id	sid	tid	token	lemma	pos
cord-002542-f7l4ty2j	1	1	key	key	NN
cord-002542-f7l4ty2j	1	2	:	:	:
cord-002542-f7l4ty2j	2	1	cord-002542-f7l4ty2j	cord-002542-f7l4ty2j	NNP
cord-002542-f7l4ty2j	3	1	authors	author	NNS
cord-002542-f7l4ty2j	3	2	:	:	:
cord-002542-f7l4ty2j	3	3	Jaworski	Jaworski	NNP
cord-002542-f7l4ty2j	3	4	,	,	,
cord-002542-f7l4ty2j	3	5	Elizabeth	Elizabeth	NNP
cord-002542-f7l4ty2j	3	6	;	;	:
cord-002542-f7l4ty2j	3	7	Routh	Routh	NNP
cord-002542-f7l4ty2j	3	8	,	,	,
cord-002542-f7l4ty2j	3	9	Andrew	Andrew	NNP
cord-002542-f7l4ty2j	3	10	title	title	NN
cord-002542-f7l4ty2j	3	11	:	:	:
cord-002542-f7l4ty2j	4	1	Parallel	parallel	JJ
cord-002542-f7l4ty2j	4	2	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	4	3	and	and	CC
cord-002542-f7l4ty2j	4	4	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	4	5	sequencing	sequencing	NN
cord-002542-f7l4ty2j	4	6	elucidates	elucidate	VBZ
cord-002542-f7l4ty2j	4	7	the	the	DT
cord-002542-f7l4ty2j	4	8	rapid	rapid	JJ
cord-002542-f7l4ty2j	4	9	evolution	evolution	NN
cord-002542-f7l4ty2j	4	10	of	of	IN
cord-002542-f7l4ty2j	4	11	defective	defective	JJ
cord-002542-f7l4ty2j	4	12	-	-	HYPH
cord-002542-f7l4ty2j	4	13	interfering	interfere	VBG
cord-002542-f7l4ty2j	4	14	RNAs	rna	NNS
cord-002542-f7l4ty2j	4	15	in	in	IN
cord-002542-f7l4ty2j	4	16	Flock	Flock	NNP
cord-002542-f7l4ty2j	4	17	House	House	NNP
cord-002542-f7l4ty2j	4	18	virus	virus	NN
cord-002542-f7l4ty2j	4	19	date	date	NN
cord-002542-f7l4ty2j	4	20	:	:	:
cord-002542-f7l4ty2j	4	21	2017	2017	CD
cord-002542-f7l4ty2j	4	22	-	-	HYPH
cord-002542-f7l4ty2j	4	23	05	05	CD
cord-002542-f7l4ty2j	4	24	-	-	HYPH
cord-002542-f7l4ty2j	4	25	05	05	CD
cord-002542-f7l4ty2j	4	26	journal	journal	NN
cord-002542-f7l4ty2j	4	27	:	:	:
cord-002542-f7l4ty2j	5	1	PLoS	PLoS	NNP
cord-002542-f7l4ty2j	5	2	Pathog	Pathog	NNP
cord-002542-f7l4ty2j	5	3	DOI	DOI	NNP
cord-002542-f7l4ty2j	5	4	:	:	:
cord-002542-f7l4ty2j	6	1	10.1371	10.1371	CD
cord-002542-f7l4ty2j	6	2	/	/	SYM
cord-002542-f7l4ty2j	6	3	journal.ppat.1006365	journal.ppat.1006365	NNP
cord-002542-f7l4ty2j	6	4	sha	sha	NNP
cord-002542-f7l4ty2j	6	5	:	:	:
cord-002542-f7l4ty2j	6	6	e69a0c654041707c6ffefca96f14c2f1fe05296c	e69a0c654041707c6ffefca96f14c2f1fe05296c	NNP
cord-002542-f7l4ty2j	6	7	doc_id	doc_id	CD
cord-002542-f7l4ty2j	6	8	:	:	:
cord-002542-f7l4ty2j	6	9	2542	2542	CD
cord-002542-f7l4ty2j	6	10	cord_uid	cord_uid	NNS
cord-002542-f7l4ty2j	6	11	:	:	:
cord-002542-f7l4ty2j	7	1	f7l4ty2j	f7l4ty2j	RB
cord-002542-f7l4ty2j	8	1	Defective	defective	JJ
cord-002542-f7l4ty2j	8	2	-	-	HYPH
cord-002542-f7l4ty2j	8	3	Interfering	interfere	VBG
cord-002542-f7l4ty2j	8	4	RNAs	rna	NNS
cord-002542-f7l4ty2j	8	5	(	(	-LRB-
cord-002542-f7l4ty2j	8	6	DI	DI	NNP
cord-002542-f7l4ty2j	8	7	-	-	HYPH
cord-002542-f7l4ty2j	8	8	RNAs	rna	NNS
cord-002542-f7l4ty2j	8	9	)	)	-RRB-
cord-002542-f7l4ty2j	8	10	have	have	VBP
cord-002542-f7l4ty2j	8	11	long	long	RB
cord-002542-f7l4ty2j	8	12	been	be	VBN
cord-002542-f7l4ty2j	8	13	known	know	VBN
cord-002542-f7l4ty2j	8	14	to	to	TO
cord-002542-f7l4ty2j	8	15	play	play	VB
cord-002542-f7l4ty2j	8	16	an	an	DT
cord-002542-f7l4ty2j	8	17	important	important	JJ
cord-002542-f7l4ty2j	8	18	role	role	NN
cord-002542-f7l4ty2j	8	19	in	in	IN
cord-002542-f7l4ty2j	8	20	virus	virus	NN
cord-002542-f7l4ty2j	8	21	replication	replication	NN
cord-002542-f7l4ty2j	8	22	and	and	CC
cord-002542-f7l4ty2j	8	23	transmission	transmission	NN
cord-002542-f7l4ty2j	8	24	.	.	.
cord-002542-f7l4ty2j	9	1	DI	DI	NNP
cord-002542-f7l4ty2j	9	2	-	-	HYPH
cord-002542-f7l4ty2j	9	3	RNAs	rna	NNS
cord-002542-f7l4ty2j	9	4	emerge	emerge	VBP
cord-002542-f7l4ty2j	9	5	during	during	IN
cord-002542-f7l4ty2j	9	6	virus	virus	NN
cord-002542-f7l4ty2j	9	7	passaging	passaging	NN
cord-002542-f7l4ty2j	9	8	in	in	IN
cord-002542-f7l4ty2j	9	9	both	both	DT
cord-002542-f7l4ty2j	9	10	cell	cell	NN
cord-002542-f7l4ty2j	9	11	-	-	HYPH
cord-002542-f7l4ty2j	9	12	culture	culture	NN
cord-002542-f7l4ty2j	9	13	and	and	CC
cord-002542-f7l4ty2j	9	14	their	-PRON-	PRP$
cord-002542-f7l4ty2j	9	15	hosts	host	NNS
cord-002542-f7l4ty2j	9	16	as	as	IN
cord-002542-f7l4ty2j	9	17	a	a	DT
cord-002542-f7l4ty2j	9	18	result	result	NN
cord-002542-f7l4ty2j	9	19	of	of	IN
cord-002542-f7l4ty2j	9	20	non	non	JJ
cord-002542-f7l4ty2j	9	21	-	-	JJ
cord-002542-f7l4ty2j	9	22	homologous	homologous	JJ
cord-002542-f7l4ty2j	9	23	RNA	RNA	NNP
cord-002542-f7l4ty2j	9	24	recombination	recombination	NN
cord-002542-f7l4ty2j	9	25	.	.	.
cord-002542-f7l4ty2j	10	1	However	however	RB
cord-002542-f7l4ty2j	10	2	,	,	,
cord-002542-f7l4ty2j	10	3	the	the	DT
cord-002542-f7l4ty2j	10	4	principles	principle	NNS
cord-002542-f7l4ty2j	10	5	of	of	IN
cord-002542-f7l4ty2j	10	6	DI	DI	NNP
cord-002542-f7l4ty2j	10	7	-	-	HYPH
cord-002542-f7l4ty2j	10	8	RNA	RNA	NNP
cord-002542-f7l4ty2j	10	9	emergence	emergence	NN
cord-002542-f7l4ty2j	10	10	and	and	CC
cord-002542-f7l4ty2j	10	11	their	-PRON-	PRP$
cord-002542-f7l4ty2j	10	12	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	10	13	evolution	evolution	NN
cord-002542-f7l4ty2j	10	14	have	have	VBP
cord-002542-f7l4ty2j	10	15	remained	remain	VBN
cord-002542-f7l4ty2j	10	16	elusive	elusive	JJ
cord-002542-f7l4ty2j	10	17	.	.	.
cord-002542-f7l4ty2j	11	1	Using	use	VBG
cord-002542-f7l4ty2j	11	2	a	a	DT
cord-002542-f7l4ty2j	11	3	combination	combination	NN
cord-002542-f7l4ty2j	11	4	of	of	IN
cord-002542-f7l4ty2j	11	5	long-	long-	NNS
cord-002542-f7l4ty2j	11	6	and	and	CC
cord-002542-f7l4ty2j	11	7	short	short	RB
cord-002542-f7l4ty2j	11	8	-	-	HYPH
cord-002542-f7l4ty2j	11	9	read	read	VBN
cord-002542-f7l4ty2j	11	10	Next	Next	NNP
cord-002542-f7l4ty2j	11	11	-	-	HYPH
cord-002542-f7l4ty2j	11	12	Generation	Generation	NNP
cord-002542-f7l4ty2j	11	13	Sequencing	Sequencing	NNP
cord-002542-f7l4ty2j	11	14	,	,	,
cord-002542-f7l4ty2j	11	15	we	-PRON-	PRP
cord-002542-f7l4ty2j	11	16	have	have	VBP
cord-002542-f7l4ty2j	11	17	characterized	characterize	VBN
cord-002542-f7l4ty2j	11	18	the	the	DT
cord-002542-f7l4ty2j	11	19	formation	formation	NN
cord-002542-f7l4ty2j	11	20	of	of	IN
cord-002542-f7l4ty2j	11	21	DI	DI	NNP
cord-002542-f7l4ty2j	11	22	-	-	HYPH
cord-002542-f7l4ty2j	11	23	RNAs	rna	NNS
cord-002542-f7l4ty2j	11	24	during	during	IN
cord-002542-f7l4ty2j	11	25	serial	serial	JJ
cord-002542-f7l4ty2j	11	26	passaging	passaging	NN
cord-002542-f7l4ty2j	11	27	of	of	IN
cord-002542-f7l4ty2j	11	28	Flock	Flock	NNP
cord-002542-f7l4ty2j	11	29	House	House	NNP
cord-002542-f7l4ty2j	11	30	virus	virus	NN
cord-002542-f7l4ty2j	11	31	(	(	-LRB-
cord-002542-f7l4ty2j	11	32	FHV	FHV	NNP
cord-002542-f7l4ty2j	11	33	)	)	-RRB-
cord-002542-f7l4ty2j	11	34	in	in	IN
cord-002542-f7l4ty2j	11	35	cell	cell	NN
cord-002542-f7l4ty2j	11	36	-	-	HYPH
cord-002542-f7l4ty2j	11	37	culture	culture	NN
cord-002542-f7l4ty2j	11	38	over	over	IN
cord-002542-f7l4ty2j	11	39	a	a	DT
cord-002542-f7l4ty2j	11	40	period	period	NN
cord-002542-f7l4ty2j	11	41	of	of	IN
cord-002542-f7l4ty2j	11	42	30	30	CD
cord-002542-f7l4ty2j	11	43	days	day	NNS
cord-002542-f7l4ty2j	11	44	in	in	IN
cord-002542-f7l4ty2j	11	45	order	order	NN
cord-002542-f7l4ty2j	11	46	to	to	TO
cord-002542-f7l4ty2j	11	47	elucidate	elucidate	VB
cord-002542-f7l4ty2j	11	48	the	the	DT
cord-002542-f7l4ty2j	11	49	pathways	pathway	NNS
cord-002542-f7l4ty2j	11	50	and	and	CC
cord-002542-f7l4ty2j	11	51	potential	potential	JJ
cord-002542-f7l4ty2j	11	52	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	11	53	of	of	IN
cord-002542-f7l4ty2j	11	54	DI	DI	NNP
cord-002542-f7l4ty2j	11	55	-	-	HYPH
cord-002542-f7l4ty2j	11	56	RNA	RNA	NNP
cord-002542-f7l4ty2j	11	57	emergence	emergence	NN
cord-002542-f7l4ty2j	11	58	and	and	CC
cord-002542-f7l4ty2j	11	59	evolution	evolution	NN
cord-002542-f7l4ty2j	11	60	.	.	.
cord-002542-f7l4ty2j	12	1	For	for	IN
cord-002542-f7l4ty2j	12	2	short	short	RB
cord-002542-f7l4ty2j	12	3	-	-	HYPH
cord-002542-f7l4ty2j	12	4	read	read	NN
cord-002542-f7l4ty2j	12	5	RNAseq	RNAseq	NNP
cord-002542-f7l4ty2j	12	6	,	,	,
cord-002542-f7l4ty2j	12	7	we	-PRON-	PRP
cord-002542-f7l4ty2j	12	8	employed	employ	VBD
cord-002542-f7l4ty2j	12	9	‘	'	``
cord-002542-f7l4ty2j	12	10	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	12	11	’	'	''
cord-002542-f7l4ty2j	12	12	due	due	IN
cord-002542-f7l4ty2j	12	13	to	to	IN
cord-002542-f7l4ty2j	12	14	its	-PRON-	PRP$
cord-002542-f7l4ty2j	12	15	ability	ability	NN
cord-002542-f7l4ty2j	12	16	to	to	TO
cord-002542-f7l4ty2j	12	17	sensitively	sensitively	RB
cord-002542-f7l4ty2j	12	18	and	and	CC
cord-002542-f7l4ty2j	12	19	confidently	confidently	RB
cord-002542-f7l4ty2j	12	20	detect	detect	VB
cord-002542-f7l4ty2j	12	21	RNA	RNA	NNP
cord-002542-f7l4ty2j	12	22	recombination	recombination	NN
cord-002542-f7l4ty2j	12	23	events	event	NNS
cord-002542-f7l4ty2j	12	24	with	with	IN
cord-002542-f7l4ty2j	12	25	nucleotide	nucleotide	JJ
cord-002542-f7l4ty2j	12	26	resolution	resolution	NN
cord-002542-f7l4ty2j	12	27	.	.	.
cord-002542-f7l4ty2j	13	1	In	in	IN
cord-002542-f7l4ty2j	13	2	parallel	parallel	NN
cord-002542-f7l4ty2j	13	3	,	,	,
cord-002542-f7l4ty2j	13	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	13	5	used	use	VBD
cord-002542-f7l4ty2j	13	6	the	the	DT
cord-002542-f7l4ty2j	13	7	Oxford	Oxford	NNP
cord-002542-f7l4ty2j	13	8	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	13	9	Technologies	Technologies	NNP
cord-002542-f7l4ty2j	13	10	’s	’s	POS
cord-002542-f7l4ty2j	13	11	(	(	-LRB-
cord-002542-f7l4ty2j	13	12	ONT	ONT	NNP
cord-002542-f7l4ty2j	13	13	)	)	-RRB-
cord-002542-f7l4ty2j	13	14	MinION	MinION	NNS
cord-002542-f7l4ty2j	13	15	to	to	TO
cord-002542-f7l4ty2j	13	16	resolve	resolve	VB
cord-002542-f7l4ty2j	13	17	full	full	JJ
cord-002542-f7l4ty2j	13	18	-	-	HYPH
cord-002542-f7l4ty2j	13	19	length	length	NN
cord-002542-f7l4ty2j	13	20	defective	defective	JJ
cord-002542-f7l4ty2j	13	21	and	and	CC
cord-002542-f7l4ty2j	13	22	wild	wild	JJ
cord-002542-f7l4ty2j	13	23	-	-	HYPH
cord-002542-f7l4ty2j	13	24	type	type	NN
cord-002542-f7l4ty2j	13	25	viral	viral	JJ
cord-002542-f7l4ty2j	13	26	genomes	genome	NNS
cord-002542-f7l4ty2j	13	27	.	.	.
cord-002542-f7l4ty2j	14	1	Together	together	RB
cord-002542-f7l4ty2j	14	2	,	,	,
cord-002542-f7l4ty2j	14	3	these	these	DT
cord-002542-f7l4ty2j	14	4	accurately	accurately	RB
cord-002542-f7l4ty2j	14	5	resolve	resolve	VBP
cord-002542-f7l4ty2j	14	6	both	both	CC
cord-002542-f7l4ty2j	14	7	rare	rare	JJ
cord-002542-f7l4ty2j	14	8	and	and	CC
cord-002542-f7l4ty2j	14	9	common	common	JJ
cord-002542-f7l4ty2j	14	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	14	11	recombination	recombination	NN
cord-002542-f7l4ty2j	14	12	events	event	NNS
cord-002542-f7l4ty2j	14	13	,	,	,
cord-002542-f7l4ty2j	14	14	determine	determine	VB
cord-002542-f7l4ty2j	14	15	the	the	DT
cord-002542-f7l4ty2j	14	16	correlation	correlation	NN
cord-002542-f7l4ty2j	14	17	between	between	IN
cord-002542-f7l4ty2j	14	18	recombination	recombination	NN
cord-002542-f7l4ty2j	14	19	events	event	NNS
cord-002542-f7l4ty2j	14	20	,	,	,
cord-002542-f7l4ty2j	14	21	and	and	CC
cord-002542-f7l4ty2j	14	22	quantifies	quantify	VBZ
cord-002542-f7l4ty2j	14	23	the	the	DT
cord-002542-f7l4ty2j	14	24	relative	relative	JJ
cord-002542-f7l4ty2j	14	25	abundance	abundance	NN
cord-002542-f7l4ty2j	14	26	of	of	IN
cord-002542-f7l4ty2j	14	27	different	different	JJ
cord-002542-f7l4ty2j	14	28	DI	DI	NNP
cord-002542-f7l4ty2j	14	29	-	-	HYPH
cord-002542-f7l4ty2j	14	30	RNAs	rna	NNS
cord-002542-f7l4ty2j	14	31	throughout	throughout	IN
cord-002542-f7l4ty2j	14	32	passaging	passage	VBG
cord-002542-f7l4ty2j	14	33	.	.	.
cord-002542-f7l4ty2j	15	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	15	2	observe	observe	VBP
cord-002542-f7l4ty2j	15	3	the	the	DT
cord-002542-f7l4ty2j	15	4	formation	formation	NN
cord-002542-f7l4ty2j	15	5	of	of	IN
cord-002542-f7l4ty2j	15	6	a	a	DT
cord-002542-f7l4ty2j	15	7	diverse	diverse	JJ
cord-002542-f7l4ty2j	15	8	pool	pool	NN
cord-002542-f7l4ty2j	15	9	of	of	IN
cord-002542-f7l4ty2j	15	10	defective	defective	JJ
cord-002542-f7l4ty2j	15	11	RNAs	rna	NNS
cord-002542-f7l4ty2j	15	12	at	at	IN
cord-002542-f7l4ty2j	15	13	each	each	DT
cord-002542-f7l4ty2j	15	14	stage	stage	NN
cord-002542-f7l4ty2j	15	15	of	of	IN
cord-002542-f7l4ty2j	15	16	viral	viral	JJ
cord-002542-f7l4ty2j	15	17	passaging	passaging	NN
cord-002542-f7l4ty2j	15	18	.	.	.
cord-002542-f7l4ty2j	16	1	However	however	RB
cord-002542-f7l4ty2j	16	2	,	,	,
cord-002542-f7l4ty2j	16	3	many	many	JJ
cord-002542-f7l4ty2j	16	4	of	of	IN
cord-002542-f7l4ty2j	16	5	these	these	DT
cord-002542-f7l4ty2j	16	6	‘	'	``
cord-002542-f7l4ty2j	16	7	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	16	8	’	'	''
cord-002542-f7l4ty2j	16	9	species	specie	NNS
cord-002542-f7l4ty2j	16	10	,	,	,
cord-002542-f7l4ty2j	16	11	while	while	IN
cord-002542-f7l4ty2j	16	12	present	present	JJ
cord-002542-f7l4ty2j	16	13	in	in	IN
cord-002542-f7l4ty2j	16	14	early	early	JJ
cord-002542-f7l4ty2j	16	15	stages	stage	NNS
cord-002542-f7l4ty2j	16	16	of	of	IN
cord-002542-f7l4ty2j	16	17	passaging	passaging	NN
cord-002542-f7l4ty2j	16	18	,	,	,
cord-002542-f7l4ty2j	16	19	do	do	VBP
cord-002542-f7l4ty2j	16	20	not	not	RB
cord-002542-f7l4ty2j	16	21	accumulate	accumulate	VB
cord-002542-f7l4ty2j	16	22	.	.	.
cord-002542-f7l4ty2j	17	1	After	after	IN
cord-002542-f7l4ty2j	17	2	approximately	approximately	RB
cord-002542-f7l4ty2j	17	3	9	9	CD
cord-002542-f7l4ty2j	17	4	days	day	NNS
cord-002542-f7l4ty2j	17	5	of	of	IN
cord-002542-f7l4ty2j	17	6	passaging	passaging	NN
cord-002542-f7l4ty2j	17	7	we	-PRON-	PRP
cord-002542-f7l4ty2j	17	8	observe	observe	VBP
cord-002542-f7l4ty2j	17	9	the	the	DT
cord-002542-f7l4ty2j	17	10	rapid	rapid	JJ
cord-002542-f7l4ty2j	17	11	accumulation	accumulation	NN
cord-002542-f7l4ty2j	17	12	of	of	IN
cord-002542-f7l4ty2j	17	13	DI	DI	NNP
cord-002542-f7l4ty2j	17	14	-	-	HYPH
cord-002542-f7l4ty2j	17	15	RNAs	rna	NNS
cord-002542-f7l4ty2j	17	16	with	with	IN
cord-002542-f7l4ty2j	17	17	a	a	DT
cord-002542-f7l4ty2j	17	18	correlated	correlate	VBN
cord-002542-f7l4ty2j	17	19	reduction	reduction	NN
cord-002542-f7l4ty2j	17	20	in	in	IN
cord-002542-f7l4ty2j	17	21	specific	specific	JJ
cord-002542-f7l4ty2j	17	22	infectivity	infectivity	NN
cord-002542-f7l4ty2j	17	23	and	and	CC
cord-002542-f7l4ty2j	17	24	with	with	IN
cord-002542-f7l4ty2j	17	25	the	the	DT
cord-002542-f7l4ty2j	17	26	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	17	27	data	datum	NNS
cord-002542-f7l4ty2j	18	1	find	find	VB
cord-002542-f7l4ty2j	18	2	that	that	IN
cord-002542-f7l4ty2j	18	3	DI	DI	NNP
cord-002542-f7l4ty2j	18	4	-	-	HYPH
cord-002542-f7l4ty2j	18	5	RNAs	rna	NNS
cord-002542-f7l4ty2j	18	6	are	be	VBP
cord-002542-f7l4ty2j	18	7	characterized	characterize	VBN
cord-002542-f7l4ty2j	18	8	by	by	IN
cord-002542-f7l4ty2j	18	9	multiple	multiple	JJ
cord-002542-f7l4ty2j	18	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	18	11	recombination	recombination	NN
cord-002542-f7l4ty2j	18	12	events	event	NNS
cord-002542-f7l4ty2j	18	13	.	.	.
cord-002542-f7l4ty2j	19	1	This	this	DT
cord-002542-f7l4ty2j	19	2	suggests	suggest	VBZ
cord-002542-f7l4ty2j	19	3	that	that	IN
cord-002542-f7l4ty2j	19	4	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	19	5	DI	DI	NNP
cord-002542-f7l4ty2j	19	6	-	-	HYPH
cord-002542-f7l4ty2j	19	7	RNA	RNA	NNP
cord-002542-f7l4ty2j	19	8	species	specie	NNS
cord-002542-f7l4ty2j	19	9	are	be	VBP
cord-002542-f7l4ty2j	19	10	not	not	RB
cord-002542-f7l4ty2j	19	11	competitive	competitive	JJ
cord-002542-f7l4ty2j	19	12	and	and	CC
cord-002542-f7l4ty2j	19	13	that	that	IN
cord-002542-f7l4ty2j	19	14	multiple	multiple	JJ
cord-002542-f7l4ty2j	19	15	recombination	recombination	NN
cord-002542-f7l4ty2j	19	16	events	event	NNS
cord-002542-f7l4ty2j	19	17	interact	interact	VBP
cord-002542-f7l4ty2j	19	18	epistatically	epistatically	RB
cord-002542-f7l4ty2j	19	19	to	to	TO
cord-002542-f7l4ty2j	19	20	confer	confer	VB
cord-002542-f7l4ty2j	19	21	‘	'	``
cord-002542-f7l4ty2j	19	22	mature	mature	JJ
cord-002542-f7l4ty2j	19	23	’	'	''
cord-002542-f7l4ty2j	19	24	DI	di	NN
cord-002542-f7l4ty2j	19	25	-	-	HYPH
cord-002542-f7l4ty2j	19	26	RNAs	rna	NNS
cord-002542-f7l4ty2j	19	27	with	with	IN
cord-002542-f7l4ty2j	19	28	their	-PRON-	PRP$
cord-002542-f7l4ty2j	19	29	selective	selective	JJ
cord-002542-f7l4ty2j	19	30	advantage	advantage	NN
cord-002542-f7l4ty2j	19	31	allowing	allow	VBG
cord-002542-f7l4ty2j	19	32	for	for	IN
cord-002542-f7l4ty2j	19	33	their	-PRON-	PRP$
cord-002542-f7l4ty2j	19	34	rapid	rapid	JJ
cord-002542-f7l4ty2j	19	35	accumulation	accumulation	NN
cord-002542-f7l4ty2j	19	36	.	.	.
cord-002542-f7l4ty2j	20	1	Alternatively	alternatively	RB
cord-002542-f7l4ty2j	20	2	,	,	,
cord-002542-f7l4ty2j	20	3	it	-PRON-	PRP
cord-002542-f7l4ty2j	20	4	is	be	VBZ
cord-002542-f7l4ty2j	20	5	possible	possible	JJ
cord-002542-f7l4ty2j	20	6	that	that	IN
cord-002542-f7l4ty2j	20	7	mature	mature	JJ
cord-002542-f7l4ty2j	20	8	DI	DI	NNP
cord-002542-f7l4ty2j	20	9	-	-	HYPH
cord-002542-f7l4ty2j	20	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	20	11	species	specie	NNS
cord-002542-f7l4ty2j	20	12	are	be	VBP
cord-002542-f7l4ty2j	20	13	generated	generate	VBN
cord-002542-f7l4ty2j	20	14	in	in	IN
cord-002542-f7l4ty2j	20	15	a	a	DT
cord-002542-f7l4ty2j	20	16	single	single	JJ
cord-002542-f7l4ty2j	20	17	event	event	NN
cord-002542-f7l4ty2j	20	18	involving	involve	VBG
cord-002542-f7l4ty2j	20	19	multiple	multiple	JJ
cord-002542-f7l4ty2j	20	20	RNA	RNA	NNP
cord-002542-f7l4ty2j	20	21	rearrangements	rearrangement	NNS
cord-002542-f7l4ty2j	20	22	.	.	.
cord-002542-f7l4ty2j	21	1	These	these	DT
cord-002542-f7l4ty2j	21	2	insights	insight	NNS
cord-002542-f7l4ty2j	21	3	have	have	VBP
cord-002542-f7l4ty2j	21	4	important	important	JJ
cord-002542-f7l4ty2j	21	5	consequences	consequence	NNS
cord-002542-f7l4ty2j	21	6	for	for	IN
cord-002542-f7l4ty2j	21	7	our	-PRON-	PRP$
cord-002542-f7l4ty2j	21	8	understanding	understanding	NN
cord-002542-f7l4ty2j	21	9	of	of	IN
cord-002542-f7l4ty2j	21	10	the	the	DT
cord-002542-f7l4ty2j	21	11	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	21	12	,	,	,
cord-002542-f7l4ty2j	21	13	determinants	determinant	NNS
cord-002542-f7l4ty2j	21	14	and	and	CC
cord-002542-f7l4ty2j	21	15	limitations	limitation	NNS
cord-002542-f7l4ty2j	21	16	in	in	IN
cord-002542-f7l4ty2j	21	17	the	the	DT
cord-002542-f7l4ty2j	21	18	emergence	emergence	NN
cord-002542-f7l4ty2j	21	19	and	and	CC
cord-002542-f7l4ty2j	21	20	evolution	evolution	NN
cord-002542-f7l4ty2j	21	21	of	of	IN
cord-002542-f7l4ty2j	21	22	DI	DI	NNP
cord-002542-f7l4ty2j	21	23	-	-	HYPH
cord-002542-f7l4ty2j	21	24	RNAs	rna	NNS
cord-002542-f7l4ty2j	21	25	.	.	.
cord-002542-f7l4ty2j	22	1	Introduction	Introduction	NNP
cord-002542-f7l4ty2j	22	2	RNA	RNA	NNP
cord-002542-f7l4ty2j	22	3	viruses	virus	NNS
cord-002542-f7l4ty2j	22	4	are	be	VBP
cord-002542-f7l4ty2j	22	5	extremely	extremely	RB
cord-002542-f7l4ty2j	22	6	diverse	diverse	JJ
cord-002542-f7l4ty2j	22	7	and	and	CC
cord-002542-f7l4ty2j	22	8	rapidly	rapidly	RB
cord-002542-f7l4ty2j	22	9	evolving	evolve	VBG
cord-002542-f7l4ty2j	22	10	.	.	.
cord-002542-f7l4ty2j	23	1	Their	-PRON-	PRP$
cord-002542-f7l4ty2j	23	2	RNA	RNA	NNP
cord-002542-f7l4ty2j	23	3	-	-	HYPH
cord-002542-f7l4ty2j	23	4	dependent	dependent	JJ
cord-002542-f7l4ty2j	23	5	RNA	RNA	NNP
cord-002542-f7l4ty2j	23	6	polymerases	polymerase	NNS
cord-002542-f7l4ty2j	23	7	(	(	-LRB-
cord-002542-f7l4ty2j	23	8	RdRps	RdRps	NNP
cord-002542-f7l4ty2j	23	9	)	)	-RRB-
cord-002542-f7l4ty2j	23	10	readily	readily	RB
cord-002542-f7l4ty2j	23	11	generate	generate	VBP
cord-002542-f7l4ty2j	23	12	single	single	JJ
cord-002542-f7l4ty2j	23	13	-	-	HYPH
cord-002542-f7l4ty2j	23	14	nucleotide	nucleotide	NN
cord-002542-f7l4ty2j	23	15	variants	variant	NNS
cord-002542-f7l4ty2j	23	16	whilst	whilst	IN
cord-002542-f7l4ty2j	23	17	lacking	lack	VBG
cord-002542-f7l4ty2j	23	18	proof	proof	NN
cord-002542-f7l4ty2j	23	19	-	-	HYPH
cord-002542-f7l4ty2j	23	20	reading	reading	NN
cord-002542-f7l4ty2j	23	21	capabilities	capability	NNS
cord-002542-f7l4ty2j	23	22	[	[	-LRB-
cord-002542-f7l4ty2j	23	23	1	1	CD
cord-002542-f7l4ty2j	23	24	]	]	-RRB-
cord-002542-f7l4ty2j	23	25	.	.	.
cord-002542-f7l4ty2j	24	1	RdRps	RdRps	NNP
cord-002542-f7l4ty2j	24	2	are	be	VBP
cord-002542-f7l4ty2j	24	3	also	also	RB
cord-002542-f7l4ty2j	24	4	highly	highly	RB
cord-002542-f7l4ty2j	24	5	prone	prone	JJ
cord-002542-f7l4ty2j	24	6	to	to	IN
cord-002542-f7l4ty2j	24	7	RNA	rna	NN
cord-002542-f7l4ty2j	24	8	recombination	recombination	NN
cord-002542-f7l4ty2j	24	9	[	[	-LRB-
cord-002542-f7l4ty2j	24	10	2	2	CD
cord-002542-f7l4ty2j	24	11	]	]	-RRB-
cord-002542-f7l4ty2j	24	12	;	;	:
cord-002542-f7l4ty2j	24	13	either	either	CC
cord-002542-f7l4ty2j	24	14	through	through	IN
cord-002542-f7l4ty2j	24	15	template	template	NN
cord-002542-f7l4ty2j	24	16	-	-	HYPH
cord-002542-f7l4ty2j	24	17	switching	switch	VBG
cord-002542-f7l4ty2j	24	18	[	[	-LRB-
cord-002542-f7l4ty2j	24	19	3	3	CD
cord-002542-f7l4ty2j	24	20	]	]	-RRB-
cord-002542-f7l4ty2j	24	21	or	or	CC
cord-002542-f7l4ty2j	24	22	through	through	IN
cord-002542-f7l4ty2j	24	23	non	non	JJ
cord-002542-f7l4ty2j	24	24	-	-	JJ
cord-002542-f7l4ty2j	24	25	replicative	replicative	JJ
cord-002542-f7l4ty2j	24	26	end	end	NN
cord-002542-f7l4ty2j	24	27	-	-	HYPH
cord-002542-f7l4ty2j	24	28	joining	join	VBG
cord-002542-f7l4ty2j	24	29	[	[	-LRB-
cord-002542-f7l4ty2j	24	30	4	4	CD
cord-002542-f7l4ty2j	24	31	]	]	-RRB-
cord-002542-f7l4ty2j	24	32	.	.	.
cord-002542-f7l4ty2j	25	1	RNA	RNA	NNP
cord-002542-f7l4ty2j	25	2	recombination	recombination	NN
cord-002542-f7l4ty2j	25	3	has	have	VBZ
cord-002542-f7l4ty2j	25	4	been	be	VBN
cord-002542-f7l4ty2j	25	5	demonstrated	demonstrate	VBN
cord-002542-f7l4ty2j	25	6	to	to	TO
cord-002542-f7l4ty2j	25	7	be	be	VB
cord-002542-f7l4ty2j	25	8	responsible	responsible	JJ
cord-002542-f7l4ty2j	25	9	for	for	IN
cord-002542-f7l4ty2j	25	10	the	the	DT
cord-002542-f7l4ty2j	25	11	emergence	emergence	NN
cord-002542-f7l4ty2j	25	12	of	of	IN
cord-002542-f7l4ty2j	25	13	new	new	JJ
cord-002542-f7l4ty2j	25	14	strains	strain	NNS
cord-002542-f7l4ty2j	25	15	or	or	CC
cord-002542-f7l4ty2j	25	16	species	specie	NNS
cord-002542-f7l4ty2j	25	17	of	of	IN
cord-002542-f7l4ty2j	25	18	viruses	virus	NNS
cord-002542-f7l4ty2j	25	19	such	such	JJ
cord-002542-f7l4ty2j	25	20	as	as	IN
cord-002542-f7l4ty2j	25	21	rhinoviruses	rhinovirus	NNS
cord-002542-f7l4ty2j	25	22	[	[	-LRB-
cord-002542-f7l4ty2j	25	23	5	5	CD
cord-002542-f7l4ty2j	25	24	]	]	-RRB-
cord-002542-f7l4ty2j	25	25	and	and	CC
cord-002542-f7l4ty2j	25	26	dengue	dengue	NN
cord-002542-f7l4ty2j	25	27	virus	virus	NN
cord-002542-f7l4ty2j	25	28	[	[	-LRB-
cord-002542-f7l4ty2j	25	29	6	6	CD
cord-002542-f7l4ty2j	25	30	]	]	-RRB-
cord-002542-f7l4ty2j	25	31	,	,	,
cord-002542-f7l4ty2j	25	32	and	and	CC
cord-002542-f7l4ty2j	25	33	the	the	DT
cord-002542-f7l4ty2j	25	34	formation	formation	NN
cord-002542-f7l4ty2j	25	35	of	of	IN
cord-002542-f7l4ty2j	25	36	vaccine	vaccine	NN
cord-002542-f7l4ty2j	25	37	-	-	HYPH
cord-002542-f7l4ty2j	25	38	derived	derive	VBN
cord-002542-f7l4ty2j	25	39	poliovirus	poliovirus	NN
cord-002542-f7l4ty2j	25	40	[	[	-LRB-
cord-002542-f7l4ty2j	25	41	7	7	CD
cord-002542-f7l4ty2j	25	42	]	]	-RRB-
cord-002542-f7l4ty2j	25	43	.	.	.
cord-002542-f7l4ty2j	26	1	Non	non	JJ
cord-002542-f7l4ty2j	26	2	-	-	JJ
cord-002542-f7l4ty2j	26	3	homologous	homologous	JJ
cord-002542-f7l4ty2j	26	4	RNA	RNA	NNP
cord-002542-f7l4ty2j	26	5	recombination	recombination	NN
cord-002542-f7l4ty2j	26	6	is	be	VBZ
cord-002542-f7l4ty2j	26	7	also	also	RB
cord-002542-f7l4ty2j	26	8	responsible	responsible	JJ
cord-002542-f7l4ty2j	26	9	for	for	IN
cord-002542-f7l4ty2j	26	10	the	the	DT
cord-002542-f7l4ty2j	26	11	generation	generation	NN
cord-002542-f7l4ty2j	26	12	of	of	IN
cord-002542-f7l4ty2j	26	13	defective	defective	JJ
cord-002542-f7l4ty2j	26	14	RNAs	rna	NNS
cord-002542-f7l4ty2j	26	15	[	[	-LRB-
cord-002542-f7l4ty2j	26	16	8	8	CD
cord-002542-f7l4ty2j	26	17	,	,	,
cord-002542-f7l4ty2j	26	18	9	9	CD
cord-002542-f7l4ty2j	26	19	]	]	-RRB-
cord-002542-f7l4ty2j	26	20	.	.	.
cord-002542-f7l4ty2j	27	1	These	these	DT
cord-002542-f7l4ty2j	27	2	are	be	VBP
cord-002542-f7l4ty2j	27	3	versions	version	NNS
cord-002542-f7l4ty2j	27	4	of	of	IN
cord-002542-f7l4ty2j	27	5	the	the	DT
cord-002542-f7l4ty2j	27	6	parental	parental	JJ
cord-002542-f7l4ty2j	27	7	viral	viral	JJ
cord-002542-f7l4ty2j	27	8	genome	genome	NN
cord-002542-f7l4ty2j	27	9	that	that	WDT
cord-002542-f7l4ty2j	27	10	can	can	MD
cord-002542-f7l4ty2j	27	11	arise	arise	VB
cord-002542-f7l4ty2j	27	12	naturally	naturally	RB
cord-002542-f7l4ty2j	27	13	during	during	IN
cord-002542-f7l4ty2j	27	14	the	the	DT
cord-002542-f7l4ty2j	27	15	course	course	NN
cord-002542-f7l4ty2j	27	16	of	of	IN
cord-002542-f7l4ty2j	27	17	viral	viral	JJ
cord-002542-f7l4ty2j	27	18	passaging	passaging	NN
cord-002542-f7l4ty2j	27	19	but	but	CC
cord-002542-f7l4ty2j	27	20	have	have	VBP
cord-002542-f7l4ty2j	27	21	been	be	VBN
cord-002542-f7l4ty2j	27	22	truncated	truncate	VBN
cord-002542-f7l4ty2j	27	23	and	and	CC
cord-002542-f7l4ty2j	27	24	rearranged	rearrange	VBN
cord-002542-f7l4ty2j	27	25	by	by	IN
cord-002542-f7l4ty2j	27	26	RNA	RNA	NNP
cord-002542-f7l4ty2j	27	27	recombination	recombination	NN
cord-002542-f7l4ty2j	27	28	.	.	.
cord-002542-f7l4ty2j	28	1	While	while	IN
cord-002542-f7l4ty2j	28	2	not	not	RB
cord-002542-f7l4ty2j	28	3	encoding	encode	VBG
cord-002542-f7l4ty2j	28	4	for	for	IN
cord-002542-f7l4ty2j	28	5	functional	functional	JJ
cord-002542-f7l4ty2j	28	6	viruses	virus	NNS
cord-002542-f7l4ty2j	28	7	themselves	-PRON-	PRP
cord-002542-f7l4ty2j	28	8	,	,	,
cord-002542-f7l4ty2j	28	9	they	-PRON-	PRP
cord-002542-f7l4ty2j	28	10	can	can	MD
cord-002542-f7l4ty2j	28	11	be	be	VB
cord-002542-f7l4ty2j	28	12	amplified	amplify	VBN
cord-002542-f7l4ty2j	28	13	and	and	CC
cord-002542-f7l4ty2j	28	14	co	co	JJ
cord-002542-f7l4ty2j	28	15	-	-	JJ
cord-002542-f7l4ty2j	28	16	passaged	passaged	JJ
cord-002542-f7l4ty2j	28	17	with	with	IN
cord-002542-f7l4ty2j	28	18	the	the	DT
cord-002542-f7l4ty2j	28	19	help	help	NN
cord-002542-f7l4ty2j	28	20	of	of	IN
cord-002542-f7l4ty2j	28	21	the	the	DT
cord-002542-f7l4ty2j	28	22	wild	wild	JJ
cord-002542-f7l4ty2j	28	23	-	-	HYPH
cord-002542-f7l4ty2j	28	24	type	type	NN
cord-002542-f7l4ty2j	28	25	'	'	``
cord-002542-f7l4ty2j	28	26	helper	helper	NN
cord-002542-f7l4ty2j	28	27	'	'	''
cord-002542-f7l4ty2j	28	28	virus	virus	NN
cord-002542-f7l4ty2j	28	29	that	that	WDT
cord-002542-f7l4ty2j	28	30	provides	provide	VBZ
cord-002542-f7l4ty2j	28	31	the	the	DT
cord-002542-f7l4ty2j	28	32	necessary	necessary	JJ
cord-002542-f7l4ty2j	28	33	machinery	machinery	NN
cord-002542-f7l4ty2j	28	34	for	for	IN
cord-002542-f7l4ty2j	28	35	replication	replication	NN
cord-002542-f7l4ty2j	28	36	,	,	,
cord-002542-f7l4ty2j	28	37	encapsidation	encapsidation	NN
cord-002542-f7l4ty2j	28	38	and	and	CC
cord-002542-f7l4ty2j	28	39	transmission	transmission	NN
cord-002542-f7l4ty2j	28	40	.	.	.
cord-002542-f7l4ty2j	29	1	A	a	DT
cord-002542-f7l4ty2j	29	2	defective	defective	JJ
cord-002542-f7l4ty2j	29	3	RNA	RNA	NNP
cord-002542-f7l4ty2j	29	4	that	that	WDT
cord-002542-f7l4ty2j	29	5	accumulates	accumulate	VBZ
cord-002542-f7l4ty2j	29	6	to	to	IN
cord-002542-f7l4ty2j	29	7	such	such	PDT
cord-002542-f7l4ty2j	29	8	an	an	DT
cord-002542-f7l4ty2j	29	9	extent	extent	NN
cord-002542-f7l4ty2j	29	10	as	as	IN
cord-002542-f7l4ty2j	29	11	to	to	TO
cord-002542-f7l4ty2j	29	12	compete	compete	VB
cord-002542-f7l4ty2j	29	13	with	with	IN
cord-002542-f7l4ty2j	29	14	or	or	CC
cord-002542-f7l4ty2j	29	15	otherwise	otherwise	RB
cord-002542-f7l4ty2j	29	16	attenuate	attenuate	VB
cord-002542-f7l4ty2j	29	17	the	the	DT
cord-002542-f7l4ty2j	29	18	replication	replication	NN
cord-002542-f7l4ty2j	29	19	of	of	IN
cord-002542-f7l4ty2j	29	20	the	the	DT
cord-002542-f7l4ty2j	29	21	parental	parental	JJ
cord-002542-f7l4ty2j	29	22	virus	virus	NN
cord-002542-f7l4ty2j	29	23	is	be	VBZ
cord-002542-f7l4ty2j	29	24	known	know	VBN
cord-002542-f7l4ty2j	29	25	as	as	IN
cord-002542-f7l4ty2j	29	26	a	a	DT
cord-002542-f7l4ty2j	29	27	Defective	Defective	NNP
cord-002542-f7l4ty2j	29	28	-	-	HYPH
cord-002542-f7l4ty2j	29	29	Interfering	interfere	VBG
cord-002542-f7l4ty2j	29	30	RNA	RNA	NNP
cord-002542-f7l4ty2j	29	31	(	(	-LRB-
cord-002542-f7l4ty2j	29	32	DI	DI	NNP
cord-002542-f7l4ty2j	29	33	-	-	HYPH
cord-002542-f7l4ty2j	29	34	RNA	RNA	NNP
cord-002542-f7l4ty2j	29	35	)	)	-RRB-
cord-002542-f7l4ty2j	29	36	[	[	-LRB-
cord-002542-f7l4ty2j	29	37	10	10	CD
cord-002542-f7l4ty2j	29	38	]	]	-RRB-
cord-002542-f7l4ty2j	29	39	.	.	.
cord-002542-f7l4ty2j	30	1	DI	DI	NNP
cord-002542-f7l4ty2j	30	2	-	-	HYPH
cord-002542-f7l4ty2j	30	3	RNAs	rna	NNS
cord-002542-f7l4ty2j	30	4	can	can	MD
cord-002542-f7l4ty2j	30	5	attenuate	attenuate	VB
cord-002542-f7l4ty2j	30	6	the	the	DT
cord-002542-f7l4ty2j	30	7	viral	viral	JJ
cord-002542-f7l4ty2j	30	8	infection	infection	NN
cord-002542-f7l4ty2j	30	9	via	via	IN
cord-002542-f7l4ty2j	30	10	a	a	DT
cord-002542-f7l4ty2j	30	11	variety	variety	NN
cord-002542-f7l4ty2j	30	12	of	of	IN
cord-002542-f7l4ty2j	30	13	proposed	propose	VBN
cord-002542-f7l4ty2j	30	14	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	30	15	such	such	JJ
cord-002542-f7l4ty2j	30	16	as	as	IN
cord-002542-f7l4ty2j	30	17	the	the	DT
cord-002542-f7l4ty2j	30	18	saturation	saturation	NN
cord-002542-f7l4ty2j	30	19	of	of	IN
cord-002542-f7l4ty2j	30	20	the	the	DT
cord-002542-f7l4ty2j	30	21	viral	viral	JJ
cord-002542-f7l4ty2j	30	22	replicative	replicative	JJ
cord-002542-f7l4ty2j	30	23	machinery	machinery	NN
cord-002542-f7l4ty2j	30	24	,	,	,
cord-002542-f7l4ty2j	30	25	sequestration	sequestration	NN
cord-002542-f7l4ty2j	30	26	of	of	IN
cord-002542-f7l4ty2j	30	27	essential	essential	JJ
cord-002542-f7l4ty2j	30	28	cellular	cellular	JJ
cord-002542-f7l4ty2j	30	29	cofactors	cofactor	NNS
cord-002542-f7l4ty2j	30	30	,	,	,
cord-002542-f7l4ty2j	30	31	and/	and/	CD
cord-002542-f7l4ty2j	30	32	or	or	CC
cord-002542-f7l4ty2j	30	33	induction	induction	NN
cord-002542-f7l4ty2j	30	34	of	of	IN
cord-002542-f7l4ty2j	30	35	innate	innate	JJ
cord-002542-f7l4ty2j	30	36	immune	immune	JJ
cord-002542-f7l4ty2j	30	37	responses	response	NNS
cord-002542-f7l4ty2j	30	38	[	[	-LRB-
cord-002542-f7l4ty2j	30	39	10	10	CD
cord-002542-f7l4ty2j	30	40	]	]	-RRB-
cord-002542-f7l4ty2j	30	41	[	[	-LRB-
cord-002542-f7l4ty2j	30	42	11	11	CD
cord-002542-f7l4ty2j	30	43	]	]	-RRB-
cord-002542-f7l4ty2j	30	44	[	[	-LRB-
cord-002542-f7l4ty2j	30	45	12	12	CD
cord-002542-f7l4ty2j	30	46	]	]	-RRB-
cord-002542-f7l4ty2j	30	47	[	[	-LRB-
cord-002542-f7l4ty2j	30	48	13	13	CD
cord-002542-f7l4ty2j	30	49	]	]	-RRB-
cord-002542-f7l4ty2j	30	50	[	[	-LRB-
cord-002542-f7l4ty2j	30	51	14	14	CD
cord-002542-f7l4ty2j	30	52	]	]	-RRB-
cord-002542-f7l4ty2j	30	53	.	.	.
cord-002542-f7l4ty2j	31	1	DI	DI	NNP
cord-002542-f7l4ty2j	31	2	-	-	HYPH
cord-002542-f7l4ty2j	31	3	RNAs	rna	NNS
cord-002542-f7l4ty2j	31	4	have	have	VBP
cord-002542-f7l4ty2j	31	5	been	be	VBN
cord-002542-f7l4ty2j	31	6	well	well	RB
cord-002542-f7l4ty2j	31	7	characterized	characterize	VBN
cord-002542-f7l4ty2j	31	8	for	for	IN
cord-002542-f7l4ty2j	31	9	a	a	DT
cord-002542-f7l4ty2j	31	10	number	number	NN
cord-002542-f7l4ty2j	31	11	of	of	IN
cord-002542-f7l4ty2j	31	12	RNA	RNA	NNP
cord-002542-f7l4ty2j	31	13	viruses	virus	NNS
cord-002542-f7l4ty2j	31	14	as	as	IN
cord-002542-f7l4ty2j	31	15	they	-PRON-	PRP
cord-002542-f7l4ty2j	31	16	provide	provide	VBP
cord-002542-f7l4ty2j	31	17	valuable	valuable	JJ
cord-002542-f7l4ty2j	31	18	tools	tool	NNS
cord-002542-f7l4ty2j	31	19	to	to	IN
cord-002542-f7l4ty2j	31	20	molecular	molecular	JJ
cord-002542-f7l4ty2j	31	21	virologists	virologist	NNS
cord-002542-f7l4ty2j	31	22	by	by	IN
cord-002542-f7l4ty2j	31	23	revealing	reveal	VBG
cord-002542-f7l4ty2j	31	24	conserved	conserved	JJ
cord-002542-f7l4ty2j	31	25	regions	region	NNS
cord-002542-f7l4ty2j	31	26	and	and	CC
cord-002542-f7l4ty2j	31	27	functional	functional	JJ
cord-002542-f7l4ty2j	31	28	domains	domain	NNS
cord-002542-f7l4ty2j	31	29	in	in	IN
cord-002542-f7l4ty2j	31	30	the	the	DT
cord-002542-f7l4ty2j	31	31	RNA	RNA	NNP
cord-002542-f7l4ty2j	31	32	genome	genome	NN
cord-002542-f7l4ty2j	31	33	such	such	JJ
cord-002542-f7l4ty2j	31	34	as	as	IN
cord-002542-f7l4ty2j	31	35	binding	bind	VBG
cord-002542-f7l4ty2j	31	36	sites	site	NNS
cord-002542-f7l4ty2j	31	37	for	for	IN
cord-002542-f7l4ty2j	31	38	viral	viral	JJ
cord-002542-f7l4ty2j	31	39	or	or	CC
cord-002542-f7l4ty2j	31	40	host	host	NN
cord-002542-f7l4ty2j	31	41	factors	factor	NNS
cord-002542-f7l4ty2j	31	42	.	.	.
cord-002542-f7l4ty2j	32	1	Moreover	moreover	RB
cord-002542-f7l4ty2j	32	2	,	,	,
cord-002542-f7l4ty2j	32	3	characterizing	characterize	VBG
cord-002542-f7l4ty2j	32	4	recombination	recombination	NN
cord-002542-f7l4ty2j	32	5	loci	locus	NNS
cord-002542-f7l4ty2j	32	6	reveal	reveal	VBP
cord-002542-f7l4ty2j	32	7	the	the	DT
cord-002542-f7l4ty2j	32	8	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	32	9	of	of	IN
cord-002542-f7l4ty2j	32	10	recombination	recombination	NN
cord-002542-f7l4ty2j	32	11	,	,	,
cord-002542-f7l4ty2j	32	12	impacting	impact	VBG
cord-002542-f7l4ty2j	32	13	our	-PRON-	PRP$
cord-002542-f7l4ty2j	32	14	understanding	understanding	NN
cord-002542-f7l4ty2j	32	15	of	of	IN
cord-002542-f7l4ty2j	32	16	viral	viral	JJ
cord-002542-f7l4ty2j	32	17	evolution	evolution	NN
cord-002542-f7l4ty2j	32	18	[	[	-LRB-
cord-002542-f7l4ty2j	32	19	8	8	CD
cord-002542-f7l4ty2j	32	20	,	,	,
cord-002542-f7l4ty2j	32	21	15	15	CD
cord-002542-f7l4ty2j	32	22	,	,	,
cord-002542-f7l4ty2j	32	23	16	16	CD
cord-002542-f7l4ty2j	32	24	]	]	-RRB-
cord-002542-f7l4ty2j	32	25	.	.	.
cord-002542-f7l4ty2j	33	1	Until	until	IN
cord-002542-f7l4ty2j	33	2	recently	recently	RB
cord-002542-f7l4ty2j	33	3	[	[	-LRB-
cord-002542-f7l4ty2j	33	4	17	17	CD
cord-002542-f7l4ty2j	33	5	]	]	-RRB-
cord-002542-f7l4ty2j	33	6	,	,	,
cord-002542-f7l4ty2j	33	7	due	due	IN
cord-002542-f7l4ty2j	33	8	to	to	IN
cord-002542-f7l4ty2j	33	9	difficulties	difficulty	NNS
cord-002542-f7l4ty2j	33	10	in	in	IN
cord-002542-f7l4ty2j	33	11	capturing	capture	VBG
cord-002542-f7l4ty2j	33	12	and	and	CC
cord-002542-f7l4ty2j	33	13	characterizing	characterize	VBG
cord-002542-f7l4ty2j	33	14	DI	DI	NNP
cord-002542-f7l4ty2j	33	15	-	-	HYPH
cord-002542-f7l4ty2j	33	16	RNAs	rna	NNS
cord-002542-f7l4ty2j	33	17	in	in	IN
cord-002542-f7l4ty2j	33	18	vivo	vivo	NN
cord-002542-f7l4ty2j	33	19	,	,	,
cord-002542-f7l4ty2j	33	20	DI	DI	NNP
cord-002542-f7l4ty2j	33	21	-	-	HYPH
cord-002542-f7l4ty2j	33	22	RNAs	rna	NNS
cord-002542-f7l4ty2j	33	23	were	be	VBD
cord-002542-f7l4ty2j	33	24	considered	consider	VBN
cord-002542-f7l4ty2j	33	25	to	to	TO
cord-002542-f7l4ty2j	33	26	be	be	VB
cord-002542-f7l4ty2j	33	27	a	a	DT
cord-002542-f7l4ty2j	33	28	curious	curious	JJ
cord-002542-f7l4ty2j	33	29	epiphenomenon	epiphenomenon	NN
cord-002542-f7l4ty2j	33	30	of	of	IN
cord-002542-f7l4ty2j	33	31	cell	cell	NN
cord-002542-f7l4ty2j	33	32	-	-	HYPH
cord-002542-f7l4ty2j	33	33	culturing	culture	VBG
cord-002542-f7l4ty2j	33	34	practices	practice	NNS
cord-002542-f7l4ty2j	33	35	.	.	.
cord-002542-f7l4ty2j	34	1	As	as	IN
cord-002542-f7l4ty2j	34	2	a	a	DT
cord-002542-f7l4ty2j	34	3	result	result	NN
cord-002542-f7l4ty2j	34	4	,	,	,
cord-002542-f7l4ty2j	34	5	our	-PRON-	PRP$
cord-002542-f7l4ty2j	34	6	appreciation	appreciation	NN
cord-002542-f7l4ty2j	34	7	of	of	IN
cord-002542-f7l4ty2j	34	8	the	the	DT
cord-002542-f7l4ty2j	34	9	diversity	diversity	NN
cord-002542-f7l4ty2j	34	10	of	of	IN
cord-002542-f7l4ty2j	34	11	DI	DI	NNP
cord-002542-f7l4ty2j	34	12	-	-	HYPH
cord-002542-f7l4ty2j	34	13	RNAs	rna	NNS
cord-002542-f7l4ty2j	34	14	and	and	CC
cord-002542-f7l4ty2j	34	15	the	the	DT
cord-002542-f7l4ty2j	34	16	range	range	NN
cord-002542-f7l4ty2j	34	17	of	of	IN
cord-002542-f7l4ty2j	34	18	situations	situation	NNS
cord-002542-f7l4ty2j	34	19	in	in	IN
cord-002542-f7l4ty2j	34	20	which	which	WDT
cord-002542-f7l4ty2j	34	21	they	-PRON-	PRP
cord-002542-f7l4ty2j	34	22	could	could	MD
cord-002542-f7l4ty2j	34	23	play	play	VB
cord-002542-f7l4ty2j	34	24	a	a	DT
cord-002542-f7l4ty2j	34	25	role	role	NN
cord-002542-f7l4ty2j	34	26	was	be	VBD
cord-002542-f7l4ty2j	34	27	greatly	greatly	RB
cord-002542-f7l4ty2j	34	28	limited	limited	JJ
cord-002542-f7l4ty2j	34	29	.	.	.
cord-002542-f7l4ty2j	35	1	Increasingly	increasingly	RB
cord-002542-f7l4ty2j	35	2	,	,	,
cord-002542-f7l4ty2j	35	3	due	due	IN
cord-002542-f7l4ty2j	35	4	to	to	IN
cord-002542-f7l4ty2j	35	5	the	the	DT
cord-002542-f7l4ty2j	35	6	use	use	NN
cord-002542-f7l4ty2j	35	7	and	and	CC
cord-002542-f7l4ty2j	35	8	sensitivity	sensitivity	NN
cord-002542-f7l4ty2j	35	9	of	of	IN
cord-002542-f7l4ty2j	35	10	Next	Next	NNP
cord-002542-f7l4ty2j	35	11	-	-	HYPH
cord-002542-f7l4ty2j	35	12	Generation	Generation	NNP
cord-002542-f7l4ty2j	35	13	Sequencing	Sequencing	NNP
cord-002542-f7l4ty2j	35	14	(	(	-LRB-
cord-002542-f7l4ty2j	35	15	NGS	NGS	NNP
cord-002542-f7l4ty2j	35	16	)	)	-RRB-
cord-002542-f7l4ty2j	35	17	technologies	technology	NNS
cord-002542-f7l4ty2j	35	18	,	,	,
cord-002542-f7l4ty2j	35	19	DI	DI	NNP
cord-002542-f7l4ty2j	35	20	-	-	HYPH
cord-002542-f7l4ty2j	35	21	RNAs	rna	NNS
cord-002542-f7l4ty2j	35	22	have	have	VBP
cord-002542-f7l4ty2j	35	23	been	be	VBN
cord-002542-f7l4ty2j	35	24	observed	observe	VBN
cord-002542-f7l4ty2j	35	25	in	in	IN
cord-002542-f7l4ty2j	35	26	a	a	DT
cord-002542-f7l4ty2j	35	27	multitude	multitude	NN
cord-002542-f7l4ty2j	35	28	of	of	IN
cord-002542-f7l4ty2j	35	29	viral	viral	JJ
cord-002542-f7l4ty2j	35	30	systems	system	NNS
cord-002542-f7l4ty2j	35	31	under	under	IN
cord-002542-f7l4ty2j	35	32	laboratory	laboratory	NN
cord-002542-f7l4ty2j	35	33	conditions	condition	NNS
cord-002542-f7l4ty2j	35	34	(	(	-LRB-
cord-002542-f7l4ty2j	35	35	e.g.	e.g.	IN
cord-002542-f7l4ty2j	35	36	SARS	SARS	NNP
cord-002542-f7l4ty2j	35	37	coronavirus	coronavirus	NN
cord-002542-f7l4ty2j	35	38	[	[	-LRB-
cord-002542-f7l4ty2j	35	39	18	18	CD
cord-002542-f7l4ty2j	35	40	]	]	-RRB-
cord-002542-f7l4ty2j	35	41	,	,	,
cord-002542-f7l4ty2j	35	42	HIV	HIV	NNP
cord-002542-f7l4ty2j	35	43	[	[	-LRB-
cord-002542-f7l4ty2j	35	44	19	19	CD
cord-002542-f7l4ty2j	35	45	]	]	-RRB-
cord-002542-f7l4ty2j	35	46	)	)	-RRB-
cord-002542-f7l4ty2j	35	47	,	,	,
cord-002542-f7l4ty2j	35	48	in	in	IN
cord-002542-f7l4ty2j	35	49	clinical	clinical	JJ
cord-002542-f7l4ty2j	35	50	settings	setting	NNS
cord-002542-f7l4ty2j	35	51	(	(	-LRB-
cord-002542-f7l4ty2j	35	52	e.g.	e.g.	IN
cord-002542-f7l4ty2j	35	53	measles	measle	NNS
cord-002542-f7l4ty2j	35	54	[	[	-LRB-
cord-002542-f7l4ty2j	35	55	20	20	CD
cord-002542-f7l4ty2j	35	56	]	]	-RRB-
cord-002542-f7l4ty2j	35	57	,	,	,
cord-002542-f7l4ty2j	35	58	dengue	dengue	NN
cord-002542-f7l4ty2j	35	59	[	[	-LRB-
cord-002542-f7l4ty2j	35	60	21	21	CD
cord-002542-f7l4ty2j	35	61	]	]	-RRB-
cord-002542-f7l4ty2j	35	62	and	and	CC
cord-002542-f7l4ty2j	35	63	chronic	chronic	JJ
cord-002542-f7l4ty2j	35	64	hepatitis	hepatitis	NN
cord-002542-f7l4ty2j	35	65	C	c	NN
cord-002542-f7l4ty2j	35	66	[	[	-LRB-
cord-002542-f7l4ty2j	35	67	22	22	CD
cord-002542-f7l4ty2j	35	68	]	]	-RRB-
cord-002542-f7l4ty2j	35	69	)	)	-RRB-
cord-002542-f7l4ty2j	35	70	and	and	CC
cord-002542-f7l4ty2j	35	71	in	in	IN
cord-002542-f7l4ty2j	35	72	metagenomic	metagenomic	NNP
cord-002542-f7l4ty2j	35	73	or	or	CC
cord-002542-f7l4ty2j	35	74	'	'	``
cord-002542-f7l4ty2j	35	75	wild	wild	JJ
cord-002542-f7l4ty2j	35	76	'	'	''
cord-002542-f7l4ty2j	35	77	samples	sample	NNS
cord-002542-f7l4ty2j	35	78	(	(	-LRB-
cord-002542-f7l4ty2j	35	79	e.g.	e.g.	RB
cord-002542-f7l4ty2j	35	80	West	West	NNP
cord-002542-f7l4ty2j	35	81	Nile	Nile	NNP
cord-002542-f7l4ty2j	35	82	virus	virus	NN
cord-002542-f7l4ty2j	35	83	[	[	-LRB-
cord-002542-f7l4ty2j	35	84	23	23	CD
cord-002542-f7l4ty2j	35	85	]	]	-RRB-
cord-002542-f7l4ty2j	35	86	,	,	,
cord-002542-f7l4ty2j	35	87	influenza	influenza	NN
cord-002542-f7l4ty2j	35	88	virus	virus	NN
cord-002542-f7l4ty2j	35	89	[	[	-LRB-
cord-002542-f7l4ty2j	35	90	24	24	CD
cord-002542-f7l4ty2j	35	91	]	]	-RRB-
cord-002542-f7l4ty2j	35	92	)	)	-RRB-
cord-002542-f7l4ty2j	35	93	.	.	.
cord-002542-f7l4ty2j	36	1	Despite	despite	IN
cord-002542-f7l4ty2j	36	2	this	this	DT
cord-002542-f7l4ty2j	36	3	burgeoning	burgeon	VBG
cord-002542-f7l4ty2j	36	4	range	range	NN
cord-002542-f7l4ty2j	36	5	of	of	IN
cord-002542-f7l4ty2j	36	6	hosts	host	NNS
cord-002542-f7l4ty2j	36	7	for	for	IN
cord-002542-f7l4ty2j	36	8	DI	DI	NNP
cord-002542-f7l4ty2j	36	9	-	-	HYPH
cord-002542-f7l4ty2j	36	10	RNAs	rna	NNS
cord-002542-f7l4ty2j	36	11	,	,	,
cord-002542-f7l4ty2j	36	12	limitations	limitation	NNS
cord-002542-f7l4ty2j	36	13	in	in	IN
cord-002542-f7l4ty2j	36	14	NGS	NGS	NNP
cord-002542-f7l4ty2j	36	15	technologies	technology	NNS
cord-002542-f7l4ty2j	36	16	including	include	VBG
cord-002542-f7l4ty2j	36	17	high	high	JJ
cord-002542-f7l4ty2j	36	18	artifactual	artifactual	JJ
cord-002542-f7l4ty2j	36	19	recombination	recombination	NN
cord-002542-f7l4ty2j	36	20	rates	rate	NNS
cord-002542-f7l4ty2j	36	21	,	,	,
cord-002542-f7l4ty2j	36	22	short	short	JJ
cord-002542-f7l4ty2j	36	23	reads	read	NNS
cord-002542-f7l4ty2j	36	24	and	and	CC
cord-002542-f7l4ty2j	36	25	a	a	DT
cord-002542-f7l4ty2j	36	26	limited	limited	JJ
cord-002542-f7l4ty2j	36	27	range	range	NN
cord-002542-f7l4ty2j	36	28	of	of	IN
cord-002542-f7l4ty2j	36	29	bioinformatics	bioinformatics	NN
cord-002542-f7l4ty2j	36	30	tools	tool	NNS
cord-002542-f7l4ty2j	36	31	tailored	tailor	VBN
cord-002542-f7l4ty2j	36	32	to	to	IN
cord-002542-f7l4ty2j	36	33	viral	viral	JJ
cord-002542-f7l4ty2j	36	34	RNA	RNA	NNP
cord-002542-f7l4ty2j	36	35	recombination	recombination	NN
cord-002542-f7l4ty2j	36	36	discovery	discovery	NN
cord-002542-f7l4ty2j	36	37	has	have	VBZ
cord-002542-f7l4ty2j	36	38	hindered	hinder	VBN
cord-002542-f7l4ty2j	36	39	our	-PRON-	PRP$
cord-002542-f7l4ty2j	36	40	ability	ability	NN
cord-002542-f7l4ty2j	36	41	to	to	TO
cord-002542-f7l4ty2j	36	42	detect	detect	VB
cord-002542-f7l4ty2j	36	43	and	and	CC
cord-002542-f7l4ty2j	36	44	characterize	characterize	VB
cord-002542-f7l4ty2j	36	45	DI	DI	NNP
cord-002542-f7l4ty2j	36	46	-	-	HYPH
cord-002542-f7l4ty2j	36	47	RNAs	rna	NNS
cord-002542-f7l4ty2j	36	48	in	in	IN
cord-002542-f7l4ty2j	36	49	complex	complex	JJ
cord-002542-f7l4ty2j	36	50	or	or	CC
cord-002542-f7l4ty2j	36	51	clinical	clinical	JJ
cord-002542-f7l4ty2j	36	52	samples	sample	NNS
cord-002542-f7l4ty2j	36	53	.	.	.
cord-002542-f7l4ty2j	37	1	Flock	Flock	NNP
cord-002542-f7l4ty2j	37	2	House	House	NNP
cord-002542-f7l4ty2j	37	3	virus	virus	NN
cord-002542-f7l4ty2j	37	4	(	(	-LRB-
cord-002542-f7l4ty2j	37	5	FHV	FHV	NNP
cord-002542-f7l4ty2j	37	6	)	)	-RRB-
cord-002542-f7l4ty2j	37	7	is	be	VBZ
cord-002542-f7l4ty2j	37	8	a	a	DT
cord-002542-f7l4ty2j	37	9	positive	positive	JJ
cord-002542-f7l4ty2j	37	10	-	-	HYPH
cord-002542-f7l4ty2j	37	11	sense	sense	NN
cord-002542-f7l4ty2j	37	12	single	single	JJ
cord-002542-f7l4ty2j	37	13	-	-	HYPH
cord-002542-f7l4ty2j	37	14	stranded	strand	VBN
cord-002542-f7l4ty2j	37	15	RNA	RNA	NNP
cord-002542-f7l4ty2j	37	16	(	(	-LRB-
cord-002542-f7l4ty2j	37	17	+	+	CC
cord-002542-f7l4ty2j	37	18	ssRNA	ssrna	NN
cord-002542-f7l4ty2j	37	19	)	)	-RRB-
cord-002542-f7l4ty2j	37	20	virus	virus	NN
cord-002542-f7l4ty2j	37	21	originally	originally	RB
cord-002542-f7l4ty2j	37	22	isolated	isolate	VBN
cord-002542-f7l4ty2j	37	23	from	from	IN
cord-002542-f7l4ty2j	37	24	grass	grass	NN
cord-002542-f7l4ty2j	37	25	grubs	grub	NNS
cord-002542-f7l4ty2j	37	26	in	in	IN
cord-002542-f7l4ty2j	37	27	New	New	NNP
cord-002542-f7l4ty2j	37	28	Zealand	Zealand	NNP
cord-002542-f7l4ty2j	37	29	[	[	-LRB-
cord-002542-f7l4ty2j	37	30	25	25	CD
cord-002542-f7l4ty2j	37	31	]	]	-RRB-
cord-002542-f7l4ty2j	37	32	and	and	CC
cord-002542-f7l4ty2j	37	33	is	be	VBZ
cord-002542-f7l4ty2j	37	34	perhaps	perhaps	RB
cord-002542-f7l4ty2j	37	35	the	the	DT
cord-002542-f7l4ty2j	37	36	best	well	RBS
cord-002542-f7l4ty2j	37	37	-	-	HYPH
cord-002542-f7l4ty2j	37	38	studied	study	VBN
cord-002542-f7l4ty2j	37	39	Alphanodavirus	Alphanodavirus	NNP
cord-002542-f7l4ty2j	37	40	from	from	IN
cord-002542-f7l4ty2j	37	41	the	the	DT
cord-002542-f7l4ty2j	37	42	Nodaviridae	Nodaviridae	NNP
cord-002542-f7l4ty2j	37	43	family	family	NN
cord-002542-f7l4ty2j	37	44	.	.	.
cord-002542-f7l4ty2j	38	1	FHV	FHV	NNP
cord-002542-f7l4ty2j	38	2	infects	infect	VBZ
cord-002542-f7l4ty2j	38	3	Drosophila	Drosophila	NNP
cord-002542-f7l4ty2j	38	4	flies	fly	NNS
cord-002542-f7l4ty2j	38	5	and	and	CC
cord-002542-f7l4ty2j	38	6	cells	cell	NNS
cord-002542-f7l4ty2j	38	7	in	in	IN
cord-002542-f7l4ty2j	38	8	culture	culture	NN
cord-002542-f7l4ty2j	38	9	as	as	RB
cord-002542-f7l4ty2j	38	10	well	well	RB
cord-002542-f7l4ty2j	38	11	as	as	IN
cord-002542-f7l4ty2j	38	12	medically	medically	RB
cord-002542-f7l4ty2j	38	13	important	important	JJ
cord-002542-f7l4ty2j	38	14	genera	genus	NNS
cord-002542-f7l4ty2j	38	15	of	of	IN
cord-002542-f7l4ty2j	38	16	insects	insect	NNS
cord-002542-f7l4ty2j	38	17	including	include	VBG
cord-002542-f7l4ty2j	38	18	mosquitos	mosquitos	NN
cord-002542-f7l4ty2j	38	19	,	,	,
cord-002542-f7l4ty2j	38	20	(	(	-LRB-
cord-002542-f7l4ty2j	38	21	Anopheles	Anopheles	NNP
cord-002542-f7l4ty2j	38	22	gambiae	gambiae	NN
cord-002542-f7l4ty2j	38	23	)	)	-RRB-
cord-002542-f7l4ty2j	38	24	,	,	,
cord-002542-f7l4ty2j	38	25	the	the	DT
cord-002542-f7l4ty2j	38	26	tsetse	tsetse	NN
cord-002542-f7l4ty2j	38	27	fly	fly	NN
cord-002542-f7l4ty2j	38	28	(	(	-LRB-
cord-002542-f7l4ty2j	38	29	Glossina	Glossina	NNP
cord-002542-f7l4ty2j	38	30	morsitans	morsitan	VBD
cord-002542-f7l4ty2j	38	31	morsitans	morsitans	NNP
cord-002542-f7l4ty2j	38	32	Westwood	Westwood	NNP
cord-002542-f7l4ty2j	38	33	)	)	-RRB-
cord-002542-f7l4ty2j	38	34	,	,	,
cord-002542-f7l4ty2j	38	35	and	and	CC
cord-002542-f7l4ty2j	38	36	the	the	DT
cord-002542-f7l4ty2j	38	37	Chagas	Chagas	NNP
cord-002542-f7l4ty2j	38	38	vector	vector	NN
cord-002542-f7l4ty2j	38	39	(	(	-LRB-
cord-002542-f7l4ty2j	38	40	Rhodnius	Rhodnius	NNP
cord-002542-f7l4ty2j	38	41	prolixus	prolixus	NN
cord-002542-f7l4ty2j	38	42	Stal	Stal	NNP
cord-002542-f7l4ty2j	38	43	)	)	-RRB-
cord-002542-f7l4ty2j	38	44	[	[	-LRB-
cord-002542-f7l4ty2j	38	45	26	26	CD
cord-002542-f7l4ty2j	38	46	]	]	-RRB-
cord-002542-f7l4ty2j	38	47	.	.	.
cord-002542-f7l4ty2j	39	1	Infection	infection	NN
cord-002542-f7l4ty2j	39	2	of	of	IN
cord-002542-f7l4ty2j	39	3	these	these	DT
cord-002542-f7l4ty2j	39	4	organisms	organism	NNS
cord-002542-f7l4ty2j	39	5	by	by	IN
cord-002542-f7l4ty2j	39	6	FHV	FHV	NNP
cord-002542-f7l4ty2j	39	7	has	have	VBZ
cord-002542-f7l4ty2j	39	8	been	be	VBN
cord-002542-f7l4ty2j	39	9	demonstrated	demonstrate	VBN
cord-002542-f7l4ty2j	39	10	to	to	TO
cord-002542-f7l4ty2j	39	11	have	have	VB
cord-002542-f7l4ty2j	39	12	similar	similar	JJ
cord-002542-f7l4ty2j	39	13	characteristics	characteristic	NNS
cord-002542-f7l4ty2j	39	14	in	in	IN
cord-002542-f7l4ty2j	39	15	terms	term	NNS
cord-002542-f7l4ty2j	39	16	of	of	IN
cord-002542-f7l4ty2j	39	17	viral	viral	JJ
cord-002542-f7l4ty2j	39	18	titer	titer	NN
cord-002542-f7l4ty2j	39	19	,	,	,
cord-002542-f7l4ty2j	39	20	virus	virus	NN
cord-002542-f7l4ty2j	39	21	dissemination	dissemination	NN
cord-002542-f7l4ty2j	39	22	and	and	CC
cord-002542-f7l4ty2j	39	23	mortality	mortality	NN
cord-002542-f7l4ty2j	39	24	as	as	IN
cord-002542-f7l4ty2j	39	25	has	have	VBZ
cord-002542-f7l4ty2j	39	26	been	be	VBN
cord-002542-f7l4ty2j	39	27	shown	show	VBN
cord-002542-f7l4ty2j	39	28	for	for	IN
cord-002542-f7l4ty2j	39	29	fruit	fruit	NN
cord-002542-f7l4ty2j	39	30	fly	fly	NN
cord-002542-f7l4ty2j	39	31	infections	infection	NNS
cord-002542-f7l4ty2j	39	32	.	.	.
cord-002542-f7l4ty2j	40	1	FHV	FHV	NNP
cord-002542-f7l4ty2j	40	2	provides	provide	VBZ
cord-002542-f7l4ty2j	40	3	an	an	DT
cord-002542-f7l4ty2j	40	4	excellent	excellent	JJ
cord-002542-f7l4ty2j	40	5	model	model	NN
cord-002542-f7l4ty2j	40	6	system	system	NN
cord-002542-f7l4ty2j	40	7	to	to	TO
cord-002542-f7l4ty2j	40	8	study	study	VB
cord-002542-f7l4ty2j	40	9	+	+	CC
cord-002542-f7l4ty2j	40	10	ssRNA	ssRNA	-RRB-
cord-002542-f7l4ty2j	40	11	virus	virus	NN
cord-002542-f7l4ty2j	40	12	evolution	evolution	NN
cord-002542-f7l4ty2j	40	13	by	by	IN
cord-002542-f7l4ty2j	40	14	virtue	virtue	NN
cord-002542-f7l4ty2j	40	15	of	of	IN
cord-002542-f7l4ty2j	40	16	having	have	VBG
cord-002542-f7l4ty2j	40	17	one	one	CD
cord-002542-f7l4ty2j	40	18	of	of	IN
cord-002542-f7l4ty2j	40	19	the	the	DT
cord-002542-f7l4ty2j	40	20	smallest	smallest	RBS
cord-002542-f7l4ty2j	40	21	known	know	VBN
cord-002542-f7l4ty2j	40	22	eukaryotic	eukaryotic	JJ
cord-002542-f7l4ty2j	40	23	virus	virus	NN
cord-002542-f7l4ty2j	40	24	genomes	genome	NNS
cord-002542-f7l4ty2j	40	25	[	[	-LRB-
cord-002542-f7l4ty2j	40	26	27	27	CD
cord-002542-f7l4ty2j	40	27	]	]	-RRB-
cord-002542-f7l4ty2j	40	28	.	.	.
cord-002542-f7l4ty2j	41	1	Moreover	moreover	RB
cord-002542-f7l4ty2j	41	2	,	,	,
cord-002542-f7l4ty2j	41	3	the	the	DT
cord-002542-f7l4ty2j	41	4	viral	viral	JJ
cord-002542-f7l4ty2j	41	5	life	life	NN
cord-002542-f7l4ty2j	41	6	-	-	HYPH
cord-002542-f7l4ty2j	41	7	cycle	cycle	NN
cord-002542-f7l4ty2j	41	8	and	and	CC
cord-002542-f7l4ty2j	41	9	details	detail	NNS
cord-002542-f7l4ty2j	41	10	of	of	IN
cord-002542-f7l4ty2j	41	11	the	the	DT
cord-002542-f7l4ty2j	41	12	molecular	molecular	JJ
cord-002542-f7l4ty2j	41	13	biology	biology	NN
cord-002542-f7l4ty2j	41	14	of	of	IN
cord-002542-f7l4ty2j	41	15	virus	virus	NN
cord-002542-f7l4ty2j	41	16	particle	particle	NN
cord-002542-f7l4ty2j	41	17	assembly	assembly	NN
cord-002542-f7l4ty2j	41	18	,	,	,
cord-002542-f7l4ty2j	41	19	cell	cell	NN
cord-002542-f7l4ty2j	41	20	entry	entry	NN
cord-002542-f7l4ty2j	41	21	and	and	CC
cord-002542-f7l4ty2j	41	22	particle	particle	NN
cord-002542-f7l4ty2j	41	23	disassembly	disassembly	NN
cord-002542-f7l4ty2j	41	24	are	be	VBP
cord-002542-f7l4ty2j	41	25	highly	highly	RB
cord-002542-f7l4ty2j	41	26	-	-	HYPH
cord-002542-f7l4ty2j	41	27	characterized	characterize	VBN
cord-002542-f7l4ty2j	41	28	.	.	.
cord-002542-f7l4ty2j	42	1	FHV	FHV	NNP
cord-002542-f7l4ty2j	42	2	contains	contain	VBZ
cord-002542-f7l4ty2j	42	3	two	two	CD
cord-002542-f7l4ty2j	42	4	genomic	genomic	JJ
cord-002542-f7l4ty2j	42	5	RNAs	rna	NNS
cord-002542-f7l4ty2j	42	6	.	.	.
cord-002542-f7l4ty2j	43	1	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	43	2	(	(	-LRB-
cord-002542-f7l4ty2j	43	3	3107	3107	CD
cord-002542-f7l4ty2j	43	4	nts	nt	NNS
cord-002542-f7l4ty2j	43	5	)	)	-RRB-
cord-002542-f7l4ty2j	43	6	encodes	encode	VBZ
cord-002542-f7l4ty2j	43	7	the	the	DT
cord-002542-f7l4ty2j	43	8	viral	viral	JJ
cord-002542-f7l4ty2j	43	9	RdRp	RdRp	NNP
cord-002542-f7l4ty2j	43	10	and	and	CC
cord-002542-f7l4ty2j	43	11	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	43	12	(	(	-LRB-
cord-002542-f7l4ty2j	43	13	1400	1400	CD
cord-002542-f7l4ty2j	43	14	nts	nt	NNS
cord-002542-f7l4ty2j	43	15	)	)	-RRB-
cord-002542-f7l4ty2j	43	16	encodes	encode	VBZ
cord-002542-f7l4ty2j	43	17	the	the	DT
cord-002542-f7l4ty2j	43	18	viral	viral	JJ
cord-002542-f7l4ty2j	43	19	capsid	capsid	NN
cord-002542-f7l4ty2j	43	20	protein	protein	NN
cord-002542-f7l4ty2j	43	21	.	.	.
cord-002542-f7l4ty2j	44	1	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	44	2	also	also	RB
cord-002542-f7l4ty2j	44	3	expresses	express	VBZ
cord-002542-f7l4ty2j	44	4	a	a	DT
cord-002542-f7l4ty2j	44	5	small	small	JJ
cord-002542-f7l4ty2j	44	6	sub	sub	JJ
cord-002542-f7l4ty2j	44	7	-	-	JJ
cord-002542-f7l4ty2j	44	8	genomic	genomic	JJ
cord-002542-f7l4ty2j	44	9	RNA	RNA	NNP
cord-002542-f7l4ty2j	44	10	,	,	,
cord-002542-f7l4ty2j	44	11	called	call	VBN
cord-002542-f7l4ty2j	44	12	RNA3	RNA3	NNP
cord-002542-f7l4ty2j	44	13	,	,	,
cord-002542-f7l4ty2j	44	14	that	that	WDT
cord-002542-f7l4ty2j	44	15	encodes	encode	VBZ
cord-002542-f7l4ty2j	44	16	the	the	DT
cord-002542-f7l4ty2j	44	17	B2	b2	NN
cord-002542-f7l4ty2j	44	18	protein	protein	NN
cord-002542-f7l4ty2j	44	19	responsible	responsible	JJ
cord-002542-f7l4ty2j	44	20	for	for	IN
cord-002542-f7l4ty2j	44	21	inhibition	inhibition	NN
cord-002542-f7l4ty2j	44	22	of	of	IN
cord-002542-f7l4ty2j	44	23	the	the	DT
cord-002542-f7l4ty2j	44	24	anti	anti	JJ
cord-002542-f7l4ty2j	44	25	-	-	JJ
cord-002542-f7l4ty2j	44	26	viral	viral	JJ
cord-002542-f7l4ty2j	44	27	RNAi	RNAi	NNS
cord-002542-f7l4ty2j	44	28	machinery	machinery	NN
cord-002542-f7l4ty2j	44	29	[	[	-LRB-
cord-002542-f7l4ty2j	44	30	28	28	CD
cord-002542-f7l4ty2j	44	31	]	]	-RRB-
cord-002542-f7l4ty2j	44	32	.	.	.
cord-002542-f7l4ty2j	45	1	FHV	FHV	NNP
cord-002542-f7l4ty2j	45	2	has	have	VBZ
cord-002542-f7l4ty2j	45	3	been	be	VBN
cord-002542-f7l4ty2j	45	4	demonstrated	demonstrate	VBN
cord-002542-f7l4ty2j	45	5	to	to	TO
cord-002542-f7l4ty2j	45	6	form	form	VB
cord-002542-f7l4ty2j	45	7	DI	DI	NNP
cord-002542-f7l4ty2j	45	8	-	-	HYPH
cord-002542-f7l4ty2j	45	9	RNAs	rna	NNS
cord-002542-f7l4ty2j	45	10	in	in	IN
cord-002542-f7l4ty2j	45	11	multiple	multiple	JJ
cord-002542-f7l4ty2j	45	12	independent	independent	JJ
cord-002542-f7l4ty2j	45	13	studies	study	NNS
cord-002542-f7l4ty2j	45	14	spanning	span	VBG
cord-002542-f7l4ty2j	45	15	three	three	CD
cord-002542-f7l4ty2j	45	16	decades	decade	NNS
cord-002542-f7l4ty2j	45	17	both	both	CC
cord-002542-f7l4ty2j	45	18	in	in	IN
cord-002542-f7l4ty2j	45	19	cell	cell	NN
cord-002542-f7l4ty2j	45	20	-	-	HYPH
cord-002542-f7l4ty2j	45	21	culture	culture	NN
cord-002542-f7l4ty2j	45	22	[	[	-LRB-
cord-002542-f7l4ty2j	45	23	8	8	CD
cord-002542-f7l4ty2j	45	24	,	,	,
cord-002542-f7l4ty2j	45	25	26	26	CD
cord-002542-f7l4ty2j	45	26	,	,	,
cord-002542-f7l4ty2j	45	27	[	[	-LRB-
cord-002542-f7l4ty2j	45	28	29	29	CD
cord-002542-f7l4ty2j	45	29	]	]	-RRB-
cord-002542-f7l4ty2j	46	1	[	[	-LRB-
cord-002542-f7l4ty2j	46	2	30	30	CD
cord-002542-f7l4ty2j	46	3	]	]	-RRB-
cord-002542-f7l4ty2j	46	4	[	[	-LRB-
cord-002542-f7l4ty2j	46	5	31	31	CD
cord-002542-f7l4ty2j	46	6	]	]	-RRB-
cord-002542-f7l4ty2j	47	1	[	[	-LRB-
cord-002542-f7l4ty2j	47	2	32	32	CD
cord-002542-f7l4ty2j	47	3	]	]	-RRB-
cord-002542-f7l4ty2j	47	4	and	and	CC
cord-002542-f7l4ty2j	47	5	in	in	IN
cord-002542-f7l4ty2j	47	6	Drosophila	Drosophila	NNP
cord-002542-f7l4ty2j	47	7	melanogaster	melanogaster	NN
cord-002542-f7l4ty2j	47	8	[	[	-LRB-
cord-002542-f7l4ty2j	47	9	33	33	CD
cord-002542-f7l4ty2j	47	10	]	]	-RRB-
cord-002542-f7l4ty2j	47	11	.	.	.
cord-002542-f7l4ty2j	48	1	Many	many	JJ
cord-002542-f7l4ty2j	48	2	of	of	IN
cord-002542-f7l4ty2j	48	3	these	these	DT
cord-002542-f7l4ty2j	48	4	studies	study	NNS
cord-002542-f7l4ty2j	48	5	characterized	characterize	VBD
cord-002542-f7l4ty2j	48	6	individual	individual	JJ
cord-002542-f7l4ty2j	48	7	DI	DI	NNP
cord-002542-f7l4ty2j	48	8	-	-	HYPH
cord-002542-f7l4ty2j	48	9	RNA	RNA	NNP
cord-002542-f7l4ty2j	48	10	genomes	genome	NNS
cord-002542-f7l4ty2j	48	11	through	through	IN
cord-002542-f7l4ty2j	48	12	sub	sub	NN
cord-002542-f7l4ty2j	48	13	-	-	JJ
cord-002542-f7l4ty2j	48	14	cloning	cloning	JJ
cord-002542-f7l4ty2j	48	15	and	and	CC
cord-002542-f7l4ty2j	48	16	Sanger	Sanger	NNP
cord-002542-f7l4ty2j	48	17	sequencing	sequencing	NN
cord-002542-f7l4ty2j	48	18	.	.	.
cord-002542-f7l4ty2j	49	1	Intriguingly	intriguingly	RB
cord-002542-f7l4ty2j	49	2	,	,	,
cord-002542-f7l4ty2j	49	3	many	many	JJ
cord-002542-f7l4ty2j	49	4	of	of	IN
cord-002542-f7l4ty2j	49	5	these	these	DT
cord-002542-f7l4ty2j	49	6	DI	DI	NNP
cord-002542-f7l4ty2j	49	7	-	-	HYPH
cord-002542-f7l4ty2j	49	8	RNAs	rna	NNS
cord-002542-f7l4ty2j	49	9	are	be	VBP
cord-002542-f7l4ty2j	49	10	highly	highly	RB
cord-002542-f7l4ty2j	49	11	similar	similar	JJ
cord-002542-f7l4ty2j	49	12	.	.	.
cord-002542-f7l4ty2j	50	1	This	this	DT
cord-002542-f7l4ty2j	50	2	indicates	indicate	VBZ
cord-002542-f7l4ty2j	50	3	that	that	IN
cord-002542-f7l4ty2j	50	4	either	either	CC
cord-002542-f7l4ty2j	50	5	the	the	DT
cord-002542-f7l4ty2j	50	6	DI	DI	NNP
cord-002542-f7l4ty2j	50	7	-	-	HYPH
cord-002542-f7l4ty2j	50	8	RNAs	rna	NNS
cord-002542-f7l4ty2j	50	9	have	have	VBP
cord-002542-f7l4ty2j	50	10	emerged	emerge	VBN
cord-002542-f7l4ty2j	50	11	due	due	IN
cord-002542-f7l4ty2j	50	12	to	to	IN
cord-002542-f7l4ty2j	50	13	a	a	DT
cord-002542-f7l4ty2j	50	14	common	common	JJ
cord-002542-f7l4ty2j	50	15	mechanism	mechanism	NN
cord-002542-f7l4ty2j	50	16	of	of	IN
cord-002542-f7l4ty2j	50	17	formation	formation	NN
cord-002542-f7l4ty2j	50	18	or	or	CC
cord-002542-f7l4ty2j	50	19	the	the	DT
cord-002542-f7l4ty2j	50	20	presence	presence	NN
cord-002542-f7l4ty2j	50	21	of	of	IN
cord-002542-f7l4ty2j	50	22	a	a	DT
cord-002542-f7l4ty2j	50	23	common	common	JJ
cord-002542-f7l4ty2j	50	24	selectivity	selectivity	NN
cord-002542-f7l4ty2j	50	25	filter	filter	NN
cord-002542-f7l4ty2j	50	26	,	,	,
cord-002542-f7l4ty2j	50	27	or	or	CC
cord-002542-f7l4ty2j	50	28	both	both	DT
cord-002542-f7l4ty2j	50	29	.	.	.
cord-002542-f7l4ty2j	51	1	Our	-PRON-	PRP$
cord-002542-f7l4ty2j	51	2	recent	recent	JJ
cord-002542-f7l4ty2j	51	3	NGS	NGS	NNP
cord-002542-f7l4ty2j	51	4	studies	study	NNS
cord-002542-f7l4ty2j	51	5	of	of	IN
cord-002542-f7l4ty2j	51	6	RNA	RNA	NNP
cord-002542-f7l4ty2j	51	7	recombination	recombination	NN
cord-002542-f7l4ty2j	51	8	in	in	IN
cord-002542-f7l4ty2j	51	9	FHV	FHV	NNP
cord-002542-f7l4ty2j	51	10	revealed	reveal	VBD
cord-002542-f7l4ty2j	51	11	a	a	DT
cord-002542-f7l4ty2j	51	12	diverse	diverse	JJ
cord-002542-f7l4ty2j	51	13	array	array	NN
cord-002542-f7l4ty2j	51	14	of	of	IN
cord-002542-f7l4ty2j	51	15	RNA	rna	NN
cord-002542-f7l4ty2j	51	16	recombination	recombination	NN
cord-002542-f7l4ty2j	51	17	events	event	NNS
cord-002542-f7l4ty2j	51	18	,	,	,
cord-002542-f7l4ty2j	51	19	suggesting	suggest	VBG
cord-002542-f7l4ty2j	51	20	that	that	IN
cord-002542-f7l4ty2j	51	21	the	the	DT
cord-002542-f7l4ty2j	51	22	genomic	genomic	JJ
cord-002542-f7l4ty2j	51	23	landscape	landscape	NN
cord-002542-f7l4ty2j	51	24	of	of	IN
cord-002542-f7l4ty2j	51	25	DI	DI	NNP
cord-002542-f7l4ty2j	51	26	-	-	HYPH
cord-002542-f7l4ty2j	51	27	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	51	28	is	be	VBZ
cord-002542-f7l4ty2j	51	29	highly	highly	RB
cord-002542-f7l4ty2j	51	30	dynamic	dynamic	JJ
cord-002542-f7l4ty2j	51	31	and	and	CC
cord-002542-f7l4ty2j	51	32	likely	likely	RB
cord-002542-f7l4ty2j	51	33	contributes	contribute	VBZ
cord-002542-f7l4ty2j	51	34	significantly	significantly	RB
cord-002542-f7l4ty2j	51	35	to	to	IN
cord-002542-f7l4ty2j	51	36	the	the	DT
cord-002542-f7l4ty2j	51	37	diversity	diversity	NN
cord-002542-f7l4ty2j	51	38	of	of	IN
cord-002542-f7l4ty2j	51	39	viral	viral	JJ
cord-002542-f7l4ty2j	51	40	genomes	genome	NNS
cord-002542-f7l4ty2j	51	41	that	that	WDT
cord-002542-f7l4ty2j	51	42	form	form	VBP
cord-002542-f7l4ty2j	51	43	the	the	DT
cord-002542-f7l4ty2j	51	44	viral	viral	JJ
cord-002542-f7l4ty2j	51	45	quasi	quasi	JJ
cord-002542-f7l4ty2j	51	46	-	-	NN
cord-002542-f7l4ty2j	51	47	species	species	JJ
cord-002542-f7l4ty2j	51	48	[	[	-LRB-
cord-002542-f7l4ty2j	51	49	34	34	CD
cord-002542-f7l4ty2j	51	50	]	]	-RRB-
cord-002542-f7l4ty2j	51	51	.	.	.
cord-002542-f7l4ty2j	52	1	Despite	despite	IN
cord-002542-f7l4ty2j	52	2	these	these	DT
cord-002542-f7l4ty2j	52	3	findings	finding	NNS
cord-002542-f7l4ty2j	52	4	,	,	,
cord-002542-f7l4ty2j	52	5	studies	study	NNS
cord-002542-f7l4ty2j	52	6	to	to	IN
cord-002542-f7l4ty2j	52	7	-	-	HYPH
cord-002542-f7l4ty2j	52	8	date	date	NN
cord-002542-f7l4ty2j	52	9	present	present	NN
cord-002542-f7l4ty2j	52	10	only	only	RB
cord-002542-f7l4ty2j	52	11	a	a	DT
cord-002542-f7l4ty2j	52	12	single	single	JJ
cord-002542-f7l4ty2j	52	13	snap	snap	NN
cord-002542-f7l4ty2j	52	14	-	-	HYPH
cord-002542-f7l4ty2j	52	15	shot	shot	NN
cord-002542-f7l4ty2j	52	16	of	of	IN
cord-002542-f7l4ty2j	52	17	the	the	DT
cord-002542-f7l4ty2j	52	18	DI	DI	NNP
cord-002542-f7l4ty2j	52	19	-	-	HYPH
cord-002542-f7l4ty2j	52	20	RNA	RNA	NNP
cord-002542-f7l4ty2j	52	21	genome	genome	NN
cord-002542-f7l4ty2j	52	22	landscape	landscape	NN
cord-002542-f7l4ty2j	52	23	and	and	CC
cord-002542-f7l4ty2j	52	24	do	do	VBP
cord-002542-f7l4ty2j	52	25	not	not	RB
cord-002542-f7l4ty2j	52	26	capture	capture	VB
cord-002542-f7l4ty2j	52	27	the	the	DT
cord-002542-f7l4ty2j	52	28	pathways	pathway	NNS
cord-002542-f7l4ty2j	52	29	of	of	IN
cord-002542-f7l4ty2j	52	30	their	-PRON-	PRP$
cord-002542-f7l4ty2j	52	31	emergence	emergence	NN
cord-002542-f7l4ty2j	52	32	and	and	CC
cord-002542-f7l4ty2j	52	33	evolution	evolution	NN
cord-002542-f7l4ty2j	52	34	nor	nor	CC
cord-002542-f7l4ty2j	52	35	characterize	characterize	VB
cord-002542-f7l4ty2j	52	36	any	any	DT
cord-002542-f7l4ty2j	52	37	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	52	38	DI	DI	NNP
cord-002542-f7l4ty2j	52	39	-	-	HYPH
cord-002542-f7l4ty2j	52	40	RNA	RNA	NNP
cord-002542-f7l4ty2j	52	41	species	specie	NNS
cord-002542-f7l4ty2j	52	42	that	that	WDT
cord-002542-f7l4ty2j	52	43	might	may	MD
cord-002542-f7l4ty2j	52	44	arise	arise	VB
cord-002542-f7l4ty2j	52	45	during	during	IN
cord-002542-f7l4ty2j	52	46	these	these	DT
cord-002542-f7l4ty2j	52	47	processes	process	NNS
cord-002542-f7l4ty2j	52	48	.	.	.
cord-002542-f7l4ty2j	53	1	In	in	IN
cord-002542-f7l4ty2j	53	2	order	order	NN
cord-002542-f7l4ty2j	53	3	to	to	TO
cord-002542-f7l4ty2j	53	4	resolve	resolve	VB
cord-002542-f7l4ty2j	53	5	the	the	DT
cord-002542-f7l4ty2j	53	6	potential	potential	JJ
cord-002542-f7l4ty2j	53	7	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	53	8	of	of	IN
cord-002542-f7l4ty2j	53	9	DI	DI	NNP
cord-002542-f7l4ty2j	53	10	-	-	HYPH
cord-002542-f7l4ty2j	53	11	RNA	RNA	NNP
cord-002542-f7l4ty2j	53	12	emergence	emergence	NN
cord-002542-f7l4ty2j	53	13	and	and	CC
cord-002542-f7l4ty2j	53	14	elucidate	elucidate	VB
cord-002542-f7l4ty2j	53	15	the	the	DT
cord-002542-f7l4ty2j	53	16	evolutionary	evolutionary	JJ
cord-002542-f7l4ty2j	53	17	pathways	pathway	NNS
cord-002542-f7l4ty2j	53	18	that	that	WDT
cord-002542-f7l4ty2j	53	19	lead	lead	VBP
cord-002542-f7l4ty2j	53	20	to	to	IN
cord-002542-f7l4ty2j	53	21	the	the	DT
cord-002542-f7l4ty2j	53	22	formation	formation	NN
cord-002542-f7l4ty2j	53	23	of	of	IN
cord-002542-f7l4ty2j	53	24	'	'	``
cord-002542-f7l4ty2j	53	25	mature	mature	JJ
cord-002542-f7l4ty2j	53	26	'	'	''
cord-002542-f7l4ty2j	53	27	DI	di	NN
cord-002542-f7l4ty2j	53	28	-	-	HYPH
cord-002542-f7l4ty2j	53	29	RNAs	rna	NNS
cord-002542-f7l4ty2j	53	30	,	,	,
cord-002542-f7l4ty2j	53	31	we	-PRON-	PRP
cord-002542-f7l4ty2j	53	32	performed	perform	VBD
cord-002542-f7l4ty2j	53	33	high	high	JJ
cord-002542-f7l4ty2j	53	34	-	-	HYPH
cord-002542-f7l4ty2j	53	35	titer	titer	NN
cord-002542-f7l4ty2j	53	36	serial	serial	JJ
cord-002542-f7l4ty2j	53	37	passaging	passaging	NN
cord-002542-f7l4ty2j	53	38	of	of	IN
cord-002542-f7l4ty2j	53	39	FHV	FHV	NNP
cord-002542-f7l4ty2j	53	40	in	in	IN
cord-002542-f7l4ty2j	53	41	cell	cell	NN
cord-002542-f7l4ty2j	53	42	culture	culture	NN
cord-002542-f7l4ty2j	53	43	and	and	CC
cord-002542-f7l4ty2j	53	44	characterized	characterize	VBD
cord-002542-f7l4ty2j	53	45	the	the	DT
cord-002542-f7l4ty2j	53	46	encapsidated	encapsidate	VBN
cord-002542-f7l4ty2j	53	47	RNA	RNA	NNP
cord-002542-f7l4ty2j	53	48	using	use	VBG
cord-002542-f7l4ty2j	53	49	RNAseq	RNAseq	NNP
cord-002542-f7l4ty2j	53	50	.	.	.
cord-002542-f7l4ty2j	54	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	54	2	used	use	VBD
cord-002542-f7l4ty2j	54	3	Illumina	Illumina	NNP
cord-002542-f7l4ty2j	54	4	HiSeq	HiSeq	NNP
cord-002542-f7l4ty2j	54	5	sequencing	sequencing	NN
cord-002542-f7l4ty2j	54	6	of	of	IN
cord-002542-f7l4ty2j	54	7	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	54	8	generated	generate	VBD
cord-002542-f7l4ty2j	54	9	libraries	library	NNS
cord-002542-f7l4ty2j	54	10	to	to	TO
cord-002542-f7l4ty2j	54	11	provide	provide	VB
cord-002542-f7l4ty2j	54	12	a	a	DT
cord-002542-f7l4ty2j	54	13	high	high	JJ
cord-002542-f7l4ty2j	54	14	-	-	HYPH
cord-002542-f7l4ty2j	54	15	resolution	resolution	NN
cord-002542-f7l4ty2j	54	16	and	and	CC
cord-002542-f7l4ty2j	54	17	high	high	JJ
cord-002542-f7l4ty2j	54	18	-	-	HYPH
cord-002542-f7l4ty2j	54	19	confidence	confidence	NN
cord-002542-f7l4ty2j	54	20	quantification	quantification	NN
cord-002542-f7l4ty2j	54	21	of	of	IN
cord-002542-f7l4ty2j	54	22	individual	individual	JJ
cord-002542-f7l4ty2j	54	23	recombination	recombination	NN
cord-002542-f7l4ty2j	54	24	events	event	NNS
cord-002542-f7l4ty2j	54	25	.	.	.
cord-002542-f7l4ty2j	55	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	55	2	combined	combine	VBD
cord-002542-f7l4ty2j	55	3	this	this	DT
cord-002542-f7l4ty2j	55	4	information	information	NN
cord-002542-f7l4ty2j	55	5	with	with	IN
cord-002542-f7l4ty2j	55	6	long	long	RB
cord-002542-f7l4ty2j	55	7	-	-	HYPH
cord-002542-f7l4ty2j	55	8	read	read	VBN
cord-002542-f7l4ty2j	55	9	Oxford	Oxford	NNP
cord-002542-f7l4ty2j	55	10	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	55	11	Technologies	Technologies	NNP
cord-002542-f7l4ty2j	55	12	's	's	POS
cord-002542-f7l4ty2j	55	13	(	(	-LRB-
cord-002542-f7l4ty2j	55	14	ONT	ONT	NNP
cord-002542-f7l4ty2j	55	15	)	)	-RRB-
cord-002542-f7l4ty2j	55	16	MinION	minion	NN
cord-002542-f7l4ty2j	55	17	sequencing	sequencing	NN
cord-002542-f7l4ty2j	55	18	to	to	TO
cord-002542-f7l4ty2j	55	19	resolve	resolve	VB
cord-002542-f7l4ty2j	55	20	the	the	DT
cord-002542-f7l4ty2j	55	21	topology	topology	NN
cord-002542-f7l4ty2j	55	22	of	of	IN
cord-002542-f7l4ty2j	55	23	full	full	JJ
cord-002542-f7l4ty2j	55	24	-	-	HYPH
cord-002542-f7l4ty2j	55	25	length	length	NN
cord-002542-f7l4ty2j	55	26	and	and	CC
cord-002542-f7l4ty2j	55	27	defective	defective	JJ
cord-002542-f7l4ty2j	55	28	RNA	RNA	NNP
cord-002542-f7l4ty2j	55	29	genomes	genome	NNS
cord-002542-f7l4ty2j	55	30	.	.	.
cord-002542-f7l4ty2j	56	1	By	by	IN
cord-002542-f7l4ty2j	56	2	combining	combine	VBG
cord-002542-f7l4ty2j	56	3	these	these	DT
cord-002542-f7l4ty2j	56	4	data	datum	NNS
cord-002542-f7l4ty2j	56	5	,	,	,
cord-002542-f7l4ty2j	56	6	we	-PRON-	PRP
cord-002542-f7l4ty2j	56	7	aimed	aim	VBD
cord-002542-f7l4ty2j	56	8	to	to	TO
cord-002542-f7l4ty2j	56	9	determine	determine	VB
cord-002542-f7l4ty2j	56	10	the	the	DT
cord-002542-f7l4ty2j	56	11	correlation	correlation	NN
cord-002542-f7l4ty2j	56	12	of	of	IN
cord-002542-f7l4ty2j	56	13	recombination	recombination	NN
cord-002542-f7l4ty2j	56	14	events	event	NNS
cord-002542-f7l4ty2j	56	15	within	within	IN
cord-002542-f7l4ty2j	56	16	single	single	JJ
cord-002542-f7l4ty2j	56	17	RNA	RNA	NNP
cord-002542-f7l4ty2j	56	18	virus	virus	NN
cord-002542-f7l4ty2j	56	19	genomes	genome	NNS
cord-002542-f7l4ty2j	56	20	,	,	,
cord-002542-f7l4ty2j	56	21	characterize	characterize	VB
cord-002542-f7l4ty2j	56	22	the	the	DT
cord-002542-f7l4ty2j	56	23	distribution	distribution	NN
cord-002542-f7l4ty2j	56	24	of	of	IN
cord-002542-f7l4ty2j	56	25	defective	defective	JJ
cord-002542-f7l4ty2j	56	26	RNA	RNA	NNP
cord-002542-f7l4ty2j	56	27	genomes	genome	NNS
cord-002542-f7l4ty2j	56	28	,	,	,
cord-002542-f7l4ty2j	56	29	and	and	CC
cord-002542-f7l4ty2j	56	30	determine	determine	VB
cord-002542-f7l4ty2j	56	31	the	the	DT
cord-002542-f7l4ty2j	56	32	exact	exact	JJ
cord-002542-f7l4ty2j	56	33	make	make	NN
cord-002542-f7l4ty2j	56	34	-	-	HYPH
cord-002542-f7l4ty2j	56	35	up	up	NN
cord-002542-f7l4ty2j	56	36	of	of	IN
cord-002542-f7l4ty2j	56	37	DI	DI	NNP
cord-002542-f7l4ty2j	56	38	-	-	HYPH
cord-002542-f7l4ty2j	56	39	RNAs	rna	NNS
cord-002542-f7l4ty2j	56	40	during	during	IN
cord-002542-f7l4ty2j	56	41	serial	serial	JJ
cord-002542-f7l4ty2j	56	42	passaging	passaging	NN
cord-002542-f7l4ty2j	56	43	of	of	IN
cord-002542-f7l4ty2j	56	44	FHV	FHV	NNP
cord-002542-f7l4ty2j	56	45	in	in	IN
cord-002542-f7l4ty2j	56	46	cell	cell	NN
cord-002542-f7l4ty2j	56	47	culture	culture	NN
cord-002542-f7l4ty2j	56	48	.	.	.
cord-002542-f7l4ty2j	57	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	57	2	recently	recently	RB
cord-002542-f7l4ty2j	57	3	developed	develop	VBD
cord-002542-f7l4ty2j	57	4	the	the	DT
cord-002542-f7l4ty2j	57	5	'	'	``
cord-002542-f7l4ty2j	57	6	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	57	7	'	'	''
cord-002542-f7l4ty2j	57	8	method	method	NN
cord-002542-f7l4ty2j	57	9	for	for	IN
cord-002542-f7l4ty2j	57	10	RNAseq	RNAseq	NNP
cord-002542-f7l4ty2j	57	11	that	that	WDT
cord-002542-f7l4ty2j	57	12	uses	use	VBZ
cord-002542-f7l4ty2j	57	13	copper	copper	NN
cord-002542-f7l4ty2j	57	14	-	-	HYPH
cord-002542-f7l4ty2j	57	15	catalyzed	catalyze	VBN
cord-002542-f7l4ty2j	57	16	alkyne	alkyne	NN
cord-002542-f7l4ty2j	57	17	-	-	HYPH
cord-002542-f7l4ty2j	57	18	azide	azide	NN
cord-002542-f7l4ty2j	57	19	cycloaddition	cycloaddition	NN
cord-002542-f7l4ty2j	57	20	(	(	-LRB-
cord-002542-f7l4ty2j	57	21	CuAAC	CuAAC	NNP
cord-002542-f7l4ty2j	57	22	)	)	-RRB-
cord-002542-f7l4ty2j	57	23	,	,	,
cord-002542-f7l4ty2j	57	24	a	a	DT
cord-002542-f7l4ty2j	57	25	click	click	VB
cord-002542-f7l4ty2j	57	26	-	-	HYPH
cord-002542-f7l4ty2j	57	27	chemistry	chemistry	NN
cord-002542-f7l4ty2j	57	28	reaction	reaction	NN
cord-002542-f7l4ty2j	57	29	,	,	,
cord-002542-f7l4ty2j	57	30	for	for	IN
cord-002542-f7l4ty2j	57	31	RNAseq	rnaseq	NN
cord-002542-f7l4ty2j	57	32	library	library	NN
cord-002542-f7l4ty2j	57	33	synthesis	synthesis	NN
cord-002542-f7l4ty2j	57	34	[	[	-LRB-
cord-002542-f7l4ty2j	57	35	35	35	CD
cord-002542-f7l4ty2j	57	36	]	]	-RRB-
cord-002542-f7l4ty2j	57	37	.	.	.
cord-002542-f7l4ty2j	58	1	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	58	2	provides	provide	VBZ
cord-002542-f7l4ty2j	58	3	a	a	DT
cord-002542-f7l4ty2j	58	4	robust	robust	JJ
cord-002542-f7l4ty2j	58	5	platform	platform	NN
cord-002542-f7l4ty2j	58	6	on	on	IN
cord-002542-f7l4ty2j	58	7	which	which	WDT
cord-002542-f7l4ty2j	58	8	to	to	TO
cord-002542-f7l4ty2j	58	9	study	study	VB
cord-002542-f7l4ty2j	58	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	58	11	recombination	recombination	NN
cord-002542-f7l4ty2j	58	12	in	in	IN
cord-002542-f7l4ty2j	58	13	RNA	RNA	NNP
cord-002542-f7l4ty2j	58	14	viruses	virus	NNS
cord-002542-f7l4ty2j	58	15	.	.	.
cord-002542-f7l4ty2j	59	1	Artifactual	artifactual	JJ
cord-002542-f7l4ty2j	59	2	recombination	recombination	NN
cord-002542-f7l4ty2j	59	3	is	be	VBZ
cord-002542-f7l4ty2j	59	4	a	a	DT
cord-002542-f7l4ty2j	59	5	common	common	JJ
cord-002542-f7l4ty2j	59	6	contaminant	contaminant	NN
cord-002542-f7l4ty2j	59	7	in	in	IN
cord-002542-f7l4ty2j	59	8	NGS	NGS	NNP
cord-002542-f7l4ty2j	59	9	library	library	NN
cord-002542-f7l4ty2j	59	10	generation	generation	NN
cord-002542-f7l4ty2j	59	11	and	and	CC
cord-002542-f7l4ty2j	59	12	can	can	MD
cord-002542-f7l4ty2j	59	13	easily	easily	RB
cord-002542-f7l4ty2j	59	14	obscure	obscure	VB
cord-002542-f7l4ty2j	59	15	rare	rare	JJ
cord-002542-f7l4ty2j	59	16	or	or	CC
cord-002542-f7l4ty2j	59	17	non	non	JJ
cord-002542-f7l4ty2j	59	18	-	-	JJ
cord-002542-f7l4ty2j	59	19	canonical	canonical	JJ
cord-002542-f7l4ty2j	59	20	recombinant	recombinant	JJ
cord-002542-f7l4ty2j	59	21	species	specie	NNS
cord-002542-f7l4ty2j	59	22	.	.	.
cord-002542-f7l4ty2j	60	1	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	60	2	does	do	VBZ
cord-002542-f7l4ty2j	60	3	not	not	RB
cord-002542-f7l4ty2j	60	4	require	require	VB
cord-002542-f7l4ty2j	60	5	template	template	NN
cord-002542-f7l4ty2j	60	6	fragmentation	fragmentation	NN
cord-002542-f7l4ty2j	60	7	and	and	CC
cord-002542-f7l4ty2j	60	8	replaces	replace	VBZ
cord-002542-f7l4ty2j	60	9	enzymatic	enzymatic	JJ
cord-002542-f7l4ty2j	60	10	ligation	ligation	NN
cord-002542-f7l4ty2j	60	11	steps	step	NNS
cord-002542-f7l4ty2j	60	12	commonly	commonly	RB
cord-002542-f7l4ty2j	60	13	required	require	VBN
cord-002542-f7l4ty2j	60	14	in	in	IN
cord-002542-f7l4ty2j	60	15	NGS	NGS	NNP
cord-002542-f7l4ty2j	60	16	library	library	NN
cord-002542-f7l4ty2j	60	17	generation	generation	NN
cord-002542-f7l4ty2j	60	18	with	with	IN
cord-002542-f7l4ty2j	60	19	click	click	NN
cord-002542-f7l4ty2j	60	20	-	-	HYPH
cord-002542-f7l4ty2j	60	21	chemistry	chemistry	NN
cord-002542-f7l4ty2j	60	22	.	.	.
cord-002542-f7l4ty2j	61	1	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	61	2	works	work	VBZ
cord-002542-f7l4ty2j	61	3	by	by	IN
cord-002542-f7l4ty2j	61	4	introducing	introduce	VBG
cord-002542-f7l4ty2j	61	5	small	small	JJ
cord-002542-f7l4ty2j	61	6	amounts	amount	NNS
cord-002542-f7l4ty2j	61	7	of	of	IN
cord-002542-f7l4ty2j	61	8	azido	azido	NN
cord-002542-f7l4ty2j	61	9	-	-	HYPH
cord-002542-f7l4ty2j	61	10	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	61	11	(	(	-LRB-
cord-002542-f7l4ty2j	61	12	AzNTPs	AzNTPs	NNP
cord-002542-f7l4ty2j	61	13	)	)	-RRB-
cord-002542-f7l4ty2j	61	14	into	into	IN
cord-002542-f7l4ty2j	61	15	RT	RT	NNP
cord-002542-f7l4ty2j	61	16	-	-	HYPH
cord-002542-f7l4ty2j	61	17	PCR	PCR	NNP
cord-002542-f7l4ty2j	61	18	reactions	reaction	NNS
cord-002542-f7l4ty2j	61	19	to	to	TO
cord-002542-f7l4ty2j	61	20	generate	generate	VB
cord-002542-f7l4ty2j	61	21	azido	azido	NNP
cord-002542-f7l4ty2j	61	22	-	-	HYPH
cord-002542-f7l4ty2j	61	23	terminated	terminate	VBN
cord-002542-f7l4ty2j	61	24	cDNA	cdna	NN
cord-002542-f7l4ty2j	61	25	transcripts	transcript	NNS
cord-002542-f7l4ty2j	61	26	.	.	.
cord-002542-f7l4ty2j	62	1	These	these	DT
cord-002542-f7l4ty2j	62	2	cDNA	cdna	NN
cord-002542-f7l4ty2j	62	3	fragments	fragment	NNS
cord-002542-f7l4ty2j	62	4	are	be	VBP
cord-002542-f7l4ty2j	62	5	subsequently	subsequently	RB
cord-002542-f7l4ty2j	62	6	mixed	mix	VBN
cord-002542-f7l4ty2j	62	7	with	with	IN
cord-002542-f7l4ty2j	62	8	alkyne	alkyne	NN
cord-002542-f7l4ty2j	62	9	-	-	HYPH
cord-002542-f7l4ty2j	62	10	labelled	label	VBN
cord-002542-f7l4ty2j	62	11	DNA	dna	NN
cord-002542-f7l4ty2j	62	12	adaptors	adaptor	NNS
cord-002542-f7l4ty2j	62	13	.	.	.
cord-002542-f7l4ty2j	63	1	The	the	DT
cord-002542-f7l4ty2j	63	2	addition	addition	NN
cord-002542-f7l4ty2j	63	3	of	of	IN
cord-002542-f7l4ty2j	63	4	a	a	DT
cord-002542-f7l4ty2j	63	5	copper	copper	NN
cord-002542-f7l4ty2j	63	6	catalyst	catalyst	NN
cord-002542-f7l4ty2j	63	7	results	result	NNS
cord-002542-f7l4ty2j	63	8	in	in	IN
cord-002542-f7l4ty2j	63	9	the	the	DT
cord-002542-f7l4ty2j	63	10	'	'	``
cord-002542-f7l4ty2j	63	11	click	click	NN
cord-002542-f7l4ty2j	63	12	-	-	HYPH
cord-002542-f7l4ty2j	63	13	ligation	ligation	NN
cord-002542-f7l4ty2j	63	14	'	'	''
cord-002542-f7l4ty2j	63	15	of	of	IN
cord-002542-f7l4ty2j	63	16	the	the	DT
cord-002542-f7l4ty2j	63	17	two	two	CD
cord-002542-f7l4ty2j	63	18	chemically	chemically	RB
cord-002542-f7l4ty2j	63	19	-	-	HYPH
cord-002542-f7l4ty2j	63	20	functionalized	functionalize	VBN
cord-002542-f7l4ty2j	63	21	DNA	dna	NN
cord-002542-f7l4ty2j	63	22	substrates	substrate	NNS
cord-002542-f7l4ty2j	63	23	to	to	TO
cord-002542-f7l4ty2j	63	24	produce	produce	VB
cord-002542-f7l4ty2j	63	25	an	an	DT
cord-002542-f7l4ty2j	63	26	unnatural	unnatural	JJ
cord-002542-f7l4ty2j	63	27	triazole	triazole	NN
cord-002542-f7l4ty2j	63	28	-	-	HYPH
cord-002542-f7l4ty2j	63	29	linked	link	VBN
cord-002542-f7l4ty2j	63	30	single	single	RB
cord-002542-f7l4ty2j	63	31	-	-	HYPH
cord-002542-f7l4ty2j	63	32	stranded	strand	VBN
cord-002542-f7l4ty2j	63	33	DNA	dna	NN
cord-002542-f7l4ty2j	63	34	molecule	molecule	NN
cord-002542-f7l4ty2j	63	35	[	[	-LRB-
cord-002542-f7l4ty2j	63	36	36	36	CD
cord-002542-f7l4ty2j	63	37	]	]	-RRB-
cord-002542-f7l4ty2j	63	38	.	.	.
cord-002542-f7l4ty2j	64	1	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	64	2	prevents	prevent	VBZ
cord-002542-f7l4ty2j	64	3	template	template	NN
cord-002542-f7l4ty2j	64	4	switching	switch	VBG
cord-002542-f7l4ty2j	64	5	during	during	IN
cord-002542-f7l4ty2j	64	6	RT	RT	NNP
cord-002542-f7l4ty2j	64	7	-	-	HYPH
cord-002542-f7l4ty2j	64	8	PCR	PCR	NNP
cord-002542-f7l4ty2j	64	9	as	as	RB
cord-002542-f7l4ty2j	64	10	well	well	RB
cord-002542-f7l4ty2j	64	11	as	as	IN
cord-002542-f7l4ty2j	64	12	non	non	JJ
cord-002542-f7l4ty2j	64	13	-	-	JJ
cord-002542-f7l4ty2j	64	14	specific	specific	JJ
cord-002542-f7l4ty2j	64	15	ligation	ligation	NN
cord-002542-f7l4ty2j	64	16	of	of	IN
cord-002542-f7l4ty2j	64	17	RNA	RNA	NNP
cord-002542-f7l4ty2j	64	18	fragments	fragment	NNS
cord-002542-f7l4ty2j	64	19	.	.	.
cord-002542-f7l4ty2j	65	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	65	2	demonstrated	demonstrate	VBD
cord-002542-f7l4ty2j	65	3	that	that	IN
cord-002542-f7l4ty2j	65	4	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	65	5	reduces	reduce	VBZ
cord-002542-f7l4ty2j	65	6	artifactual	artifactual	JJ
cord-002542-f7l4ty2j	65	7	recombination	recombination	NN
cord-002542-f7l4ty2j	65	8	to	to	IN
cord-002542-f7l4ty2j	65	9	fewer	few	JJR
cord-002542-f7l4ty2j	65	10	than	than	IN
cord-002542-f7l4ty2j	65	11	3	3	CD
cord-002542-f7l4ty2j	65	12	events	event	NNS
cord-002542-f7l4ty2j	65	13	per	per	IN
cord-002542-f7l4ty2j	65	14	million	million	CD
cord-002542-f7l4ty2j	65	15	mapped	mapped	NNS
cord-002542-f7l4ty2j	65	16	reads	read	VBZ
cord-002542-f7l4ty2j	65	17	[	[	-LRB-
cord-002542-f7l4ty2j	65	18	35	35	CD
cord-002542-f7l4ty2j	65	19	]	]	-RRB-
cord-002542-f7l4ty2j	65	20	.	.	.
cord-002542-f7l4ty2j	66	1	As	as	IN
cord-002542-f7l4ty2j	66	2	a	a	DT
cord-002542-f7l4ty2j	66	3	result	result	NN
cord-002542-f7l4ty2j	66	4	,	,	,
cord-002542-f7l4ty2j	66	5	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	66	6	provides	provide	VBZ
cord-002542-f7l4ty2j	66	7	a	a	DT
cord-002542-f7l4ty2j	66	8	superior	superior	JJ
cord-002542-f7l4ty2j	66	9	method	method	NN
cord-002542-f7l4ty2j	66	10	for	for	IN
cord-002542-f7l4ty2j	66	11	the	the	DT
cord-002542-f7l4ty2j	66	12	detection	detection	NN
cord-002542-f7l4ty2j	66	13	of	of	IN
cord-002542-f7l4ty2j	66	14	DI	DI	NNP
cord-002542-f7l4ty2j	66	15	-	-	HYPH
cord-002542-f7l4ty2j	66	16	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	66	17	and	and	CC
cord-002542-f7l4ty2j	66	18	RNA	RNA	NNP
cord-002542-f7l4ty2j	66	19	recombination	recombination	NN
cord-002542-f7l4ty2j	66	20	events	event	NNS
cord-002542-f7l4ty2j	66	21	.	.	.
cord-002542-f7l4ty2j	67	1	The	the	DT
cord-002542-f7l4ty2j	67	2	Oxford	Oxford	NNP
cord-002542-f7l4ty2j	67	3	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	67	4	Technologies	Technologies	NNPS
cord-002542-f7l4ty2j	67	5	's	's	POS
cord-002542-f7l4ty2j	67	6	(	(	-LRB-
cord-002542-f7l4ty2j	67	7	ONT	ONT	NNP
cord-002542-f7l4ty2j	67	8	)	)	-RRB-
cord-002542-f7l4ty2j	67	9	MinION	MinION	NNP
cord-002542-f7l4ty2j	67	10	is	be	VBZ
cord-002542-f7l4ty2j	67	11	a	a	DT
cord-002542-f7l4ty2j	67	12	small	small	JJ
cord-002542-f7l4ty2j	67	13	handheld	handheld	JJ
cord-002542-f7l4ty2j	67	14	sequencing	sequencing	NN
cord-002542-f7l4ty2j	67	15	device	device	NN
cord-002542-f7l4ty2j	67	16	[	[	-LRB-
cord-002542-f7l4ty2j	67	17	37	37	CD
cord-002542-f7l4ty2j	67	18	]	]	-RRB-
cord-002542-f7l4ty2j	67	19	poised	poise	VBN
cord-002542-f7l4ty2j	67	20	to	to	TO
cord-002542-f7l4ty2j	67	21	revolutionize	revolutionize	VB
cord-002542-f7l4ty2j	67	22	the	the	DT
cord-002542-f7l4ty2j	67	23	next	next	JJ
cord-002542-f7l4ty2j	67	24	-	-	HYPH
cord-002542-f7l4ty2j	67	25	generation	generation	NN
cord-002542-f7l4ty2j	67	26	sequencing	sequencing	NN
cord-002542-f7l4ty2j	67	27	field	field	NN
cord-002542-f7l4ty2j	67	28	by	by	IN
cord-002542-f7l4ty2j	67	29	providing	provide	VBG
cord-002542-f7l4ty2j	67	30	realtime	realtime	NN
cord-002542-f7l4ty2j	67	31	,	,	,
cord-002542-f7l4ty2j	67	32	high	high	JJ
cord-002542-f7l4ty2j	67	33	-	-	HYPH
cord-002542-f7l4ty2j	67	34	throughput	throughput	NN
cord-002542-f7l4ty2j	67	35	and	and	CC
cord-002542-f7l4ty2j	67	36	long	long	JJ
cord-002542-f7l4ty2j	67	37	-	-	HYPH
cord-002542-f7l4ty2j	67	38	range	range	NN
cord-002542-f7l4ty2j	67	39	(	(	-LRB-
cord-002542-f7l4ty2j	67	40	over	over	IN
cord-002542-f7l4ty2j	67	41	882	882	CD
cord-002542-f7l4ty2j	67	42	kbp	kbp	NNS
cord-002542-f7l4ty2j	67	43	[	[	-LRB-
cord-002542-f7l4ty2j	67	44	38	38	CD
cord-002542-f7l4ty2j	67	45	]	]	-RRB-
cord-002542-f7l4ty2j	67	46	)	)	-RRB-
cord-002542-f7l4ty2j	67	47	sequences	sequence	NNS
cord-002542-f7l4ty2j	67	48	of	of	IN
cord-002542-f7l4ty2j	67	49	DNA	dna	NN
cord-002542-f7l4ty2j	67	50	samples	sample	NNS
cord-002542-f7l4ty2j	67	51	with	with	IN
cord-002542-f7l4ty2j	67	52	minimal	minimal	JJ
cord-002542-f7l4ty2j	67	53	sample	sample	NN
cord-002542-f7l4ty2j	67	54	prep	prep	NN
cord-002542-f7l4ty2j	67	55	.	.	.
cord-002542-f7l4ty2j	68	1	ONT	ONT	NNP
cord-002542-f7l4ty2j	68	2	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	68	3	sequencing	sequencing	NN
cord-002542-f7l4ty2j	68	4	has	have	VBZ
cord-002542-f7l4ty2j	68	5	been	be	VBN
cord-002542-f7l4ty2j	68	6	used	use	VBN
cord-002542-f7l4ty2j	68	7	to	to	TO
cord-002542-f7l4ty2j	68	8	rapidly	rapidly	RB
cord-002542-f7l4ty2j	68	9	characterize	characterize	VB
cord-002542-f7l4ty2j	68	10	virus	virus	NN
cord-002542-f7l4ty2j	68	11	genomes	genome	NNS
cord-002542-f7l4ty2j	68	12	from	from	IN
cord-002542-f7l4ty2j	68	13	metagenomic	metagenomic	NNP
cord-002542-f7l4ty2j	68	14	samples	sample	NNS
cord-002542-f7l4ty2j	68	15	[	[	-LRB-
cord-002542-f7l4ty2j	68	16	39	39	CD
cord-002542-f7l4ty2j	68	17	]	]	-RRB-
cord-002542-f7l4ty2j	68	18	,	,	,
cord-002542-f7l4ty2j	68	19	in	in	IN
cord-002542-f7l4ty2j	68	20	the	the	DT
cord-002542-f7l4ty2j	68	21	midst	midst	NN
cord-002542-f7l4ty2j	68	22	of	of	IN
cord-002542-f7l4ty2j	68	23	Ebola	Ebola	NNP
cord-002542-f7l4ty2j	68	24	virus	virus	NN
cord-002542-f7l4ty2j	68	25	outbreaks	outbreak	NNS
cord-002542-f7l4ty2j	68	26	[	[	-LRB-
cord-002542-f7l4ty2j	68	27	40	40	CD
cord-002542-f7l4ty2j	68	28	]	]	-RRB-
cord-002542-f7l4ty2j	68	29	,	,	,
cord-002542-f7l4ty2j	68	30	and	and	CC
cord-002542-f7l4ty2j	68	31	in	in	IN
cord-002542-f7l4ty2j	68	32	targeted	target	VBN
cord-002542-f7l4ty2j	68	33	studies	study	NNS
cord-002542-f7l4ty2j	68	34	aimed	aim	VBN
cord-002542-f7l4ty2j	68	35	at	at	IN
cord-002542-f7l4ty2j	68	36	characterizing	characterize	VBG
cord-002542-f7l4ty2j	68	37	sequence	sequence	NN
cord-002542-f7l4ty2j	68	38	variations	variation	NNS
cord-002542-f7l4ty2j	68	39	within	within	IN
cord-002542-f7l4ty2j	68	40	influenza	influenza	NN
cord-002542-f7l4ty2j	68	41	virus	virus	NN
cord-002542-f7l4ty2j	68	42	samples	sample	NNS
cord-002542-f7l4ty2j	68	43	[	[	-LRB-
cord-002542-f7l4ty2j	68	44	41	41	CD
cord-002542-f7l4ty2j	68	45	]	]	-RRB-
cord-002542-f7l4ty2j	68	46	.	.	.
cord-002542-f7l4ty2j	69	1	Highly	highly	RB
cord-002542-f7l4ty2j	69	2	parallel	parallel	JJ
cord-002542-f7l4ty2j	69	3	direct	direct	JJ
cord-002542-f7l4ty2j	69	4	RNA	rna	NN
cord-002542-f7l4ty2j	69	5	sequencing	sequencing	NN
cord-002542-f7l4ty2j	69	6	using	use	VBG
cord-002542-f7l4ty2j	69	7	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	69	8	technology	technology	NN
cord-002542-f7l4ty2j	69	9	was	be	VBD
cord-002542-f7l4ty2j	69	10	also	also	RB
cord-002542-f7l4ty2j	69	11	recently	recently	RB
cord-002542-f7l4ty2j	69	12	reported	report	VBN
cord-002542-f7l4ty2j	69	13	[	[	-LRB-
cord-002542-f7l4ty2j	69	14	42	42	CD
cord-002542-f7l4ty2j	69	15	]	]	-RRB-
cord-002542-f7l4ty2j	69	16	.	.	.
cord-002542-f7l4ty2j	70	1	Due	due	IN
cord-002542-f7l4ty2j	70	2	to	to	IN
cord-002542-f7l4ty2j	70	3	the	the	DT
cord-002542-f7l4ty2j	70	4	higher	high	JJR
cord-002542-f7l4ty2j	70	5	error	error	NN
cord-002542-f7l4ty2j	70	6	-	-	HYPH
cord-002542-f7l4ty2j	70	7	rate	rate	NN
cord-002542-f7l4ty2j	70	8	[	[	-LRB-
cord-002542-f7l4ty2j	70	9	43	43	CD
cord-002542-f7l4ty2j	70	10	]	]	-RRB-
cord-002542-f7l4ty2j	70	11	of	of	IN
cord-002542-f7l4ty2j	70	12	the	the	DT
cord-002542-f7l4ty2j	70	13	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	70	14	sequencing	sequencing	NN
cord-002542-f7l4ty2j	70	15	technology	technology	NN
cord-002542-f7l4ty2j	70	16	compared	compare	VBN
cord-002542-f7l4ty2j	70	17	to	to	IN
cord-002542-f7l4ty2j	70	18	other	other	JJ
cord-002542-f7l4ty2j	70	19	RNAseq	RNAseq	NNP
cord-002542-f7l4ty2j	70	20	platforms	platform	NNS
cord-002542-f7l4ty2j	70	21	,	,	,
cord-002542-f7l4ty2j	70	22	the	the	DT
cord-002542-f7l4ty2j	70	23	exact	exact	JJ
cord-002542-f7l4ty2j	70	24	identity	identity	NN
cord-002542-f7l4ty2j	70	25	of	of	IN
cord-002542-f7l4ty2j	70	26	recombination	recombination	NN
cord-002542-f7l4ty2j	70	27	events	event	NNS
cord-002542-f7l4ty2j	70	28	within	within	IN
cord-002542-f7l4ty2j	70	29	singlemolecule	singlemolecule	JJ
cord-002542-f7l4ty2j	70	30	genomes	genome	NNS
cord-002542-f7l4ty2j	70	31	may	may	MD
cord-002542-f7l4ty2j	70	32	be	be	VB
cord-002542-f7l4ty2j	70	33	inaccurate	inaccurate	JJ
cord-002542-f7l4ty2j	70	34	.	.	.
cord-002542-f7l4ty2j	71	1	However	however	RB
cord-002542-f7l4ty2j	71	2	,	,	,
cord-002542-f7l4ty2j	71	3	long	long	RB
cord-002542-f7l4ty2j	71	4	-	-	HYPH
cord-002542-f7l4ty2j	71	5	read	read	VBN
cord-002542-f7l4ty2j	71	6	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	71	7	reads	read	VBZ
cord-002542-f7l4ty2j	71	8	provide	provide	VB
cord-002542-f7l4ty2j	71	9	the	the	DT
cord-002542-f7l4ty2j	71	10	distinct	distinct	JJ
cord-002542-f7l4ty2j	71	11	advantage	advantage	NN
cord-002542-f7l4ty2j	71	12	of	of	IN
cord-002542-f7l4ty2j	71	13	being	be	VBG
cord-002542-f7l4ty2j	71	14	able	able	JJ
cord-002542-f7l4ty2j	71	15	to	to	TO
cord-002542-f7l4ty2j	71	16	sequence	sequence	VB
cord-002542-f7l4ty2j	71	17	full	full	JJ
cord-002542-f7l4ty2j	71	18	-	-	HYPH
cord-002542-f7l4ty2j	71	19	length	length	NN
cord-002542-f7l4ty2j	71	20	cDNA	cdna	NN
cord-002542-f7l4ty2j	71	21	copies	copy	NNS
cord-002542-f7l4ty2j	71	22	of	of	IN
cord-002542-f7l4ty2j	71	23	RNA	RNA	NNP
cord-002542-f7l4ty2j	71	24	virus	virus	NN
cord-002542-f7l4ty2j	71	25	genomes	genome	NNS
cord-002542-f7l4ty2j	71	26	and	and	CC
cord-002542-f7l4ty2j	71	27	thus	thus	RB
cord-002542-f7l4ty2j	71	28	can	can	MD
cord-002542-f7l4ty2j	71	29	resolve	resolve	VB
cord-002542-f7l4ty2j	71	30	multiple	multiple	JJ
cord-002542-f7l4ty2j	71	31	recombination	recombination	NN
cord-002542-f7l4ty2j	71	32	events	event	NNS
cord-002542-f7l4ty2j	71	33	within	within	IN
cord-002542-f7l4ty2j	71	34	a	a	DT
cord-002542-f7l4ty2j	71	35	single	single	JJ
cord-002542-f7l4ty2j	71	36	RNA	RNA	NNP
cord-002542-f7l4ty2j	71	37	virus	virus	NN
cord-002542-f7l4ty2j	71	38	genome	genome	NN
cord-002542-f7l4ty2j	71	39	.	.	.
cord-002542-f7l4ty2j	72	1	This	this	DT
cord-002542-f7l4ty2j	72	2	study	study	NN
cord-002542-f7l4ty2j	72	3	provides	provide	VBZ
cord-002542-f7l4ty2j	72	4	a	a	DT
cord-002542-f7l4ty2j	72	5	comprehensive	comprehensive	JJ
cord-002542-f7l4ty2j	72	6	analysis	analysis	NN
cord-002542-f7l4ty2j	72	7	of	of	IN
cord-002542-f7l4ty2j	72	8	the	the	DT
cord-002542-f7l4ty2j	72	9	steps	step	NNS
cord-002542-f7l4ty2j	72	10	and	and	CC
cord-002542-f7l4ty2j	72	11	pathways	pathway	NNS
cord-002542-f7l4ty2j	72	12	governing	govern	VBG
cord-002542-f7l4ty2j	72	13	DI	DI	NNP
cord-002542-f7l4ty2j	72	14	-	-	HYPH
cord-002542-f7l4ty2j	72	15	RNA	RNA	NNP
cord-002542-f7l4ty2j	72	16	emergence	emergence	NN
cord-002542-f7l4ty2j	72	17	and	and	CC
cord-002542-f7l4ty2j	72	18	evolution	evolution	NN
cord-002542-f7l4ty2j	72	19	starting	start	VBG
cord-002542-f7l4ty2j	72	20	from	from	IN
cord-002542-f7l4ty2j	72	21	a	a	DT
cord-002542-f7l4ty2j	72	22	plasmid	plasmid	NN
cord-002542-f7l4ty2j	72	23	-	-	HYPH
cord-002542-f7l4ty2j	72	24	driven	drive	VBN
cord-002542-f7l4ty2j	72	25	inoculum	inoculum	NN
cord-002542-f7l4ty2j	72	26	through	through	IN
cord-002542-f7l4ty2j	72	27	to	to	IN
cord-002542-f7l4ty2j	72	28	a	a	DT
cord-002542-f7l4ty2j	72	29	highly	highly	RB
cord-002542-f7l4ty2j	72	30	-	-	HYPH
cord-002542-f7l4ty2j	72	31	passaged	passage	VBN
cord-002542-f7l4ty2j	72	32	sample	sample	NN
cord-002542-f7l4ty2j	72	33	.	.	.
cord-002542-f7l4ty2j	73	1	By	by	IN
cord-002542-f7l4ty2j	73	2	combining	combine	VBG
cord-002542-f7l4ty2j	73	3	short	short	JJ
cord-002542-f7l4ty2j	73	4	-	-	HYPH
cord-002542-f7l4ty2j	73	5	read	read	VBN
cord-002542-f7l4ty2j	73	6	and	and	CC
cord-002542-f7l4ty2j	73	7	long	long	RB
cord-002542-f7l4ty2j	73	8	-	-	HYPH
cord-002542-f7l4ty2j	73	9	read	read	VBN
cord-002542-f7l4ty2j	73	10	sequencing	sequencing	NN
cord-002542-f7l4ty2j	73	11	technologies	technology	NNS
cord-002542-f7l4ty2j	73	12	,	,	,
cord-002542-f7l4ty2j	73	13	we	-PRON-	PRP
cord-002542-f7l4ty2j	73	14	determine	determine	VBP
cord-002542-f7l4ty2j	73	15	both	both	CC
cord-002542-f7l4ty2j	73	16	the	the	DT
cord-002542-f7l4ty2j	73	17	exact	exact	JJ
cord-002542-f7l4ty2j	73	18	identity	identity	NN
cord-002542-f7l4ty2j	73	19	of	of	IN
cord-002542-f7l4ty2j	73	20	RNA	RNA	NNP
cord-002542-f7l4ty2j	73	21	recombination	recombination	NN
cord-002542-f7l4ty2j	73	22	sites	site	NNS
cord-002542-f7l4ty2j	73	23	and	and	CC
cord-002542-f7l4ty2j	73	24	their	-PRON-	PRP$
cord-002542-f7l4ty2j	73	25	correlation	correlation	NN
cord-002542-f7l4ty2j	73	26	within	within	IN
cord-002542-f7l4ty2j	73	27	the	the	DT
cord-002542-f7l4ty2j	73	28	viral	viral	JJ
cord-002542-f7l4ty2j	73	29	quasispecies	quasispecie	NNS
cord-002542-f7l4ty2j	73	30	.	.	.
cord-002542-f7l4ty2j	74	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	74	2	find	find	VBP
cord-002542-f7l4ty2j	74	3	little	little	JJ
cord-002542-f7l4ty2j	74	4	evidence	evidence	NN
cord-002542-f7l4ty2j	74	5	for	for	IN
cord-002542-f7l4ty2j	74	6	the	the	DT
cord-002542-f7l4ty2j	74	7	accumulation	accumulation	NN
cord-002542-f7l4ty2j	74	8	of	of	IN
cord-002542-f7l4ty2j	74	9	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	74	10	defective	defective	JJ
cord-002542-f7l4ty2j	74	11	RNA	RNA	NNP
cord-002542-f7l4ty2j	74	12	species	specie	NNS
cord-002542-f7l4ty2j	74	13	that	that	WDT
cord-002542-f7l4ty2j	74	14	contain	contain	VBP
cord-002542-f7l4ty2j	74	15	either	either	CC
cord-002542-f7l4ty2j	74	16	only	only	RB
cord-002542-f7l4ty2j	74	17	one	one	CD
cord-002542-f7l4ty2j	74	18	,	,	,
cord-002542-f7l4ty2j	74	19	or	or	CC
cord-002542-f7l4ty2j	74	20	smaller	small	JJR
cord-002542-f7l4ty2j	74	21	,	,	,
cord-002542-f7l4ty2j	74	22	deletions	deletion	NNS
cord-002542-f7l4ty2j	74	23	during	during	IN
cord-002542-f7l4ty2j	74	24	the	the	DT
cord-002542-f7l4ty2j	74	25	course	course	NN
cord-002542-f7l4ty2j	74	26	of	of	IN
cord-002542-f7l4ty2j	74	27	passaging	passaging	NN
cord-002542-f7l4ty2j	74	28	.	.	.
cord-002542-f7l4ty2j	75	1	Rather	rather	RB
cord-002542-f7l4ty2j	75	2	,	,	,
cord-002542-f7l4ty2j	75	3	fully	fully	RB
cord-002542-f7l4ty2j	75	4	formed	form	VBD
cord-002542-f7l4ty2j	75	5	'	'	``
cord-002542-f7l4ty2j	75	6	mature	mature	VB
cord-002542-f7l4ty2j	75	7	'	'	''
cord-002542-f7l4ty2j	75	8	DI	di	NN
cord-002542-f7l4ty2j	75	9	-	-	HYPH
cord-002542-f7l4ty2j	75	10	RNAs	rna	NNS
cord-002542-f7l4ty2j	75	11	that	that	WDT
cord-002542-f7l4ty2j	75	12	are	be	VBP
cord-002542-f7l4ty2j	75	13	characterized	characterize	VBN
cord-002542-f7l4ty2j	75	14	by	by	IN
cord-002542-f7l4ty2j	75	15	two	two	CD
cord-002542-f7l4ty2j	75	16	to	to	TO
cord-002542-f7l4ty2j	75	17	three	three	CD
cord-002542-f7l4ty2j	75	18	deletions	deletion	NNS
cord-002542-f7l4ty2j	75	19	between	between	IN
cord-002542-f7l4ty2j	75	20	a	a	DT
cord-002542-f7l4ty2j	75	21	limited	limited	JJ
cord-002542-f7l4ty2j	75	22	number	number	NN
cord-002542-f7l4ty2j	75	23	of	of	IN
cord-002542-f7l4ty2j	75	24	positions	position	NNS
cord-002542-f7l4ty2j	75	25	in	in	IN
cord-002542-f7l4ty2j	75	26	each	each	DT
cord-002542-f7l4ty2j	75	27	of	of	IN
cord-002542-f7l4ty2j	75	28	the	the	DT
cord-002542-f7l4ty2j	75	29	FHV	FHV	NNP
cord-002542-f7l4ty2j	75	30	genomic	genomic	JJ
cord-002542-f7l4ty2j	75	31	RNAs	rna	NNS
cord-002542-f7l4ty2j	76	1	appear	appear	VB
cord-002542-f7l4ty2j	76	2	after	after	IN
cord-002542-f7l4ty2j	76	3	approximately	approximately	RB
cord-002542-f7l4ty2j	76	4	9	9	CD
cord-002542-f7l4ty2j	76	5	days	day	NNS
cord-002542-f7l4ty2j	76	6	of	of	IN
cord-002542-f7l4ty2j	76	7	viral	viral	JJ
cord-002542-f7l4ty2j	76	8	passaging	passaging	NN
cord-002542-f7l4ty2j	76	9	and	and	CC
cord-002542-f7l4ty2j	76	10	accumulate	accumulate	VBP
cord-002542-f7l4ty2j	76	11	rapidly	rapidly	RB
cord-002542-f7l4ty2j	76	12	.	.	.
cord-002542-f7l4ty2j	77	1	The	the	DT
cord-002542-f7l4ty2j	77	2	accumulation	accumulation	NN
cord-002542-f7l4ty2j	77	3	of	of	IN
cord-002542-f7l4ty2j	77	4	DI	DI	NNP
cord-002542-f7l4ty2j	77	5	-	-	HYPH
cord-002542-f7l4ty2j	77	6	RNAs	rna	NNS
cord-002542-f7l4ty2j	77	7	corresponds	correspond	VBZ
cord-002542-f7l4ty2j	77	8	with	with	IN
cord-002542-f7l4ty2j	77	9	a	a	DT
cord-002542-f7l4ty2j	77	10	reduction	reduction	NN
cord-002542-f7l4ty2j	77	11	in	in	IN
cord-002542-f7l4ty2j	77	12	the	the	DT
cord-002542-f7l4ty2j	77	13	specific	specific	JJ
cord-002542-f7l4ty2j	77	14	infectivity	infectivity	NN
cord-002542-f7l4ty2j	77	15	of	of	IN
cord-002542-f7l4ty2j	77	16	the	the	DT
cord-002542-f7l4ty2j	77	17	viral	viral	JJ
cord-002542-f7l4ty2j	77	18	samples	sample	NNS
cord-002542-f7l4ty2j	77	19	in	in	IN
cord-002542-f7l4ty2j	77	20	each	each	DT
cord-002542-f7l4ty2j	77	21	passage	passage	NN
cord-002542-f7l4ty2j	77	22	.	.	.
cord-002542-f7l4ty2j	78	1	This	this	DT
cord-002542-f7l4ty2j	78	2	implies	imply	VBZ
cord-002542-f7l4ty2j	78	3	that	that	IN
cord-002542-f7l4ty2j	78	4	partially	partially	RB
cord-002542-f7l4ty2j	78	5	formed	form	VBN
cord-002542-f7l4ty2j	78	6	DI	DI	NNP
cord-002542-f7l4ty2j	78	7	-	-	HYPH
cord-002542-f7l4ty2j	78	8	RNA	RNA	NNP
cord-002542-f7l4ty2j	78	9	species	specie	NNS
cord-002542-f7l4ty2j	78	10	are	be	VBP
cord-002542-f7l4ty2j	78	11	not	not	RB
cord-002542-f7l4ty2j	78	12	competitive	competitive	JJ
cord-002542-f7l4ty2j	78	13	and	and	CC
cord-002542-f7l4ty2j	78	14	can	can	MD
cord-002542-f7l4ty2j	78	15	not	not	RB
cord-002542-f7l4ty2j	78	16	accumulate	accumulate	VB
cord-002542-f7l4ty2j	78	17	in	in	IN
cord-002542-f7l4ty2j	78	18	the	the	DT
cord-002542-f7l4ty2j	78	19	manner	manner	NN
cord-002542-f7l4ty2j	78	20	that	that	WDT
cord-002542-f7l4ty2j	78	21	mature	mature	VBP
cord-002542-f7l4ty2j	78	22	DI	DI	NNP
cord-002542-f7l4ty2j	78	23	-	-	HYPH
cord-002542-f7l4ty2j	78	24	RNA	RNA	NNP
cord-002542-f7l4ty2j	78	25	species	specie	NNS
cord-002542-f7l4ty2j	78	26	do	do	VBP
cord-002542-f7l4ty2j	78	27	,	,	,
cord-002542-f7l4ty2j	78	28	perhaps	perhaps	RB
cord-002542-f7l4ty2j	78	29	due	due	IN
cord-002542-f7l4ty2j	78	30	to	to	IN
cord-002542-f7l4ty2j	78	31	the	the	DT
cord-002542-f7l4ty2j	78	32	epistatic	epistatic	JJ
cord-002542-f7l4ty2j	78	33	interaction	interaction	NN
cord-002542-f7l4ty2j	78	34	of	of	IN
cord-002542-f7l4ty2j	78	35	multiple	multiple	JJ
cord-002542-f7l4ty2j	78	36	recombination	recombination	NN
cord-002542-f7l4ty2j	78	37	events	event	NNS
cord-002542-f7l4ty2j	78	38	.	.	.
cord-002542-f7l4ty2j	79	1	Alternatively	alternatively	RB
cord-002542-f7l4ty2j	79	2	,	,	,
cord-002542-f7l4ty2j	79	3	the	the	DT
cord-002542-f7l4ty2j	79	4	formation	formation	NN
cord-002542-f7l4ty2j	79	5	of	of	IN
cord-002542-f7l4ty2j	79	6	mature	mature	JJ
cord-002542-f7l4ty2j	79	7	DI	DI	NNP
cord-002542-f7l4ty2j	79	8	-	-	HYPH
cord-002542-f7l4ty2j	79	9	RNAs	rna	NNS
cord-002542-f7l4ty2j	79	10	may	may	MD
cord-002542-f7l4ty2j	79	11	occur	occur	VB
cord-002542-f7l4ty2j	79	12	in	in	IN
cord-002542-f7l4ty2j	79	13	a	a	DT
cord-002542-f7l4ty2j	79	14	single	single	JJ
cord-002542-f7l4ty2j	79	15	step	step	NN
cord-002542-f7l4ty2j	79	16	involving	involve	VBG
cord-002542-f7l4ty2j	79	17	multiple	multiple	JJ
cord-002542-f7l4ty2j	79	18	simultaneous	simultaneous	JJ
cord-002542-f7l4ty2j	79	19	genome	genome	NN
cord-002542-f7l4ty2j	79	20	rearrangements	rearrangement	NNS
cord-002542-f7l4ty2j	79	21	.	.	.
cord-002542-f7l4ty2j	80	1	Cell	cell	NN
cord-002542-f7l4ty2j	80	2	culture	culture	NN
cord-002542-f7l4ty2j	80	3	and	and	CC
cord-002542-f7l4ty2j	80	4	virus	virus	NN
cord-002542-f7l4ty2j	80	5	passaging	passage	VBG
cord-002542-f7l4ty2j	80	6	D.	D.	NNP
cord-002542-f7l4ty2j	80	7	melanogaster	melanogaster	NN
cord-002542-f7l4ty2j	80	8	(	(	-LRB-
cord-002542-f7l4ty2j	80	9	S2	S2	NNP
cord-002542-f7l4ty2j	80	10	)	)	-RRB-
cord-002542-f7l4ty2j	80	11	cells	cell	NNS
cord-002542-f7l4ty2j	80	12	were	be	VBD
cord-002542-f7l4ty2j	80	13	grown	grow	VBN
cord-002542-f7l4ty2j	80	14	at	at	IN
cord-002542-f7l4ty2j	80	15	28˚C	28˚c	CD
cord-002542-f7l4ty2j	80	16	in	in	IN
cord-002542-f7l4ty2j	80	17	Schneider	Schneider	NNP
cord-002542-f7l4ty2j	80	18	's	's	POS
cord-002542-f7l4ty2j	80	19	Drosophila	Drosophila	NNP
cord-002542-f7l4ty2j	80	20	Media	medium	NNS
cord-002542-f7l4ty2j	80	21	supplemented	supplement	VBD
cord-002542-f7l4ty2j	80	22	with	with	IN
cord-002542-f7l4ty2j	80	23	10	10	CD
cord-002542-f7l4ty2j	80	24	%	%	NN
cord-002542-f7l4ty2j	80	25	fetal	fetal	JJ
cord-002542-f7l4ty2j	80	26	bovine	bovine	JJ
cord-002542-f7l4ty2j	80	27	serum	serum	NN
cord-002542-f7l4ty2j	80	28	and	and	CC
cord-002542-f7l4ty2j	80	29	1X	1x	JJ
cord-002542-f7l4ty2j	80	30	Penicillin	Penicillin	NNP
cord-002542-f7l4ty2j	80	31	-	-	HYPH
cord-002542-f7l4ty2j	80	32	Streptomycin	Streptomycin	NNP
cord-002542-f7l4ty2j	80	33	using	use	VBG
cord-002542-f7l4ty2j	80	34	standard	standard	JJ
cord-002542-f7l4ty2j	80	35	laboratory	laboratory	NN
cord-002542-f7l4ty2j	80	36	procedures	procedure	NNS
cord-002542-f7l4ty2j	80	37	.	.	.
cord-002542-f7l4ty2j	81	1	To	to	TO
cord-002542-f7l4ty2j	81	2	generate	generate	VB
cord-002542-f7l4ty2j	81	3	the	the	DT
cord-002542-f7l4ty2j	81	4	initial	initial	JJ
cord-002542-f7l4ty2j	81	5	Flock	Flock	NNP
cord-002542-f7l4ty2j	81	6	House	House	NNP
cord-002542-f7l4ty2j	81	7	virus	virus	NN
cord-002542-f7l4ty2j	81	8	inoculum	inoculum	NN
cord-002542-f7l4ty2j	81	9	,	,	,
cord-002542-f7l4ty2j	81	10	S2	s2	NN
cord-002542-f7l4ty2j	81	11	cells	cell	NNS
cord-002542-f7l4ty2j	81	12	were	be	VBD
cord-002542-f7l4ty2j	81	13	plated	plate	VBN
cord-002542-f7l4ty2j	81	14	at	at	IN
cord-002542-f7l4ty2j	81	15	50	50	CD
cord-002542-f7l4ty2j	81	16	-	-	SYM
cord-002542-f7l4ty2j	81	17	70	70	CD
cord-002542-f7l4ty2j	81	18	%	%	NN
cord-002542-f7l4ty2j	81	19	confluency	confluency	NN
cord-002542-f7l4ty2j	81	20	in	in	IN
cord-002542-f7l4ty2j	81	21	a	a	DT
cord-002542-f7l4ty2j	81	22	six	six	CD
cord-002542-f7l4ty2j	81	23	well	well	JJ
cord-002542-f7l4ty2j	81	24	plate	plate	NN
cord-002542-f7l4ty2j	81	25	and	and	CC
cord-002542-f7l4ty2j	81	26	were	be	VBD
cord-002542-f7l4ty2j	81	27	transfected	transfecte	VBN
cord-002542-f7l4ty2j	81	28	with	with	IN
cord-002542-f7l4ty2j	81	29	2.5μg	2.5μg	CD
cord-002542-f7l4ty2j	81	30	of	of	IN
cord-002542-f7l4ty2j	81	31	pMT	pMT	NNP
cord-002542-f7l4ty2j	81	32	plasmid	plasmid	NN
cord-002542-f7l4ty2j	81	33	containing	contain	VBG
cord-002542-f7l4ty2j	81	34	FHV	FHV	NNP
cord-002542-f7l4ty2j	81	35	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	81	36	(	(	-LRB-
cord-002542-f7l4ty2j	81	37	NC_004146	NC_004146	NNP
cord-002542-f7l4ty2j	81	38	)	)	-RRB-
cord-002542-f7l4ty2j	81	39	and	and	CC
cord-002542-f7l4ty2j	81	40	2.5μg	2.5μg	CD
cord-002542-f7l4ty2j	81	41	of	of	IN
cord-002542-f7l4ty2j	81	42	pMT	pMT	NNP
cord-002542-f7l4ty2j	81	43	plasmid	plasmid	NN
cord-002542-f7l4ty2j	81	44	containing	contain	VBG
cord-002542-f7l4ty2j	81	45	FHV	FHV	NNP
cord-002542-f7l4ty2j	81	46	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	81	47	(	(	-LRB-
cord-002542-f7l4ty2j	81	48	NC_004144	nc_004144	NN
cord-002542-f7l4ty2j	81	49	)	)	-RRB-
cord-002542-f7l4ty2j	81	50	using	use	VBG
cord-002542-f7l4ty2j	81	51	Lipofectamine	Lipofectamine	NNP
cord-002542-f7l4ty2j	81	52	3000	3000	CD
cord-002542-f7l4ty2j	81	53	Transfection	Transfection	NNP
cord-002542-f7l4ty2j	81	54	Reagent	Reagent	NNP
cord-002542-f7l4ty2j	81	55	as	as	IN
cord-002542-f7l4ty2j	81	56	per	per	IN
cord-002542-f7l4ty2j	81	57	the	the	DT
cord-002542-f7l4ty2j	81	58	manufacturer	manufacturer	NN
cord-002542-f7l4ty2j	81	59	's	's	POS
cord-002542-f7l4ty2j	81	60	protocol	protocol	NN
cord-002542-f7l4ty2j	81	61	.	.	.
cord-002542-f7l4ty2j	82	1	Plasmid	plasmid	NN
cord-002542-f7l4ty2j	82	2	transcription	transcription	NN
cord-002542-f7l4ty2j	82	3	was	be	VBD
cord-002542-f7l4ty2j	82	4	induced	induce	VBN
cord-002542-f7l4ty2j	82	5	24	24	CD
cord-002542-f7l4ty2j	82	6	hours	hour	NNS
cord-002542-f7l4ty2j	82	7	post	post	NN
cord-002542-f7l4ty2j	82	8	transfection	transfection	NN
cord-002542-f7l4ty2j	82	9	with	with	IN
cord-002542-f7l4ty2j	82	10	the	the	DT
cord-002542-f7l4ty2j	82	11	addition	addition	NN
cord-002542-f7l4ty2j	82	12	of	of	IN
cord-002542-f7l4ty2j	82	13	50mM	50mm	CD
cord-002542-f7l4ty2j	82	14	CuSO	CuSO	NNP
cord-002542-f7l4ty2j	82	15	4	4	CD
cord-002542-f7l4ty2j	82	16	.	.	.
cord-002542-f7l4ty2j	83	1	Virus	virus	NN
cord-002542-f7l4ty2j	83	2	was	be	VBD
cord-002542-f7l4ty2j	83	3	then	then	RB
cord-002542-f7l4ty2j	83	4	allowed	allow	VBN
cord-002542-f7l4ty2j	83	5	to	to	TO
cord-002542-f7l4ty2j	83	6	propagate	propagate	VB
cord-002542-f7l4ty2j	83	7	for	for	IN
cord-002542-f7l4ty2j	83	8	3	3	CD
cord-002542-f7l4ty2j	83	9	days	day	NNS
cord-002542-f7l4ty2j	83	10	post	post	NN
cord-002542-f7l4ty2j	83	11	induction	induction	NN
cord-002542-f7l4ty2j	83	12	.	.	.
cord-002542-f7l4ty2j	84	1	For	for	IN
cord-002542-f7l4ty2j	84	2	successive	successive	JJ
cord-002542-f7l4ty2j	84	3	passages	passage	NNS
cord-002542-f7l4ty2j	84	4	(	(	-LRB-
cord-002542-f7l4ty2j	84	5	Passages	Passages	NNP
cord-002542-f7l4ty2j	84	6	1	1	CD
cord-002542-f7l4ty2j	84	7	-	-	SYM
cord-002542-f7l4ty2j	84	8	9	9	CD
cord-002542-f7l4ty2j	84	9	)	)	-RRB-
cord-002542-f7l4ty2j	84	10	,	,	,
cord-002542-f7l4ty2j	84	11	S2	s2	NN
cord-002542-f7l4ty2j	84	12	cells	cell	NNS
cord-002542-f7l4ty2j	84	13	were	be	VBD
cord-002542-f7l4ty2j	84	14	grown	grow	VBN
cord-002542-f7l4ty2j	84	15	in	in	IN
cord-002542-f7l4ty2j	84	16	T-25	T-25	NNP
cord-002542-f7l4ty2j	84	17	flasks	flask	NNS
cord-002542-f7l4ty2j	84	18	to	to	IN
cord-002542-f7l4ty2j	84	19	70	70	CD
cord-002542-f7l4ty2j	84	20	-	-	SYM
cord-002542-f7l4ty2j	84	21	90	90	CD
cord-002542-f7l4ty2j	84	22	%	%	NN
cord-002542-f7l4ty2j	84	23	confluency	confluency	NN
cord-002542-f7l4ty2j	85	1	(	(	-LRB-
cord-002542-f7l4ty2j	85	2	~1	~1	NNP
cord-002542-f7l4ty2j	85	3	x	x	SYM
cord-002542-f7l4ty2j	85	4	10	10	CD
cord-002542-f7l4ty2j	85	5	7	7	CD
cord-002542-f7l4ty2j	85	6	cells	cell	NNS
cord-002542-f7l4ty2j	85	7	)	)	-RRB-
cord-002542-f7l4ty2j	85	8	,	,	,
cord-002542-f7l4ty2j	85	9	then	then	RB
cord-002542-f7l4ty2j	85	10	infected	infect	VBN
cord-002542-f7l4ty2j	85	11	with	with	IN
cord-002542-f7l4ty2j	85	12	1mL	1ml	CD
cord-002542-f7l4ty2j	85	13	of	of	IN
cord-002542-f7l4ty2j	85	14	viral	viral	JJ
cord-002542-f7l4ty2j	85	15	inoculum	inoculum	NN
cord-002542-f7l4ty2j	85	16	from	from	IN
cord-002542-f7l4ty2j	85	17	the	the	DT
cord-002542-f7l4ty2j	85	18	previous	previous	JJ
cord-002542-f7l4ty2j	85	19	passage	passage	NN
cord-002542-f7l4ty2j	85	20	.	.	.
cord-002542-f7l4ty2j	86	1	Virus	virus	NN
cord-002542-f7l4ty2j	86	2	was	be	VBD
cord-002542-f7l4ty2j	86	3	grown	grow	VBN
cord-002542-f7l4ty2j	86	4	for	for	IN
cord-002542-f7l4ty2j	86	5	3	3	CD
cord-002542-f7l4ty2j	86	6	days	day	NNS
cord-002542-f7l4ty2j	86	7	,	,	,
cord-002542-f7l4ty2j	86	8	then	then	RB
cord-002542-f7l4ty2j	86	9	fractions	fraction	NNS
cord-002542-f7l4ty2j	86	10	were	be	VBD
cord-002542-f7l4ty2j	86	11	harvested	harvest	VBN
cord-002542-f7l4ty2j	86	12	for	for	IN
cord-002542-f7l4ty2j	86	13	viral	viral	JJ
cord-002542-f7l4ty2j	86	14	purification	purification	NN
cord-002542-f7l4ty2j	86	15	or	or	CC
cord-002542-f7l4ty2j	86	16	inoculation	inoculation	NN
cord-002542-f7l4ty2j	86	17	of	of	IN
cord-002542-f7l4ty2j	86	18	the	the	DT
cord-002542-f7l4ty2j	86	19	next	next	JJ
cord-002542-f7l4ty2j	86	20	passage	passage	NN
cord-002542-f7l4ty2j	86	21	.	.	.
cord-002542-f7l4ty2j	87	1	To	to	TO
cord-002542-f7l4ty2j	87	2	purify	purify	VB
cord-002542-f7l4ty2j	87	3	virus	virus	NN
cord-002542-f7l4ty2j	87	4	from	from	IN
cord-002542-f7l4ty2j	87	5	each	each	DT
cord-002542-f7l4ty2j	87	6	consecutive	consecutive	JJ
cord-002542-f7l4ty2j	87	7	serial	serial	JJ
cord-002542-f7l4ty2j	87	8	passage	passage	NN
cord-002542-f7l4ty2j	87	9	,	,	,
cord-002542-f7l4ty2j	87	10	cells	cell	NNS
cord-002542-f7l4ty2j	87	11	and	and	CC
cord-002542-f7l4ty2j	87	12	supernatant	supernatant	JJ
cord-002542-f7l4ty2j	87	13	were	be	VBD
cord-002542-f7l4ty2j	87	14	subjected	subject	VBN
cord-002542-f7l4ty2j	87	15	to	to	IN
cord-002542-f7l4ty2j	87	16	a	a	DT
cord-002542-f7l4ty2j	87	17	freeze	freeze	NN
cord-002542-f7l4ty2j	87	18	-	-	HYPH
cord-002542-f7l4ty2j	87	19	thaw	thaw	NN
cord-002542-f7l4ty2j	87	20	cycle	cycle	NN
cord-002542-f7l4ty2j	87	21	in	in	IN
cord-002542-f7l4ty2j	87	22	the	the	DT
cord-002542-f7l4ty2j	87	23	presence	presence	NN
cord-002542-f7l4ty2j	87	24	of	of	IN
cord-002542-f7l4ty2j	87	25	1	1	CD
cord-002542-f7l4ty2j	87	26	%	%	NN
cord-002542-f7l4ty2j	87	27	Triton	Triton	NNP
cord-002542-f7l4ty2j	87	28	X-100	x-100	NN
cord-002542-f7l4ty2j	87	29	to	to	TO
cord-002542-f7l4ty2j	87	30	release	release	VB
cord-002542-f7l4ty2j	87	31	viral	viral	JJ
cord-002542-f7l4ty2j	87	32	particles	particle	NNS
cord-002542-f7l4ty2j	87	33	from	from	IN
cord-002542-f7l4ty2j	87	34	infected	infected	JJ
cord-002542-f7l4ty2j	87	35	cells	cell	NNS
cord-002542-f7l4ty2j	87	36	.	.	.
cord-002542-f7l4ty2j	88	1	Virus	virus	NN
cord-002542-f7l4ty2j	88	2	particles	particle	NNS
cord-002542-f7l4ty2j	88	3	were	be	VBD
cord-002542-f7l4ty2j	88	4	then	then	RB
cord-002542-f7l4ty2j	88	5	purified	purify	VBN
cord-002542-f7l4ty2j	88	6	on	on	IN
cord-002542-f7l4ty2j	88	7	a	a	DT
cord-002542-f7l4ty2j	88	8	30	30	CD
cord-002542-f7l4ty2j	88	9	%	%	NN
cord-002542-f7l4ty2j	88	10	sucrose	sucrose	NN
cord-002542-f7l4ty2j	88	11	cushion	cushion	NN
cord-002542-f7l4ty2j	88	12	by	by	IN
cord-002542-f7l4ty2j	88	13	spinning	spin	VBG
cord-002542-f7l4ty2j	88	14	the	the	DT
cord-002542-f7l4ty2j	88	15	cell	cell	NN
cord-002542-f7l4ty2j	88	16	lysate	lysate	NN
cord-002542-f7l4ty2j	88	17	at	at	IN
cord-002542-f7l4ty2j	88	18	40,000	40,000	CD
cord-002542-f7l4ty2j	88	19	RPM	rpm	NN
cord-002542-f7l4ty2j	88	20	for	for	IN
cord-002542-f7l4ty2j	88	21	2.5	2.5	CD
cord-002542-f7l4ty2j	88	22	hours	hour	NNS
cord-002542-f7l4ty2j	88	23	.	.	.
cord-002542-f7l4ty2j	89	1	The	the	DT
cord-002542-f7l4ty2j	89	2	viral	viral	JJ
cord-002542-f7l4ty2j	89	3	pellet	pellet	NN
cord-002542-f7l4ty2j	89	4	was	be	VBD
cord-002542-f7l4ty2j	89	5	resuspended	resuspend	VBN
cord-002542-f7l4ty2j	89	6	in	in	IN
cord-002542-f7l4ty2j	89	7	10mM	10mm	CD
cord-002542-f7l4ty2j	89	8	Tris	Tris	NNP
cord-002542-f7l4ty2j	89	9	(	(	-LRB-
cord-002542-f7l4ty2j	89	10	pH	pH	NNP
cord-002542-f7l4ty2j	89	11	7.4	7.4	CD
cord-002542-f7l4ty2j	89	12	)	)	-RRB-
cord-002542-f7l4ty2j	89	13	.	.	.
cord-002542-f7l4ty2j	90	1	Virus	virus	NN
cord-002542-f7l4ty2j	90	2	was	be	VBD
cord-002542-f7l4ty2j	90	3	further	further	RB
cord-002542-f7l4ty2j	90	4	purified	purify	VBN
cord-002542-f7l4ty2j	90	5	by	by	IN
cord-002542-f7l4ty2j	90	6	applying	apply	VBG
cord-002542-f7l4ty2j	90	7	resuspended	resuspended	JJ
cord-002542-f7l4ty2j	90	8	virus	virus	NN
cord-002542-f7l4ty2j	90	9	atop	atop	IN
cord-002542-f7l4ty2j	90	10	a	a	DT
cord-002542-f7l4ty2j	90	11	10	10	CD
cord-002542-f7l4ty2j	90	12	-	-	SYM
cord-002542-f7l4ty2j	90	13	40	40	CD
cord-002542-f7l4ty2j	90	14	%	%	NN
cord-002542-f7l4ty2j	90	15	sucrose	sucrose	NN
cord-002542-f7l4ty2j	90	16	gradient	gradient	NN
cord-002542-f7l4ty2j	90	17	and	and	CC
cord-002542-f7l4ty2j	90	18	spun	spin	VBD
cord-002542-f7l4ty2j	90	19	at	at	IN
cord-002542-f7l4ty2j	90	20	40,000	40,000	CD
cord-002542-f7l4ty2j	90	21	RPM	rpm	NN
cord-002542-f7l4ty2j	90	22	for	for	IN
cord-002542-f7l4ty2j	90	23	1.5	1.5	CD
cord-002542-f7l4ty2j	90	24	hours	hour	NNS
cord-002542-f7l4ty2j	90	25	.	.	.
cord-002542-f7l4ty2j	91	1	The	the	DT
cord-002542-f7l4ty2j	91	2	viral	viral	JJ
cord-002542-f7l4ty2j	91	3	band	band	NN
cord-002542-f7l4ty2j	91	4	was	be	VBD
cord-002542-f7l4ty2j	91	5	collected	collect	VBN
cord-002542-f7l4ty2j	91	6	and	and	CC
cord-002542-f7l4ty2j	91	7	subsequently	subsequently	RB
cord-002542-f7l4ty2j	91	8	treated	treat	VBN
cord-002542-f7l4ty2j	91	9	with	with	IN
cord-002542-f7l4ty2j	91	10	1	1	CD
cord-002542-f7l4ty2j	91	11	Unit	Unit	NNP
cord-002542-f7l4ty2j	91	12	DNase	DNase	NNP
cord-002542-f7l4ty2j	91	13	and	and	CC
cord-002542-f7l4ty2j	91	14	1	1	CD
cord-002542-f7l4ty2j	91	15	Unit	unit	NN
cord-002542-f7l4ty2j	91	16	RNase	rnase	NN
cord-002542-f7l4ty2j	91	17	and	and	CC
cord-002542-f7l4ty2j	91	18	incubated	incubate	VBN
cord-002542-f7l4ty2j	91	19	at	at	IN
cord-002542-f7l4ty2j	91	20	room	room	NN
cord-002542-f7l4ty2j	91	21	temperature	temperature	NN
cord-002542-f7l4ty2j	91	22	for	for	IN
cord-002542-f7l4ty2j	91	23	at	at	RB
cord-002542-f7l4ty2j	91	24	least	least	RBS
cord-002542-f7l4ty2j	91	25	one	one	CD
cord-002542-f7l4ty2j	91	26	hour	hour	NN
cord-002542-f7l4ty2j	91	27	to	to	TO
cord-002542-f7l4ty2j	91	28	remove	remove	VB
cord-002542-f7l4ty2j	91	29	any	any	DT
cord-002542-f7l4ty2j	91	30	cellular	cellular	JJ
cord-002542-f7l4ty2j	91	31	nucleic	nucleic	JJ
cord-002542-f7l4ty2j	91	32	acids	acid	NNS
cord-002542-f7l4ty2j	91	33	not	not	RB
cord-002542-f7l4ty2j	91	34	protected	protect	VBN
cord-002542-f7l4ty2j	91	35	by	by	IN
cord-002542-f7l4ty2j	91	36	the	the	DT
cord-002542-f7l4ty2j	91	37	viral	viral	JJ
cord-002542-f7l4ty2j	91	38	capsid	capsid	NN
cord-002542-f7l4ty2j	91	39	.	.	.
cord-002542-f7l4ty2j	92	1	The	the	DT
cord-002542-f7l4ty2j	92	2	virus	virus	NN
cord-002542-f7l4ty2j	92	3	sample	sample	NN
cord-002542-f7l4ty2j	92	4	was	be	VBD
cord-002542-f7l4ty2j	92	5	concentrated	concentrate	VBN
cord-002542-f7l4ty2j	92	6	on	on	IN
cord-002542-f7l4ty2j	92	7	a	a	DT
cord-002542-f7l4ty2j	92	8	100,000	100,000	CD
cord-002542-f7l4ty2j	92	9	NMWL	NMWL	NNP
cord-002542-f7l4ty2j	92	10	centrifugal	centrifugal	JJ
cord-002542-f7l4ty2j	92	11	filter	filter	NN
cord-002542-f7l4ty2j	92	12	column	column	NN
cord-002542-f7l4ty2j	92	13	and	and	CC
cord-002542-f7l4ty2j	92	14	washed	wash	VBD
cord-002542-f7l4ty2j	92	15	with	with	IN
cord-002542-f7l4ty2j	92	16	at	at	RB
cord-002542-f7l4ty2j	92	17	least	least	JJS
cord-002542-f7l4ty2j	92	18	2	2	CD
cord-002542-f7l4ty2j	92	19	volumes	volume	NNS
cord-002542-f7l4ty2j	92	20	of	of	IN
cord-002542-f7l4ty2j	92	21	10mM	10mm	CD
cord-002542-f7l4ty2j	92	22	Tris	Tris	NNP
cord-002542-f7l4ty2j	92	23	pH	pH	NNP
cord-002542-f7l4ty2j	92	24	7.4	7.4	CD
cord-002542-f7l4ty2j	92	25	.	.	.
cord-002542-f7l4ty2j	93	1	Finally	finally	RB
cord-002542-f7l4ty2j	93	2	,	,	,
cord-002542-f7l4ty2j	93	3	encapsidated	encapsidate	VBN
cord-002542-f7l4ty2j	93	4	viral	viral	NNP
cord-002542-f7l4ty2j	93	5	RNA	RNA	NNP
cord-002542-f7l4ty2j	93	6	was	be	VBD
cord-002542-f7l4ty2j	93	7	extracted	extract	VBN
cord-002542-f7l4ty2j	93	8	using	use	VBG
cord-002542-f7l4ty2j	93	9	a	a	DT
cord-002542-f7l4ty2j	93	10	QIAGEN	QIAGEN	NNP
cord-002542-f7l4ty2j	93	11	RNeasy	RNeasy	NNP
cord-002542-f7l4ty2j	93	12	Mini	Mini	NNP
cord-002542-f7l4ty2j	93	13	Kit	Kit	NNP
cord-002542-f7l4ty2j	93	14	as	as	IN
cord-002542-f7l4ty2j	93	15	per	per	IN
cord-002542-f7l4ty2j	93	16	the	the	DT
cord-002542-f7l4ty2j	93	17	manufacturer	manufacturer	NN
cord-002542-f7l4ty2j	93	18	's	's	POS
cord-002542-f7l4ty2j	93	19	protocol	protocol	NN
cord-002542-f7l4ty2j	93	20	.	.	.
cord-002542-f7l4ty2j	94	1	Next	next	JJ
cord-002542-f7l4ty2j	94	2	generation	generation	NN
cord-002542-f7l4ty2j	94	3	sequencing	sequencing	NN
cord-002542-f7l4ty2j	94	4	(	(	-LRB-
cord-002542-f7l4ty2j	94	5	NGS	NGS	NNP
cord-002542-f7l4ty2j	94	6	)	)	-RRB-
cord-002542-f7l4ty2j	94	7	libraries	library	NNS
cord-002542-f7l4ty2j	94	8	were	be	VBD
cord-002542-f7l4ty2j	94	9	generated	generate	VBN
cord-002542-f7l4ty2j	94	10	using	use	VBG
cord-002542-f7l4ty2j	94	11	100ng	100ng	NNP
cord-002542-f7l4ty2j	94	12	of	of	IN
cord-002542-f7l4ty2j	94	13	RNA	RNA	NNP
cord-002542-f7l4ty2j	94	14	using	use	VBG
cord-002542-f7l4ty2j	94	15	the	the	DT
cord-002542-f7l4ty2j	94	16	'	'	``
cord-002542-f7l4ty2j	94	17	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	94	18	'	'	''
cord-002542-f7l4ty2j	94	19	protocol	protocol	NN
cord-002542-f7l4ty2j	94	20	as	as	IN
cord-002542-f7l4ty2j	94	21	previously	previously	RB
cord-002542-f7l4ty2j	94	22	described	describe	VBN
cord-002542-f7l4ty2j	94	23	by	by	IN
cord-002542-f7l4ty2j	94	24	Routh	Routh	NNP
cord-002542-f7l4ty2j	94	25	et	et	NNP
cord-002542-f7l4ty2j	94	26	al	al	NNP
cord-002542-f7l4ty2j	94	27	.	.	.
cord-002542-f7l4ty2j	95	1	[	[	-LRB-
cord-002542-f7l4ty2j	95	2	35	35	CD
cord-002542-f7l4ty2j	95	3	,	,	,
cord-002542-f7l4ty2j	95	4	44	44	CD
cord-002542-f7l4ty2j	95	5	,	,	,
cord-002542-f7l4ty2j	95	6	45	45	CD
cord-002542-f7l4ty2j	95	7	]	]	-RRB-
cord-002542-f7l4ty2j	95	8	.	.	.
cord-002542-f7l4ty2j	96	1	Briefly	briefly	RB
cord-002542-f7l4ty2j	96	2	,	,	,
cord-002542-f7l4ty2j	96	3	cDNA	cDNA	NNP
cord-002542-f7l4ty2j	96	4	is	be	VBZ
cord-002542-f7l4ty2j	96	5	synthesized	synthesize	VBN
cord-002542-f7l4ty2j	96	6	through	through	IN
cord-002542-f7l4ty2j	96	7	RT	RT	NNP
cord-002542-f7l4ty2j	96	8	-	-	HYPH
cord-002542-f7l4ty2j	96	9	PCR	PCR	NNP
cord-002542-f7l4ty2j	96	10	initiated	initiate	VBD
cord-002542-f7l4ty2j	96	11	from	from	IN
cord-002542-f7l4ty2j	96	12	semi	semi	JJ
cord-002542-f7l4ty2j	96	13	-	-	JJ
cord-002542-f7l4ty2j	96	14	random	random	JJ
cord-002542-f7l4ty2j	96	15	(	(	-LRB-
cord-002542-f7l4ty2j	96	16	6N	6n	NN
cord-002542-f7l4ty2j	96	17	)	)	-RRB-
cord-002542-f7l4ty2j	96	18	primers	primer	NNS
cord-002542-f7l4ty2j	96	19	containing	contain	VBG
cord-002542-f7l4ty2j	96	20	a	a	DT
cord-002542-f7l4ty2j	96	21	partial	partial	JJ
cord-002542-f7l4ty2j	96	22	Illumina	Illumina	NNP
cord-002542-f7l4ty2j	96	23	p7	p7	NN
cord-002542-f7l4ty2j	96	24	adapter	adapter	NN
cord-002542-f7l4ty2j	96	25	(	(	-LRB-
cord-002542-f7l4ty2j	96	26	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN	NNP
cord-002542-f7l4ty2j	96	27	)	)	-RRB-
cord-002542-f7l4ty2j	96	28	and	and	CC
cord-002542-f7l4ty2j	96	29	stochastically	stochastically	RB
cord-002542-f7l4ty2j	96	30	terminated	terminate	VBN
cord-002542-f7l4ty2j	96	31	by	by	IN
cord-002542-f7l4ty2j	96	32	the	the	DT
cord-002542-f7l4ty2j	96	33	addition	addition	NN
cord-002542-f7l4ty2j	96	34	of	of	IN
cord-002542-f7l4ty2j	96	35	azido	azido	NNP
cord-002542-f7l4ty2j	96	36	-	-	HYPH
cord-002542-f7l4ty2j	96	37	NTPs	NTPs	NNP
cord-002542-f7l4ty2j	96	38	(	(	-LRB-
cord-002542-f7l4ty2j	96	39	AzNTP	AzNTP	NNP
cord-002542-f7l4ty2j	96	40	)	)	-RRB-
cord-002542-f7l4ty2j	96	41	at	at	IN
cord-002542-f7l4ty2j	96	42	a	a	DT
cord-002542-f7l4ty2j	96	43	ratio	ratio	NN
cord-002542-f7l4ty2j	96	44	of	of	IN
cord-002542-f7l4ty2j	96	45	1:35	1:35	CD
cord-002542-f7l4ty2j	97	1	AzNTP	azntp	NN
cord-002542-f7l4ty2j	97	2	:	:	:
cord-002542-f7l4ty2j	97	3	dNTPs	dntp	NNS
cord-002542-f7l4ty2j	97	4	.	.	.
cord-002542-f7l4ty2j	98	1	Subsequently	subsequently	RB
cord-002542-f7l4ty2j	98	2	,	,	,
cord-002542-f7l4ty2j	98	3	the	the	DT
cord-002542-f7l4ty2j	98	4	p5	p5	NNP
cord-002542-f7l4ty2j	98	5	Click	Click	NNP
cord-002542-f7l4ty2j	98	6	-	-	HYPH
cord-002542-f7l4ty2j	98	7	Adapter	Adapter	NNP
cord-002542-f7l4ty2j	98	8	(	(	-LRB-
cord-002542-f7l4ty2j	98	9	5'-Hexynyl	5'-hexynyl	CD
cord-002542-f7l4ty2j	98	10	-	-	HYPH
cord-002542-f7l4ty2j	98	11	NNNNAGATCGGAAGAGCGTCGTGTA	NNNNAGATCGGAAGAGCGTCGTGTA	NNP
cord-002542-f7l4ty2j	98	12	GGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT	GGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT	NNP
cord-002542-f7l4ty2j	98	13	,	,	,
cord-002542-f7l4ty2j	98	14	IDT	IDT	NNP
cord-002542-f7l4ty2j	98	15	)	)	-RRB-
cord-002542-f7l4ty2j	98	16	was	be	VBD
cord-002542-f7l4ty2j	98	17	click	click	NN
cord-002542-f7l4ty2j	98	18	-	-	HYPH
cord-002542-f7l4ty2j	98	19	ligated	ligate	VBN
cord-002542-f7l4ty2j	98	20	onto	onto	IN
cord-002542-f7l4ty2j	98	21	the	the	DT
cord-002542-f7l4ty2j	98	22	azido	azido	NNP
cord-002542-f7l4ty2j	98	23	-	-	HYPH
cord-002542-f7l4ty2j	98	24	terminated	terminate	VBN
cord-002542-f7l4ty2j	98	25	cDNA	cdna	NN
cord-002542-f7l4ty2j	98	26	fragment	fragment	NN
cord-002542-f7l4ty2j	98	27	using	use	VBG
cord-002542-f7l4ty2j	98	28	copper	copper	NN
cord-002542-f7l4ty2j	98	29	-	-	HYPH
cord-002542-f7l4ty2j	98	30	catalysed	catalyse	VBN
cord-002542-f7l4ty2j	98	31	azide	azide	NN
cord-002542-f7l4ty2j	98	32	-	-	HYPH
cord-002542-f7l4ty2j	98	33	alkyne	alkyne	NN
cord-002542-f7l4ty2j	98	34	cycloaddition	cycloaddition	NN
cord-002542-f7l4ty2j	98	35	(	(	-LRB-
cord-002542-f7l4ty2j	98	36	CuAAC	CuAAC	NNP
cord-002542-f7l4ty2j	98	37	)	)	-RRB-
cord-002542-f7l4ty2j	98	38	in	in	IN
cord-002542-f7l4ty2j	98	39	the	the	DT
cord-002542-f7l4ty2j	98	40	presence	presence	NN
cord-002542-f7l4ty2j	98	41	of	of	IN
cord-002542-f7l4ty2j	98	42	TBTA	TBTA	NNP
cord-002542-f7l4ty2j	98	43	ligand	ligand	NN
cord-002542-f7l4ty2j	98	44	(	(	-LRB-
cord-002542-f7l4ty2j	98	45	Lumiprobe	Lumiprobe	NNP
cord-002542-f7l4ty2j	98	46	)	)	-RRB-
cord-002542-f7l4ty2j	98	47	and	and	CC
cord-002542-f7l4ty2j	98	48	Vitamin	vitamin	NN
cord-002542-f7l4ty2j	98	49	C	c	NN
cord-002542-f7l4ty2j	98	50	catalyst	catalyst	NN
cord-002542-f7l4ty2j	98	51	in	in	IN
cord-002542-f7l4ty2j	98	52	55	55	CD
cord-002542-f7l4ty2j	98	53	%	%	NN
cord-002542-f7l4ty2j	98	54	DMSO	DMSO	NNP
cord-002542-f7l4ty2j	98	55	.	.	.
cord-002542-f7l4ty2j	99	1	After	after	IN
cord-002542-f7l4ty2j	99	2	purifying	purify	VBG
cord-002542-f7l4ty2j	99	3	the	the	DT
cord-002542-f7l4ty2j	99	4	click	click	NN
cord-002542-f7l4ty2j	99	5	-	-	HYPH
cord-002542-f7l4ty2j	99	6	linked	link	VBN
cord-002542-f7l4ty2j	99	7	cDNA	cdna	NN
cord-002542-f7l4ty2j	99	8	with	with	IN
cord-002542-f7l4ty2j	99	9	a	a	DT
cord-002542-f7l4ty2j	99	10	Zymo	Zymo	NNP
cord-002542-f7l4ty2j	99	11	DNA	dna	NN
cord-002542-f7l4ty2j	99	12	clean	clean	JJ
cord-002542-f7l4ty2j	99	13	column	column	NN
cord-002542-f7l4ty2j	99	14	,	,	,
cord-002542-f7l4ty2j	99	15	18	18	CD
cord-002542-f7l4ty2j	99	16	cycles	cycle	NNS
cord-002542-f7l4ty2j	99	17	of	of	IN
cord-002542-f7l4ty2j	99	18	OneTaq	OneTaq	NNP
cord-002542-f7l4ty2j	99	19	(	(	-LRB-
cord-002542-f7l4ty2j	99	20	NEB	NEB	NNP
cord-002542-f7l4ty2j	99	21	)	)	-RRB-
cord-002542-f7l4ty2j	99	22	PCR	PCR	NNP
cord-002542-f7l4ty2j	99	23	amplification	amplification	NN
cord-002542-f7l4ty2j	99	24	adds	add	VBZ
cord-002542-f7l4ty2j	99	25	the	the	DT
cord-002542-f7l4ty2j	99	26	remainder	remainder	NN
cord-002542-f7l4ty2j	99	27	of	of	IN
cord-002542-f7l4ty2j	99	28	the	the	DT
cord-002542-f7l4ty2j	99	29	p7	p7	NN
cord-002542-f7l4ty2j	99	30	adapter	adapter	NN
cord-002542-f7l4ty2j	99	31	along	along	IN
cord-002542-f7l4ty2j	99	32	with	with	IN
cord-002542-f7l4ty2j	99	33	the	the	DT
cord-002542-f7l4ty2j	99	34	desired	desire	VBN
cord-002542-f7l4ty2j	99	35	TruSeq	TruSeq	NNP
cord-002542-f7l4ty2j	99	36	index	index	NN
cord-002542-f7l4ty2j	99	37	sequence	sequence	NN
cord-002542-f7l4ty2j	99	38	.	.	.
cord-002542-f7l4ty2j	100	1	PCR	PCR	NNP
cord-002542-f7l4ty2j	100	2	product	product	NN
cord-002542-f7l4ty2j	100	3	was	be	VBD
cord-002542-f7l4ty2j	100	4	cleaned	clean	VBN
cord-002542-f7l4ty2j	100	5	again	again	RB
cord-002542-f7l4ty2j	100	6	with	with	IN
cord-002542-f7l4ty2j	100	7	a	a	DT
cord-002542-f7l4ty2j	100	8	Zymo	Zymo	NNP
cord-002542-f7l4ty2j	100	9	DNA	dna	NN
cord-002542-f7l4ty2j	100	10	clean	clean	JJ
cord-002542-f7l4ty2j	100	11	column	column	NN
cord-002542-f7l4ty2j	100	12	to	to	TO
cord-002542-f7l4ty2j	100	13	remove	remove	VB
cord-002542-f7l4ty2j	100	14	excess	excess	JJ
cord-002542-f7l4ty2j	100	15	primers	primer	NNS
cord-002542-f7l4ty2j	100	16	and	and	CC
cord-002542-f7l4ty2j	100	17	then	then	RB
cord-002542-f7l4ty2j	100	18	ran	run	VBD
cord-002542-f7l4ty2j	100	19	on	on	IN
cord-002542-f7l4ty2j	100	20	a	a	DT
cord-002542-f7l4ty2j	100	21	1	1	CD
cord-002542-f7l4ty2j	100	22	-	-	SYM
cord-002542-f7l4ty2j	100	23	2	2	CD
cord-002542-f7l4ty2j	100	24	%	%	NN
cord-002542-f7l4ty2j	100	25	precast	precast	NN
cord-002542-f7l4ty2j	100	26	agarose	agarose	NN
cord-002542-f7l4ty2j	100	27	e	e	NN
cord-002542-f7l4ty2j	100	28	-	-	NN
cord-002542-f7l4ty2j	100	29	gel	gel	NN
cord-002542-f7l4ty2j	100	30	(	(	-LRB-
cord-002542-f7l4ty2j	100	31	Invitrogen	Invitrogen	NNP
cord-002542-f7l4ty2j	100	32	,	,	,
cord-002542-f7l4ty2j	100	33	E	E	NNP
cord-002542-f7l4ty2j	100	34	-	-	HYPH
cord-002542-f7l4ty2j	100	35	Gel	Gel	NNP
cord-002542-f7l4ty2j	100	36	Electrophoresis	Electrophoresis	NNP
cord-002542-f7l4ty2j	100	37	System	System	NNP
cord-002542-f7l4ty2j	100	38	)	)	-RRB-
cord-002542-f7l4ty2j	100	39	.	.	.
cord-002542-f7l4ty2j	101	1	cDNA	cDNA	NNP
cord-002542-f7l4ty2j	101	2	libraries	library	NNS
cord-002542-f7l4ty2j	101	3	between	between	IN
cord-002542-f7l4ty2j	101	4	400	400	CD
cord-002542-f7l4ty2j	101	5	to	to	IN
cord-002542-f7l4ty2j	101	6	700bp	700bp	NNP
cord-002542-f7l4ty2j	101	7	were	be	VBD
cord-002542-f7l4ty2j	101	8	excised	excise	VBN
cord-002542-f7l4ty2j	101	9	corresponding	correspond	VBG
cord-002542-f7l4ty2j	101	10	to	to	TO
cord-002542-f7l4ty2j	101	11	insert	insert	VB
cord-002542-f7l4ty2j	101	12	sizes	size	NNS
cord-002542-f7l4ty2j	101	13	of	of	IN
cord-002542-f7l4ty2j	101	14	250	250	CD
cord-002542-f7l4ty2j	101	15	-	-	HYPH
cord-002542-f7l4ty2j	101	16	550bp	550bp	NN
cord-002542-f7l4ty2j	101	17	and	and	CC
cord-002542-f7l4ty2j	101	18	cleaned	clean	VBD
cord-002542-f7l4ty2j	101	19	using	use	VBG
cord-002542-f7l4ty2j	101	20	the	the	DT
cord-002542-f7l4ty2j	101	21	Zymo	Zymo	NNP
cord-002542-f7l4ty2j	101	22	Research	Research	NNP
cord-002542-f7l4ty2j	101	23	Gel	Gel	NNP
cord-002542-f7l4ty2j	101	24	DNA	DNA	NNP
cord-002542-f7l4ty2j	101	25	Recovery	Recovery	NNP
cord-002542-f7l4ty2j	101	26	Kit	kit	NN
cord-002542-f7l4ty2j	101	27	.	.	.
cord-002542-f7l4ty2j	102	1	Final	final	JJ
cord-002542-f7l4ty2j	102	2	cDNA	cdna	NN
cord-002542-f7l4ty2j	102	3	libraries	library	NNS
cord-002542-f7l4ty2j	102	4	were	be	VBD
cord-002542-f7l4ty2j	102	5	quantified	quantify	VBN
cord-002542-f7l4ty2j	102	6	using	use	VBG
cord-002542-f7l4ty2j	102	7	a	a	DT
cord-002542-f7l4ty2j	102	8	QuBit	QuBit	NNP
cord-002542-f7l4ty2j	102	9	fluorimeter	fluorimeter	NN
cord-002542-f7l4ty2j	102	10	(	(	-LRB-
cord-002542-f7l4ty2j	102	11	Life	Life	NNP
cord-002542-f7l4ty2j	102	12	Tech	Tech	NNP
cord-002542-f7l4ty2j	102	13	)	)	-RRB-
cord-002542-f7l4ty2j	102	14	and	and	CC
cord-002542-f7l4ty2j	102	15	loaded	load	VBN
cord-002542-f7l4ty2j	102	16	on	on	IN
cord-002542-f7l4ty2j	102	17	a	a	DT
cord-002542-f7l4ty2j	102	18	HiSeq	HiSeq	NNP
cord-002542-f7l4ty2j	102	19	1500	1500	CD
cord-002542-f7l4ty2j	102	20	single	single	JJ
cord-002542-f7l4ty2j	102	21	read	read	NN
cord-002542-f7l4ty2j	102	22	rapid	rapid	JJ
cord-002542-f7l4ty2j	102	23	run	run	NN
cord-002542-f7l4ty2j	102	24	flowcell	flowcell	NNP
cord-002542-f7l4ty2j	102	25	for	for	IN
cord-002542-f7l4ty2j	102	26	1x150	1x150	CD
cord-002542-f7l4ty2j	102	27	reads	read	NNS
cord-002542-f7l4ty2j	102	28	and	and	CC
cord-002542-f7l4ty2j	102	29	7	7	CD
cord-002542-f7l4ty2j	102	30	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	102	31	of	of	IN
cord-002542-f7l4ty2j	102	32	the	the	DT
cord-002542-f7l4ty2j	102	33	index	index	NN
cord-002542-f7l4ty2j	102	34	.	.	.
cord-002542-f7l4ty2j	103	1	FHV	FHV	NNP
cord-002542-f7l4ty2j	103	2	libraries	library	NNS
cord-002542-f7l4ty2j	103	3	used	use	VBN
cord-002542-f7l4ty2j	103	4	for	for	IN
cord-002542-f7l4ty2j	103	5	the	the	DT
cord-002542-f7l4ty2j	103	6	triplicate	triplicate	JJ
cord-002542-f7l4ty2j	103	7	study	study	NN
cord-002542-f7l4ty2j	103	8	shown	show	VBN
cord-002542-f7l4ty2j	103	9	in	in	IN
cord-002542-f7l4ty2j	103	10	S2	S2	NNP
cord-002542-f7l4ty2j	103	11	Fig	Fig	NNP
cord-002542-f7l4ty2j	103	12	were	be	VBD
cord-002542-f7l4ty2j	103	13	sequenced	sequence	VBN
cord-002542-f7l4ty2j	103	14	on	on	IN
cord-002542-f7l4ty2j	103	15	a	a	DT
cord-002542-f7l4ty2j	103	16	MiSeq	MiSeq	NNP
cord-002542-f7l4ty2j	103	17	platform	platform	NN
cord-002542-f7l4ty2j	103	18	with	with	IN
cord-002542-f7l4ty2j	103	19	v3	v3	NN
cord-002542-f7l4ty2j	103	20	chemistry	chemistry	NN
cord-002542-f7l4ty2j	103	21	for	for	IN
cord-002542-f7l4ty2j	103	22	600	600	CD
cord-002542-f7l4ty2j	103	23	cycles	cycle	NNS
cord-002542-f7l4ty2j	103	24	(	(	-LRB-
cord-002542-f7l4ty2j	103	25	2x300	2x300	CD
cord-002542-f7l4ty2j	103	26	)	)	-RRB-
cord-002542-f7l4ty2j	103	27	.	.	.
cord-002542-f7l4ty2j	104	1	Reads	read	NNS
cord-002542-f7l4ty2j	104	2	were	be	VBD
cord-002542-f7l4ty2j	104	3	trimmed	trim	VBN
cord-002542-f7l4ty2j	104	4	to	to	IN
cord-002542-f7l4ty2j	104	5	150nts	150nts	CD
cord-002542-f7l4ty2j	104	6	prior	prior	RB
cord-002542-f7l4ty2j	104	7	to	to	IN
cord-002542-f7l4ty2j	104	8	analysis	analysis	NN
cord-002542-f7l4ty2j	104	9	to	to	TO
cord-002542-f7l4ty2j	104	10	emulate	emulate	VB
cord-002542-f7l4ty2j	104	11	the	the	DT
cord-002542-f7l4ty2j	104	12	libraries	library	NNS
cord-002542-f7l4ty2j	104	13	sequenced	sequence	VBN
cord-002542-f7l4ty2j	104	14	on	on	IN
cord-002542-f7l4ty2j	104	15	the	the	DT
cord-002542-f7l4ty2j	104	16	HiSeq	HiSeq	NNP
cord-002542-f7l4ty2j	104	17	.	.	.
cord-002542-f7l4ty2j	105	1	Raw	raw	JJ
cord-002542-f7l4ty2j	105	2	reads	read	NNS
cord-002542-f7l4ty2j	105	3	were	be	VBD
cord-002542-f7l4ty2j	105	4	processed	process	VBN
cord-002542-f7l4ty2j	105	5	by	by	IN
cord-002542-f7l4ty2j	105	6	first	first	RB
cord-002542-f7l4ty2j	105	7	removing	remove	VBG
cord-002542-f7l4ty2j	105	8	the	the	DT
cord-002542-f7l4ty2j	105	9	Illumina	Illumina	NNP
cord-002542-f7l4ty2j	105	10	TruSeq	TruSeq	NNP
cord-002542-f7l4ty2j	105	11	adaptor	adaptor	NN
cord-002542-f7l4ty2j	105	12	using	use	VBG
cord-002542-f7l4ty2j	105	13	Cutadapt	Cutadapt	NNP
cord-002542-f7l4ty2j	105	14	[	[	-LRB-
cord-002542-f7l4ty2j	105	15	46	46	CD
cord-002542-f7l4ty2j	105	16	]	]	-RRB-
cord-002542-f7l4ty2j	105	17	with	with	IN
cord-002542-f7l4ty2j	105	18	default	default	NN
cord-002542-f7l4ty2j	105	19	parameters	parameter	NNS
cord-002542-f7l4ty2j	105	20	.	.	.
cord-002542-f7l4ty2j	106	1	Next	next	RB
cord-002542-f7l4ty2j	106	2	,	,	,
cord-002542-f7l4ty2j	106	3	the	the	DT
cord-002542-f7l4ty2j	106	4	first	first	JJ
cord-002542-f7l4ty2j	106	5	6	6	CD
cord-002542-f7l4ty2j	106	6	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	106	7	(	(	-LRB-
cord-002542-f7l4ty2j	106	8	corresponding	correspond	VBG
cord-002542-f7l4ty2j	106	9	to	to	IN
cord-002542-f7l4ty2j	106	10	the	the	DT
cord-002542-f7l4ty2j	106	11	random	random	JJ
cord-002542-f7l4ty2j	106	12	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	106	13	and	and	CC
cord-002542-f7l4ty2j	106	14	triazole	triazole	NN
cord-002542-f7l4ty2j	106	15	-	-	HYPH
cord-002542-f7l4ty2j	106	16	linkage	linkage	NN
cord-002542-f7l4ty2j	106	17	included	include	VBN
cord-002542-f7l4ty2j	106	18	in	in	IN
cord-002542-f7l4ty2j	106	19	the	the	DT
cord-002542-f7l4ty2j	106	20	Click	Click	NNP
cord-002542-f7l4ty2j	106	21	-	-	HYPH
cord-002542-f7l4ty2j	106	22	Adaptor	Adaptor	NNP
cord-002542-f7l4ty2j	106	23	)	)	-RRB-
cord-002542-f7l4ty2j	106	24	were	be	VBD
cord-002542-f7l4ty2j	106	25	trimmed	trim	VBN
cord-002542-f7l4ty2j	106	26	and	and	CC
cord-002542-f7l4ty2j	106	27	any	any	DT
cord-002542-f7l4ty2j	106	28	reads	read	NNS
cord-002542-f7l4ty2j	106	29	that	that	WDT
cord-002542-f7l4ty2j	106	30	contained	contain	VBD
cord-002542-f7l4ty2j	106	31	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	106	32	with	with	IN
cord-002542-f7l4ty2j	106	33	a	a	DT
cord-002542-f7l4ty2j	106	34	PHRED	PHRED	NNP
cord-002542-f7l4ty2j	106	35	score	score	NN
cord-002542-f7l4ty2j	106	36	<	<	XX
cord-002542-f7l4ty2j	106	37	20	20	CD
cord-002542-f7l4ty2j	106	38	were	be	VBD
cord-002542-f7l4ty2j	106	39	removed	remove	VBN
cord-002542-f7l4ty2j	106	40	using	use	VBG
cord-002542-f7l4ty2j	106	41	the	the	DT
cord-002542-f7l4ty2j	106	42	FASTX	FASTX	NNP
cord-002542-f7l4ty2j	106	43	toolkit	toolkit	NN
cord-002542-f7l4ty2j	106	44	(	(	-LRB-
cord-002542-f7l4ty2j	106	45	http://hannonlab.cshl.edu/fastx_toolkit/	http://hannonlab.cshl.edu/fastx_toolkit/	NNP
cord-002542-f7l4ty2j	106	46	)	)	-RRB-
cord-002542-f7l4ty2j	106	47	.	.	.
cord-002542-f7l4ty2j	107	1	The	the	DT
cord-002542-f7l4ty2j	107	2	remaining	remain	VBG
cord-002542-f7l4ty2j	107	3	reads	read	NNS
cord-002542-f7l4ty2j	107	4	were	be	VBD
cord-002542-f7l4ty2j	107	5	aligned	align	VBN
cord-002542-f7l4ty2j	107	6	end	end	NN
cord-002542-f7l4ty2j	107	7	-	-	HYPH
cord-002542-f7l4ty2j	107	8	to	to	IN
cord-002542-f7l4ty2j	107	9	-	-	HYPH
cord-002542-f7l4ty2j	107	10	end	end	NN
cord-002542-f7l4ty2j	107	11	with	with	IN
cord-002542-f7l4ty2j	107	12	Bowtie	Bowtie	NNP
cord-002542-f7l4ty2j	107	13	(	(	-LRB-
cord-002542-f7l4ty2j	107	14	v1.0.1	v1.0.1	NNP
cord-002542-f7l4ty2j	107	15	)	)	-RRB-
cord-002542-f7l4ty2j	108	1	[	[	-LRB-
cord-002542-f7l4ty2j	108	2	47	47	CD
cord-002542-f7l4ty2j	108	3	]	]	-RRB-
cord-002542-f7l4ty2j	109	1	(	(	-LRB-
cord-002542-f7l4ty2j	109	2	command	command	NN
cord-002542-f7l4ty2j	109	3	line	line	NN
cord-002542-f7l4ty2j	109	4	parameters	parameter	NNS
cord-002542-f7l4ty2j	109	5	:	:	:
cord-002542-f7l4ty2j	110	1	-v	-v	JJS
cord-002542-f7l4ty2j	110	2	3	3	CD
cord-002542-f7l4ty2j	110	3	--best	--b	JJS
cord-002542-f7l4ty2j	110	4	)	)	-RRB-
cord-002542-f7l4ty2j	111	1	first	first	RB
cord-002542-f7l4ty2j	111	2	to	to	IN
cord-002542-f7l4ty2j	111	3	the	the	DT
cord-002542-f7l4ty2j	111	4	FHV	FHV	NNP
cord-002542-f7l4ty2j	111	5	genome	genome	NN
cord-002542-f7l4ty2j	112	1	(	(	-LRB-
cord-002542-f7l4ty2j	112	2	NC_004414	NC_004414	NNP
cord-002542-f7l4ty2j	112	3	and	and	CC
cord-002542-f7l4ty2j	112	4	NC_004146	NC_004146	NNP
cord-002542-f7l4ty2j	112	5	)	)	-RRB-
cord-002542-f7l4ty2j	112	6	and	and	CC
cord-002542-f7l4ty2j	112	7	next	next	JJ
cord-002542-f7l4ty2j	112	8	to	to	TO
cord-002542-f7l4ty2j	112	9	host	host	VB
cord-002542-f7l4ty2j	112	10	D.	D.	NNP
cord-002542-f7l4ty2j	112	11	melanogaster	melanogaster	NN
cord-002542-f7l4ty2j	112	12	genome	genome	NNP
cord-002542-f7l4ty2j	112	13	(	(	-LRB-
cord-002542-f7l4ty2j	112	14	fb5_22	fb5_22	NN
cord-002542-f7l4ty2j	112	15	)	)	-RRB-
cord-002542-f7l4ty2j	112	16	.	.	.
cord-002542-f7l4ty2j	113	1	The	the	DT
cord-002542-f7l4ty2j	113	2	remaining	remain	VBG
cord-002542-f7l4ty2j	113	3	unmapped	unmapped	JJ
cord-002542-f7l4ty2j	113	4	reads	read	NNS
cord-002542-f7l4ty2j	113	5	were	be	VBD
cord-002542-f7l4ty2j	113	6	processed	process	VBN
cord-002542-f7l4ty2j	113	7	to	to	TO
cord-002542-f7l4ty2j	113	8	identify	identify	VB
cord-002542-f7l4ty2j	113	9	recombination	recombination	NN
cord-002542-f7l4ty2j	113	10	events	event	NNS
cord-002542-f7l4ty2j	113	11	using	use	VBG
cord-002542-f7l4ty2j	113	12	the	the	DT
cord-002542-f7l4ty2j	113	13	python	python	NNP
cord-002542-f7l4ty2j	113	14	script	script	NN
cord-002542-f7l4ty2j	113	15	'	'	``
cord-002542-f7l4ty2j	113	16	ViReMa	virema	UH
cord-002542-f7l4ty2j	113	17	'	'	''
cord-002542-f7l4ty2j	113	18	(	(	-LRB-
cord-002542-f7l4ty2j	113	19	Viral	Viral	NNP
cord-002542-f7l4ty2j	113	20	Recombination	Recombination	NNP
cord-002542-f7l4ty2j	113	21	Mapper	Mapper	NNP
cord-002542-f7l4ty2j	113	22	)	)	-RRB-
cord-002542-f7l4ty2j	113	23	[	[	-LRB-
cord-002542-f7l4ty2j	113	24	32	32	CD
cord-002542-f7l4ty2j	113	25	]	]	-RRB-
cord-002542-f7l4ty2j	114	1	(	(	-LRB-
cord-002542-f7l4ty2j	114	2	command	command	NN
cord-002542-f7l4ty2j	114	3	line	line	NN
cord-002542-f7l4ty2j	114	4	parameters:--N	parameters:--n	ADD
cord-002542-f7l4ty2j	114	5	1	1	CD
cord-002542-f7l4ty2j	114	6	--X	--x	CD
cord-002542-f7l4ty2j	114	7	5	5	CD
cord-002542-f7l4ty2j	115	1	--Seed	--seed	CD
cord-002542-f7l4ty2j	115	2	25	25	CD
cord-002542-f7l4ty2j	115	3	--Host_Seed	--host_seed	SYM
cord-002542-f7l4ty2j	115	4	30	30	CD
cord-002542-f7l4ty2j	115	5	--Defuzz	--defuzz	CD
cord-002542-f7l4ty2j	115	6	0	0	CD
cord-002542-f7l4ty2j	115	7	--MicroInDel	--microindel	CD
cord-002542-f7l4ty2j	115	8	5	5	CD
cord-002542-f7l4ty2j	115	9	)	)	-RRB-
cord-002542-f7l4ty2j	115	10	.	.	.
cord-002542-f7l4ty2j	116	1	The	the	DT
cord-002542-f7l4ty2j	116	2	frequency	frequency	NN
cord-002542-f7l4ty2j	116	3	of	of	IN
cord-002542-f7l4ty2j	116	4	a	a	DT
cord-002542-f7l4ty2j	116	5	specific	specific	JJ
cord-002542-f7l4ty2j	116	6	recombination	recombination	NN
cord-002542-f7l4ty2j	116	7	event	event	NN
cord-002542-f7l4ty2j	116	8	is	be	VBZ
cord-002542-f7l4ty2j	116	9	approximated	approximate	VBN
cord-002542-f7l4ty2j	116	10	by	by	IN
cord-002542-f7l4ty2j	116	11	dividing	divide	VBG
cord-002542-f7l4ty2j	116	12	the	the	DT
cord-002542-f7l4ty2j	116	13	number	number	NN
cord-002542-f7l4ty2j	116	14	of	of	IN
cord-002542-f7l4ty2j	116	15	reads	read	NNS
cord-002542-f7l4ty2j	116	16	mapping	mapping	NN
cord-002542-f7l4ty2j	116	17	to	to	IN
cord-002542-f7l4ty2j	116	18	this	this	DT
cord-002542-f7l4ty2j	116	19	recombination	recombination	NN
cord-002542-f7l4ty2j	116	20	(	(	-LRB-
cord-002542-f7l4ty2j	116	21	N	N	NNP
cord-002542-f7l4ty2j	116	22	)	)	-RRB-
cord-002542-f7l4ty2j	116	23	by	by	IN
cord-002542-f7l4ty2j	116	24	N	n	CD
cord-002542-f7l4ty2j	116	25	plus	plus	CC
cord-002542-f7l4ty2j	116	26	the	the	DT
cord-002542-f7l4ty2j	116	27	average	average	NN
cord-002542-f7l4ty2j	116	28	of	of	IN
cord-002542-f7l4ty2j	116	29	the	the	DT
cord-002542-f7l4ty2j	116	30	number	number	NN
cord-002542-f7l4ty2j	116	31	of	of	IN
cord-002542-f7l4ty2j	116	32	reads	read	NNS
cord-002542-f7l4ty2j	116	33	mapping	mapping	NN
cord-002542-f7l4ty2j	116	34	to	to	IN
cord-002542-f7l4ty2j	116	35	the	the	DT
cord-002542-f7l4ty2j	116	36	wild	wild	JJ
cord-002542-f7l4ty2j	116	37	-	-	HYPH
cord-002542-f7l4ty2j	116	38	type	type	NN
cord-002542-f7l4ty2j	116	39	genome	genome	NN
cord-002542-f7l4ty2j	116	40	at	at	IN
cord-002542-f7l4ty2j	116	41	each	each	DT
cord-002542-f7l4ty2j	116	42	of	of	IN
cord-002542-f7l4ty2j	116	43	the	the	DT
cord-002542-f7l4ty2j	116	44	recombination	recombination	NN
cord-002542-f7l4ty2j	116	45	coordinates	coordinate	VBZ
cord-002542-f7l4ty2j	116	46	.	.	.
cord-002542-f7l4ty2j	117	1	The	the	DT
cord-002542-f7l4ty2j	117	2	Oxford	Oxford	NNP
cord-002542-f7l4ty2j	117	3	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	117	4	Technologies	Technologies	NNPS
cord-002542-f7l4ty2j	117	5	's	's	POS
cord-002542-f7l4ty2j	117	6	(	(	-LRB-
cord-002542-f7l4ty2j	117	7	ONT	ONT	NNP
cord-002542-f7l4ty2j	117	8	)	)	-RRB-
cord-002542-f7l4ty2j	117	9	MinION	MinION	NNP
cord-002542-f7l4ty2j	117	10	and	and	CC
cord-002542-f7l4ty2j	117	11	flowcells	flowcell	NNS
cord-002542-f7l4ty2j	117	12	were	be	VBD
cord-002542-f7l4ty2j	117	13	acquired	acquire	VBN
cord-002542-f7l4ty2j	117	14	as	as	IN
cord-002542-f7l4ty2j	117	15	part	part	NN
cord-002542-f7l4ty2j	117	16	of	of	IN
cord-002542-f7l4ty2j	117	17	the	the	DT
cord-002542-f7l4ty2j	117	18	ONT	ONT	NNP
cord-002542-f7l4ty2j	117	19	early	early	JJ
cord-002542-f7l4ty2j	117	20	-	-	HYPH
cord-002542-f7l4ty2j	117	21	access	access	NN
cord-002542-f7l4ty2j	117	22	program	program	NN
cord-002542-f7l4ty2j	117	23	.	.	.
cord-002542-f7l4ty2j	118	1	To	to	TO
cord-002542-f7l4ty2j	118	2	prepare	prepare	VB
cord-002542-f7l4ty2j	118	3	sequencing	sequencing	NN
cord-002542-f7l4ty2j	118	4	libraries	library	NNS
cord-002542-f7l4ty2j	118	5	for	for	IN
cord-002542-f7l4ty2j	118	6	the	the	DT
cord-002542-f7l4ty2j	118	7	MinION	minion	NN
cord-002542-f7l4ty2j	118	8	,	,	,
cord-002542-f7l4ty2j	118	9	50ng	50ng	NN
cord-002542-f7l4ty2j	118	10	of	of	IN
cord-002542-f7l4ty2j	118	11	RNA	RNA	NNP
cord-002542-f7l4ty2j	118	12	was	be	VBD
cord-002542-f7l4ty2j	118	13	reverse	reverse	RB
cord-002542-f7l4ty2j	118	14	transcribed	transcribe	VBN
cord-002542-f7l4ty2j	118	15	using	use	VBG
cord-002542-f7l4ty2j	118	16	RNA	RNA	NNP
cord-002542-f7l4ty2j	118	17	specific	specific	JJ
cord-002542-f7l4ty2j	118	18	primers	primer	NNS
cord-002542-f7l4ty2j	118	19	that	that	WDT
cord-002542-f7l4ty2j	118	20	were	be	VBD
cord-002542-f7l4ty2j	118	21	complimentary	complimentary	JJ
cord-002542-f7l4ty2j	118	22	to	to	IN
cord-002542-f7l4ty2j	118	23	the	the	DT
cord-002542-f7l4ty2j	118	24	3	3	CD
cord-002542-f7l4ty2j	118	25	'	'	NN
cord-002542-f7l4ty2j	118	26	end	end	NN
cord-002542-f7l4ty2j	118	27	of	of	IN
cord-002542-f7l4ty2j	118	28	the	the	DT
cord-002542-f7l4ty2j	118	29	respective	respective	JJ
cord-002542-f7l4ty2j	118	30	genome	genome	NN
cord-002542-f7l4ty2j	118	31	(	(	-LRB-
cord-002542-f7l4ty2j	118	32	RNA1_RP	rna1_rp	NN
cord-002542-f7l4ty2j	118	33	:	:	:
cord-002542-f7l4ty2j	118	34	ACCTCTGCCCTTTCGGGCTA	ACCTCTGCCCTTTCGGGCTA	NNP
cord-002542-f7l4ty2j	118	35	or	or	CC
cord-002542-f7l4ty2j	118	36	RNA2_RP	rna2_rp	NN
cord-002542-f7l4ty2j	118	37	:	:	:
cord-002542-f7l4ty2j	118	38	ACCTT	ACCTT	NNP
cord-002542-f7l4ty2j	118	39	AGTCTGTTGACTTAA	AGTCTGTTGACTTAA	NNP
cord-002542-f7l4ty2j	118	40	)	)	-RRB-
cord-002542-f7l4ty2j	118	41	.	.	.
cord-002542-f7l4ty2j	119	1	cDNA	cDNA	NNP
cord-002542-f7l4ty2j	119	2	was	be	VBD
cord-002542-f7l4ty2j	119	3	then	then	RB
cord-002542-f7l4ty2j	119	4	amplified	amplify	VBN
cord-002542-f7l4ty2j	119	5	using	use	VBG
cord-002542-f7l4ty2j	119	6	the	the	DT
cord-002542-f7l4ty2j	119	7	standard	standard	JJ
cord-002542-f7l4ty2j	119	8	Phusion	Phusion	NNP
cord-002542-f7l4ty2j	119	9	(	(	-LRB-
cord-002542-f7l4ty2j	119	10	NEB	NEB	NNP
cord-002542-f7l4ty2j	119	11	)	)	-RRB-
cord-002542-f7l4ty2j	119	12	PCR	pcr	NN
cord-002542-f7l4ty2j	119	13	protocol	protocol	NN
cord-002542-f7l4ty2j	119	14	using	use	VBG
cord-002542-f7l4ty2j	119	15	genome	genome	NN
cord-002542-f7l4ty2j	119	16	specific	specific	JJ
cord-002542-f7l4ty2j	119	17	primers	primer	NNS
cord-002542-f7l4ty2j	119	18	(	(	-LRB-
cord-002542-f7l4ty2j	119	19	RNA1_FP	RNA1_FP	NNS
cord-002542-f7l4ty2j	119	20	:	:	:
cord-002542-f7l4ty2j	119	21	GTTTTCGAAACAAATAAAAC	gttttcgaaacaaataaaac	NN
cord-002542-f7l4ty2j	119	22	or	or	CC
cord-002542-f7l4ty2j	119	23	RNA2_FP	rna2_fp	XX
cord-002542-f7l4ty2j	119	24	:	:	:
cord-002542-f7l4ty2j	119	25	GTAAACAATTCCAAGTTCCA	GTAAACAATTCCAAGTTCCA	NNP
cord-002542-f7l4ty2j	119	26	)	)	-RRB-
cord-002542-f7l4ty2j	119	27	for	for	IN
cord-002542-f7l4ty2j	119	28	19	19	CD
cord-002542-f7l4ty2j	119	29	cycles	cycle	NNS
cord-002542-f7l4ty2j	119	30	.	.	.
cord-002542-f7l4ty2j	120	1	Excess	excess	JJ
cord-002542-f7l4ty2j	120	2	primers	primer	NNS
cord-002542-f7l4ty2j	120	3	were	be	VBD
cord-002542-f7l4ty2j	120	4	removed	remove	VBN
cord-002542-f7l4ty2j	120	5	from	from	IN
cord-002542-f7l4ty2j	120	6	the	the	DT
cord-002542-f7l4ty2j	120	7	PCR	PCR	NNP
cord-002542-f7l4ty2j	120	8	product	product	NN
cord-002542-f7l4ty2j	120	9	using	use	VBG
cord-002542-f7l4ty2j	120	10	AMPure	AMPure	NNP
cord-002542-f7l4ty2j	120	11	XP	XP	NNP
cord-002542-f7l4ty2j	120	12	beads	bead	NNS
cord-002542-f7l4ty2j	120	13	(	(	-LRB-
cord-002542-f7l4ty2j	120	14	Beckman	Beckman	NNP
cord-002542-f7l4ty2j	120	15	Coulter	Coulter	NNP
cord-002542-f7l4ty2j	120	16	)	)	-RRB-
cord-002542-f7l4ty2j	120	17	at	at	IN
cord-002542-f7l4ty2j	120	18	a	a	DT
cord-002542-f7l4ty2j	120	19	ratio	ratio	NN
cord-002542-f7l4ty2j	120	20	of	of	IN
cord-002542-f7l4ty2j	120	21	1:1	1:1	CD
cord-002542-f7l4ty2j	120	22	AMPure	ampure	CD
cord-002542-f7l4ty2j	120	23	bead	bead	NN
cord-002542-f7l4ty2j	120	24	:	:	:
cord-002542-f7l4ty2j	120	25	PCR	PCR	NNP
cord-002542-f7l4ty2j	120	26	product	product	NN
cord-002542-f7l4ty2j	120	27	.	.	.
cord-002542-f7l4ty2j	121	1	Samples	sample	NNS
cord-002542-f7l4ty2j	121	2	were	be	VBD
cord-002542-f7l4ty2j	121	3	then	then	RB
cord-002542-f7l4ty2j	121	4	barcoded	barcode	VBN
cord-002542-f7l4ty2j	121	5	and	and	CC
cord-002542-f7l4ty2j	121	6	prepared	prepare	VBD
cord-002542-f7l4ty2j	121	7	following	follow	VBG
cord-002542-f7l4ty2j	121	8	the	the	DT
cord-002542-f7l4ty2j	121	9	manufacture	manufacture	NN
cord-002542-f7l4ty2j	121	10	's	's	POS
cord-002542-f7l4ty2j	121	11	protocol	protocol	NN
cord-002542-f7l4ty2j	121	12	(	(	-LRB-
cord-002542-f7l4ty2j	121	13	R9	R9	NNP
cord-002542-f7l4ty2j	121	14	Native	Native	NNP
cord-002542-f7l4ty2j	121	15	Barcoding	Barcoding	NNP
cord-002542-f7l4ty2j	121	16	Kit	Kit	NNP
cord-002542-f7l4ty2j	121	17	I	-PRON-	PRP
cord-002542-f7l4ty2j	121	18	and	and	CC
cord-002542-f7l4ty2j	121	19	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	121	20	Sequencing	Sequencing	NNP
cord-002542-f7l4ty2j	121	21	Kit	Kit	NNP
cord-002542-f7l4ty2j	121	22	)	)	-RRB-
cord-002542-f7l4ty2j	121	23	with	with	IN
cord-002542-f7l4ty2j	121	24	adjustments	adjustment	NNS
cord-002542-f7l4ty2j	121	25	to	to	TO
cord-002542-f7l4ty2j	121	26	tailor	tailor	VB
cord-002542-f7l4ty2j	121	27	input	input	NN
cord-002542-f7l4ty2j	121	28	cDNA	cdna	NN
cord-002542-f7l4ty2j	121	29	quantities	quantity	NNS
cord-002542-f7l4ty2j	121	30	.	.	.
cord-002542-f7l4ty2j	122	1	A	a	DT
cord-002542-f7l4ty2j	122	2	target	target	NN
cord-002542-f7l4ty2j	122	3	of	of	IN
cord-002542-f7l4ty2j	122	4	1ug	1ug	NN
cord-002542-f7l4ty2j	122	5	of	of	IN
cord-002542-f7l4ty2j	122	6	fragmented	fragmented	JJ
cord-002542-f7l4ty2j	122	7	DNA	dna	NN
cord-002542-f7l4ty2j	122	8	at	at	IN
cord-002542-f7l4ty2j	122	9	approximately	approximately	RB
cord-002542-f7l4ty2j	122	10	8'000	8'000	CD
cord-002542-f7l4ty2j	122	11	nts	nts	NNPS
cord-002542-f7l4ty2j	122	12	is	be	VBZ
cord-002542-f7l4ty2j	122	13	considered	consider	VBN
cord-002542-f7l4ty2j	122	14	optimal	optimal	JJ
cord-002542-f7l4ty2j	122	15	for	for	IN
cord-002542-f7l4ty2j	122	16	library	library	NN
cord-002542-f7l4ty2j	122	17	generation	generation	NN
cord-002542-f7l4ty2j	122	18	using	use	VBG
cord-002542-f7l4ty2j	122	19	this	this	DT
cord-002542-f7l4ty2j	122	20	kit	kit	NN
cord-002542-f7l4ty2j	122	21	.	.	.
cord-002542-f7l4ty2j	123	1	The	the	DT
cord-002542-f7l4ty2j	123	2	input	input	NN
cord-002542-f7l4ty2j	123	3	amounts	amount	VBZ
cord-002542-f7l4ty2j	123	4	for	for	IN
cord-002542-f7l4ty2j	123	5	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	123	6	(	(	-LRB-
cord-002542-f7l4ty2j	123	7	3107	3107	CD
cord-002542-f7l4ty2j	123	8	bp	bp	NNP
cord-002542-f7l4ty2j	123	9	)	)	-RRB-
cord-002542-f7l4ty2j	123	10	and	and	CC
cord-002542-f7l4ty2j	123	11	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	123	12	(	(	-LRB-
cord-002542-f7l4ty2j	123	13	1400	1400	CD
cord-002542-f7l4ty2j	123	14	bp	bp	NNP
cord-002542-f7l4ty2j	123	15	)	)	-RRB-
cord-002542-f7l4ty2j	123	16	were	be	VBD
cord-002542-f7l4ty2j	123	17	thus	thus	RB
cord-002542-f7l4ty2j	123	18	adjusted	adjust	VBN
cord-002542-f7l4ty2j	123	19	to	to	IN
cord-002542-f7l4ty2j	123	20	192ng	192ng	JJ
cord-002542-f7l4ty2j	123	21	and	and	CC
cord-002542-f7l4ty2j	123	22	88ng	88ng	NN
cord-002542-f7l4ty2j	123	23	respectively	respectively	RB
cord-002542-f7l4ty2j	123	24	and	and	CC
cord-002542-f7l4ty2j	123	25	combined	combine	VBN
cord-002542-f7l4ty2j	123	26	in	in	IN
cord-002542-f7l4ty2j	123	27	46uL	46ul	CD
cord-002542-f7l4ty2j	123	28	water	water	NN
cord-002542-f7l4ty2j	123	29	to	to	TO
cord-002542-f7l4ty2j	123	30	maintain	maintain	VB
cord-002542-f7l4ty2j	123	31	optimal	optimal	JJ
cord-002542-f7l4ty2j	123	32	DNA	dna	NN
cord-002542-f7l4ty2j	123	33	end	end	NN
cord-002542-f7l4ty2j	123	34	molarity	molarity	NN
cord-002542-f7l4ty2j	123	35	.	.	.
cord-002542-f7l4ty2j	124	1	After	after	IN
cord-002542-f7l4ty2j	124	2	ligation	ligation	NN
cord-002542-f7l4ty2j	124	3	of	of	IN
cord-002542-f7l4ty2j	124	4	barcodes	barcode	NNS
cord-002542-f7l4ty2j	124	5	,	,	,
cord-002542-f7l4ty2j	124	6	equal	equal	JJ
cord-002542-f7l4ty2j	124	7	amount	amount	NN
cord-002542-f7l4ty2j	124	8	of	of	IN
cord-002542-f7l4ty2j	124	9	each	each	DT
cord-002542-f7l4ty2j	124	10	DNA	dna	NN
cord-002542-f7l4ty2j	124	11	library	library	NN
cord-002542-f7l4ty2j	124	12	(	(	-LRB-
cord-002542-f7l4ty2j	124	13	9	9	CD
cord-002542-f7l4ty2j	124	14	samples	sample	NNS
cord-002542-f7l4ty2j	124	15	in	in	IN
cord-002542-f7l4ty2j	124	16	total	total	NN
cord-002542-f7l4ty2j	124	17	)	)	-RRB-
cord-002542-f7l4ty2j	124	18	were	be	VBD
cord-002542-f7l4ty2j	124	19	pooled	pool	VBN
cord-002542-f7l4ty2j	124	20	and	and	CC
cord-002542-f7l4ty2j	124	21	loaded	load	VBN
cord-002542-f7l4ty2j	124	22	onto	onto	IN
cord-002542-f7l4ty2j	124	23	a	a	DT
cord-002542-f7l4ty2j	124	24	MinION	MinION	NNP
cord-002542-f7l4ty2j	124	25	MkIB	MkIB	NNP
cord-002542-f7l4ty2j	124	26	device	device	NN
cord-002542-f7l4ty2j	124	27	equipped	equip	VBN
cord-002542-f7l4ty2j	124	28	with	with	IN
cord-002542-f7l4ty2j	124	29	an	an	DT
cord-002542-f7l4ty2j	124	30	R9	R9	NNP
cord-002542-f7l4ty2j	124	31	flow	flow	NN
cord-002542-f7l4ty2j	124	32	cell	cell	NN
cord-002542-f7l4ty2j	124	33	.	.	.
cord-002542-f7l4ty2j	125	1	The	the	DT
cord-002542-f7l4ty2j	125	2	MinKNOW	minknow	JJ
cord-002542-f7l4ty2j	125	3	control	control	NN
cord-002542-f7l4ty2j	125	4	software	software	NN
cord-002542-f7l4ty2j	125	5	was	be	VBD
cord-002542-f7l4ty2j	125	6	used	use	VBN
cord-002542-f7l4ty2j	125	7	to	to	TO
cord-002542-f7l4ty2j	125	8	select	select	VB
cord-002542-f7l4ty2j	125	9	a	a	DT
cord-002542-f7l4ty2j	125	10	48-hour	48-hour	JJ
cord-002542-f7l4ty2j	125	11	sequencing	sequencing	NN
cord-002542-f7l4ty2j	125	12	protocol	protocol	NN
cord-002542-f7l4ty2j	125	13	and	and	CC
cord-002542-f7l4ty2j	125	14	was	be	VBD
cord-002542-f7l4ty2j	125	15	allowed	allow	VBN
cord-002542-f7l4ty2j	125	16	to	to	TO
cord-002542-f7l4ty2j	125	17	proceed	proceed	VB
cord-002542-f7l4ty2j	125	18	for	for	IN
cord-002542-f7l4ty2j	125	19	at	at	RB
cord-002542-f7l4ty2j	125	20	least	least	RBS
cord-002542-f7l4ty2j	125	21	36	36	CD
cord-002542-f7l4ty2j	125	22	hours	hour	NNS
cord-002542-f7l4ty2j	125	23	,	,	,
cord-002542-f7l4ty2j	125	24	until	until	IN
cord-002542-f7l4ty2j	125	25	high	high	JJ
cord-002542-f7l4ty2j	125	26	-	-	HYPH
cord-002542-f7l4ty2j	125	27	quality	quality	NN
cord-002542-f7l4ty2j	125	28	data	datum	NNS
cord-002542-f7l4ty2j	125	29	accumulation	accumulation	NN
cord-002542-f7l4ty2j	125	30	ceased	cease	VBD
cord-002542-f7l4ty2j	125	31	.	.	.
cord-002542-f7l4ty2j	126	1	Raw	raw	JJ
cord-002542-f7l4ty2j	126	2	data	datum	NNS
cord-002542-f7l4ty2j	126	3	was	be	VBD
cord-002542-f7l4ty2j	126	4	uploaded	upload	VBN
cord-002542-f7l4ty2j	126	5	automatically	automatically	RB
cord-002542-f7l4ty2j	126	6	by	by	IN
cord-002542-f7l4ty2j	126	7	Metrichor	Metrichor	NNP
cord-002542-f7l4ty2j	126	8	software	software	NN
cord-002542-f7l4ty2j	126	9	for	for	IN
cord-002542-f7l4ty2j	126	10	cloudbased	cloudbased	JJ
cord-002542-f7l4ty2j	126	11	base	base	NN
cord-002542-f7l4ty2j	126	12	-	-	HYPH
cord-002542-f7l4ty2j	126	13	calling	call	VBG
cord-002542-f7l4ty2j	126	14	using	use	VBG
cord-002542-f7l4ty2j	126	15	default	default	NN
cord-002542-f7l4ty2j	126	16	settings	setting	NNS
cord-002542-f7l4ty2j	126	17	and	and	CC
cord-002542-f7l4ty2j	126	18	quality	quality	NN
cord-002542-f7l4ty2j	126	19	filtering	filter	VBG
cord-002542-f7l4ty2j	126	20	for	for	IN
cord-002542-f7l4ty2j	126	21	2-dimensional	2-dimensional	JJ
cord-002542-f7l4ty2j	126	22	reads	read	NNS
cord-002542-f7l4ty2j	126	23	.	.	.
cord-002542-f7l4ty2j	127	1	Reads	read	NNS
cord-002542-f7l4ty2j	127	2	were	be	VBD
cord-002542-f7l4ty2j	127	3	extracted	extract	VBN
cord-002542-f7l4ty2j	127	4	from	from	IN
cord-002542-f7l4ty2j	127	5	HDF5	hdf5	JJ
cord-002542-f7l4ty2j	127	6	format	format	NN
cord-002542-f7l4ty2j	127	7	files	file	NNS
cord-002542-f7l4ty2j	127	8	(	(	-LRB-
cord-002542-f7l4ty2j	127	9	fast5	fast5	NN
cord-002542-f7l4ty2j	127	10	)	)	-RRB-
cord-002542-f7l4ty2j	127	11	using	use	VBG
cord-002542-f7l4ty2j	127	12	poretools	poretool	NNS
cord-002542-f7l4ty2j	127	13	[	[	-LRB-
cord-002542-f7l4ty2j	127	14	48	48	CD
cord-002542-f7l4ty2j	127	15	]	]	-RRB-
cord-002542-f7l4ty2j	127	16	.	.	.
cord-002542-f7l4ty2j	128	1	ONT	ONT	NNP
cord-002542-f7l4ty2j	128	2	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	128	3	data	datum	NNS
cord-002542-f7l4ty2j	128	4	processing	processing	NN
cord-002542-f7l4ty2j	128	5	and	and	CC
cord-002542-f7l4ty2j	128	6	alignment	alignment	NN
cord-002542-f7l4ty2j	128	7	Full	full	JJ
cord-002542-f7l4ty2j	128	8	-	-	HYPH
cord-002542-f7l4ty2j	128	9	length	length	NN
cord-002542-f7l4ty2j	128	10	ONT	ONT	NNP
cord-002542-f7l4ty2j	128	11	reads	read	VBZ
cord-002542-f7l4ty2j	128	12	were	be	VBD
cord-002542-f7l4ty2j	128	13	mapped	map	VBN
cord-002542-f7l4ty2j	128	14	to	to	IN
cord-002542-f7l4ty2j	128	15	the	the	DT
cord-002542-f7l4ty2j	128	16	Flock	Flock	NNP
cord-002542-f7l4ty2j	128	17	House	House	NNP
cord-002542-f7l4ty2j	128	18	virus	virus	NN
cord-002542-f7l4ty2j	128	19	genome	genome	NN
cord-002542-f7l4ty2j	128	20	using	use	VBG
cord-002542-f7l4ty2j	128	21	the	the	DT
cord-002542-f7l4ty2j	128	22	pacbio	pacbio	NNP
cord-002542-f7l4ty2j	128	23	wrapper	wrapper	NN
cord-002542-f7l4ty2j	128	24	from	from	IN
cord-002542-f7l4ty2j	128	25	the	the	DT
cord-002542-f7l4ty2j	128	26	BBMAP	BBMAP	NNP
cord-002542-f7l4ty2j	128	27	v36	v36	NN
cord-002542-f7l4ty2j	128	28	suite	suite	NN
cord-002542-f7l4ty2j	128	29	(	(	-LRB-
cord-002542-f7l4ty2j	128	30	command	command	NN
cord-002542-f7l4ty2j	128	31	line	line	NN
cord-002542-f7l4ty2j	128	32	parameters	parameter	NNS
cord-002542-f7l4ty2j	128	33	:	:	:
cord-002542-f7l4ty2j	128	34	fastareadlen	fastareadlen	NNP
cord-002542-f7l4ty2j	128	35	=	=	SYM
cord-002542-f7l4ty2j	128	36	6000	6000	CD
cord-002542-f7l4ty2j	128	37	vslow	vslow	NN
cord-002542-f7l4ty2j	128	38	=	=	SYM
cord-002542-f7l4ty2j	128	39	t	t	NNP
cord-002542-f7l4ty2j	128	40	maxindel	maxindel	NNP
cord-002542-f7l4ty2j	128	41	=	=	SYM
cord-002542-f7l4ty2j	128	42	3100	3100	CD
cord-002542-f7l4ty2j	128	43	minid	minid	NNP
cord-002542-f7l4ty2j	128	44	=	=	SYM
cord-002542-f7l4ty2j	128	45	0.5	0.5	CD
cord-002542-f7l4ty2j	128	46	local	local	JJ
cord-002542-f7l4ty2j	128	47	=	=	SYM
cord-002542-f7l4ty2j	128	48	f	f	NNP
cord-002542-f7l4ty2j	128	49	ignorebadquality	ignorebadquality	NNP
cord-002542-f7l4ty2j	128	50	=	=	SYM
cord-002542-f7l4ty2j	128	51	t	t	NNP
cord-002542-f7l4ty2j	128	52	usequality	usequality	NN
cord-002542-f7l4ty2j	128	53	=	=	SYM
cord-002542-f7l4ty2j	128	54	f	f	NNP
cord-002542-f7l4ty2j	128	55	)	)	-RRB-
cord-002542-f7l4ty2j	128	56	.	.	.
cord-002542-f7l4ty2j	129	1	Alignment	Alignment	NNP
cord-002542-f7l4ty2j	129	2	SAM	SAM	NNP
cord-002542-f7l4ty2j	129	3	files	file	NNS
cord-002542-f7l4ty2j	129	4	were	be	VBD
cord-002542-f7l4ty2j	129	5	visualized	visualize	VBN
cord-002542-f7l4ty2j	129	6	using	use	VBG
cord-002542-f7l4ty2j	129	7	the	the	DT
cord-002542-f7l4ty2j	129	8	Tablet	Tablet	NNP
cord-002542-f7l4ty2j	129	9	sequence	sequence	NN
cord-002542-f7l4ty2j	129	10	viewer	viewer	NN
cord-002542-f7l4ty2j	129	11	[	[	-LRB-
cord-002542-f7l4ty2j	129	12	49	49	CD
cord-002542-f7l4ty2j	129	13	]	]	-RRB-
cord-002542-f7l4ty2j	129	14	.	.	.
cord-002542-f7l4ty2j	130	1	SAM	SAM	NNP
cord-002542-f7l4ty2j	130	2	files	file	NNS
cord-002542-f7l4ty2j	130	3	were	be	VBD
cord-002542-f7l4ty2j	130	4	filtered	filter	VBN
cord-002542-f7l4ty2j	130	5	to	to	TO
cord-002542-f7l4ty2j	130	6	ensure	ensure	VB
cord-002542-f7l4ty2j	130	7	that	that	IN
cord-002542-f7l4ty2j	130	8	MinION	MinION	NNP
cord-002542-f7l4ty2j	130	9	reads	read	VBZ
cord-002542-f7l4ty2j	130	10	mapped	map	VBN
cord-002542-f7l4ty2j	130	11	from	from	IN
cord-002542-f7l4ty2j	130	12	the	the	DT
cord-002542-f7l4ty2j	130	13	first	first	JJ
cord-002542-f7l4ty2j	130	14	25	25	CD
cord-002542-f7l4ty2j	130	15	nts	nt	NNS
cord-002542-f7l4ty2j	130	16	to	to	IN
cord-002542-f7l4ty2j	130	17	the	the	DT
cord-002542-f7l4ty2j	130	18	final	final	JJ
cord-002542-f7l4ty2j	130	19	25	25	CD
cord-002542-f7l4ty2j	130	20	nts	nt	NNS
cord-002542-f7l4ty2j	130	21	of	of	IN
cord-002542-f7l4ty2j	130	22	the	the	DT
cord-002542-f7l4ty2j	130	23	reference	reference	NN
cord-002542-f7l4ty2j	130	24	genome	genome	NN
cord-002542-f7l4ty2j	130	25	(	(	-LRB-
cord-002542-f7l4ty2j	130	26	accounting	account	VBG
cord-002542-f7l4ty2j	130	27	for	for	IN
cord-002542-f7l4ty2j	130	28	deletions	deletion	NNS
cord-002542-f7l4ty2j	130	29	and	and	CC
cord-002542-f7l4ty2j	130	30	insertions	insertion	NNS
cord-002542-f7l4ty2j	130	31	)	)	-RRB-
cord-002542-f7l4ty2j	130	32	,	,	,
cord-002542-f7l4ty2j	130	33	due	due	IN
cord-002542-f7l4ty2j	130	34	to	to	IN
cord-002542-f7l4ty2j	130	35	the	the	DT
cord-002542-f7l4ty2j	130	36	presence	presence	NN
cord-002542-f7l4ty2j	130	37	of	of	IN
cord-002542-f7l4ty2j	130	38	truncated	truncate	VBN
cord-002542-f7l4ty2j	130	39	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	130	40	reads	read	VBZ
cord-002542-f7l4ty2j	130	41	and	and	CC
cord-002542-f7l4ty2j	130	42	mis	mis	NN
cord-002542-f7l4ty2j	130	43	-	-	NN
cord-002542-f7l4ty2j	130	44	priming	priming	NN
cord-002542-f7l4ty2j	130	45	during	during	IN
cord-002542-f7l4ty2j	130	46	the	the	DT
cord-002542-f7l4ty2j	130	47	cDNA	cdna	NN
cord-002542-f7l4ty2j	130	48	PCR	pcr	NN
cord-002542-f7l4ty2j	130	49	amplification	amplification	NN
cord-002542-f7l4ty2j	130	50	steps	step	NNS
cord-002542-f7l4ty2j	130	51	.	.	.
cord-002542-f7l4ty2j	131	1	Errors	error	NNS
cord-002542-f7l4ty2j	131	2	including	include	VBG
cord-002542-f7l4ty2j	131	3	substitutions	substitution	NNS
cord-002542-f7l4ty2j	131	4	,	,	,
cord-002542-f7l4ty2j	131	5	insertions	insertion	NNS
cord-002542-f7l4ty2j	131	6	and	and	CC
cord-002542-f7l4ty2j	131	7	deletions	deletion	NNS
cord-002542-f7l4ty2j	131	8	were	be	VBD
cord-002542-f7l4ty2j	131	9	counted	count	VBN
cord-002542-f7l4ty2j	131	10	using	use	VBG
cord-002542-f7l4ty2j	131	11	the	the	DT
cord-002542-f7l4ty2j	131	12	samtools	samtool	NNS
cord-002542-f7l4ty2j	131	13	[	[	-LRB-
cord-002542-f7l4ty2j	131	14	50	50	CD
cord-002542-f7l4ty2j	131	15	]	]	-RRB-
cord-002542-f7l4ty2j	131	16	mpileup	mpileup	NNP
cord-002542-f7l4ty2j	131	17	command	command	NN
cord-002542-f7l4ty2j	131	18	and	and	CC
cord-002542-f7l4ty2j	131	19	error	error	NN
cord-002542-f7l4ty2j	131	20	rates	rate	NNS
cord-002542-f7l4ty2j	131	21	at	at	IN
cord-002542-f7l4ty2j	131	22	each	each	DT
cord-002542-f7l4ty2j	131	23	position	position	NN
cord-002542-f7l4ty2j	131	24	were	be	VBD
cord-002542-f7l4ty2j	131	25	calculated	calculate	VBN
cord-002542-f7l4ty2j	131	26	by	by	IN
cord-002542-f7l4ty2j	131	27	dividing	divide	VBG
cord-002542-f7l4ty2j	131	28	this	this	DT
cord-002542-f7l4ty2j	131	29	value	value	NN
cord-002542-f7l4ty2j	131	30	by	by	IN
cord-002542-f7l4ty2j	131	31	the	the	DT
cord-002542-f7l4ty2j	131	32	read	read	NN
cord-002542-f7l4ty2j	131	33	depth	depth	NN
cord-002542-f7l4ty2j	131	34	at	at	IN
cord-002542-f7l4ty2j	131	35	this	this	DT
cord-002542-f7l4ty2j	131	36	position	position	NN
cord-002542-f7l4ty2j	131	37	(	(	-LRB-
cord-002542-f7l4ty2j	131	38	S5	S5	NNP
cord-002542-f7l4ty2j	131	39	Fig	Fig	NNP
cord-002542-f7l4ty2j	131	40	)	)	-RRB-
cord-002542-f7l4ty2j	131	41	.	.	.
cord-002542-f7l4ty2j	132	1	Insertion	insertion	NN
cord-002542-f7l4ty2j	132	2	and	and	CC
cord-002542-f7l4ty2j	132	3	deletion	deletion	NN
cord-002542-f7l4ty2j	132	4	events	event	NNS
cord-002542-f7l4ty2j	132	5	longer	long	RBR
cord-002542-f7l4ty2j	132	6	that	that	IN
cord-002542-f7l4ty2j	132	7	25	25	CD
cord-002542-f7l4ty2j	132	8	nts	nt	NNS
cord-002542-f7l4ty2j	132	9	were	be	VBD
cord-002542-f7l4ty2j	132	10	extracted	extract	VBN
cord-002542-f7l4ty2j	132	11	using	use	VBG
cord-002542-f7l4ty2j	132	12	the	the	DT
cord-002542-f7l4ty2j	132	13	CIGAR	cigar	NN
cord-002542-f7l4ty2j	132	14	string	string	NN
cord-002542-f7l4ty2j	132	15	of	of	IN
cord-002542-f7l4ty2j	132	16	the	the	DT
cord-002542-f7l4ty2j	132	17	SAM	SAM	NNP
cord-002542-f7l4ty2j	132	18	files	file	NNS
cord-002542-f7l4ty2j	132	19	using	use	VBG
cord-002542-f7l4ty2j	132	20	simple	simple	JJ
cord-002542-f7l4ty2j	132	21	in	in	IN
cord-002542-f7l4ty2j	132	22	-	-	HYPH
cord-002542-f7l4ty2j	132	23	house	house	NN
cord-002542-f7l4ty2j	132	24	scripts	script	NNS
cord-002542-f7l4ty2j	132	25	.	.	.
cord-002542-f7l4ty2j	133	1	For	for	IN
cord-002542-f7l4ty2j	133	2	recombination	recombination	NN
cord-002542-f7l4ty2j	133	3	sites	site	NNS
cord-002542-f7l4ty2j	133	4	containing	contain	VBG
cord-002542-f7l4ty2j	133	5	'	'	``
cord-002542-f7l4ty2j	133	6	fuzz	fuzz	NN
cord-002542-f7l4ty2j	133	7	'	'	''
cord-002542-f7l4ty2j	133	8	,	,	,
cord-002542-f7l4ty2j	133	9	where	where	WRB
cord-002542-f7l4ty2j	133	10	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	133	11	surrounding	surround	VBG
cord-002542-f7l4ty2j	133	12	the	the	DT
cord-002542-f7l4ty2j	133	13	putative	putative	JJ
cord-002542-f7l4ty2j	133	14	recombination	recombination	NN
cord-002542-f7l4ty2j	133	15	events	event	NNS
cord-002542-f7l4ty2j	133	16	are	be	VBP
cord-002542-f7l4ty2j	133	17	the	the	DT
cord-002542-f7l4ty2j	133	18	same	same	JJ
cord-002542-f7l4ty2j	133	19	for	for	IN
cord-002542-f7l4ty2j	133	20	both	both	CC
cord-002542-f7l4ty2j	133	21	the	the	DT
cord-002542-f7l4ty2j	133	22	acceptor	acceptor	NN
cord-002542-f7l4ty2j	133	23	and	and	CC
cord-002542-f7l4ty2j	133	24	donor	donor	NN
cord-002542-f7l4ty2j	133	25	sites	site	NNS
cord-002542-f7l4ty2j	133	26	,	,	,
cord-002542-f7l4ty2j	133	27	the	the	DT
cord-002542-f7l4ty2j	133	28	recombination	recombination	NN
cord-002542-f7l4ty2j	133	29	event	event	NN
cord-002542-f7l4ty2j	133	30	was	be	VBD
cord-002542-f7l4ty2j	133	31	reported	report	VBN
cord-002542-f7l4ty2j	133	32	as	as	IN
cord-002542-f7l4ty2j	133	33	occurring	occur	VBG
cord-002542-f7l4ty2j	133	34	in	in	IN
cord-002542-f7l4ty2j	133	35	the	the	DT
cord-002542-f7l4ty2j	133	36	middle	middle	NN
cord-002542-f7l4ty2j	133	37	of	of	IN
cord-002542-f7l4ty2j	133	38	the	the	DT
cord-002542-f7l4ty2j	133	39	'	'	``
cord-002542-f7l4ty2j	133	40	fuzzy	fuzzy	JJ
cord-002542-f7l4ty2j	133	41	'	'	''
cord-002542-f7l4ty2j	133	42	region	region	NN
cord-002542-f7l4ty2j	133	43	,	,	,
cord-002542-f7l4ty2j	133	44	or	or	CC
cord-002542-f7l4ty2j	133	45	at	at	IN
cord-002542-f7l4ty2j	133	46	the	the	DT
cord-002542-f7l4ty2j	133	47	5	5	CD
cord-002542-f7l4ty2j	133	48	'	'	POS
cord-002542-f7l4ty2j	133	49	side	side	NN
cord-002542-f7l4ty2j	133	50	of	of	IN
cord-002542-f7l4ty2j	133	51	the	the	DT
cord-002542-f7l4ty2j	133	52	middle	middle	JJ
cord-002542-f7l4ty2j	133	53	two	two	CD
cord-002542-f7l4ty2j	133	54	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	133	55	in	in	IN
cord-002542-f7l4ty2j	133	56	the	the	DT
cord-002542-f7l4ty2j	133	57	orientation	orientation	NN
cord-002542-f7l4ty2j	133	58	of	of	IN
cord-002542-f7l4ty2j	133	59	the	the	DT
cord-002542-f7l4ty2j	133	60	reference	reference	NN
cord-002542-f7l4ty2j	133	61	if	if	IN
cord-002542-f7l4ty2j	133	62	the	the	DT
cord-002542-f7l4ty2j	133	63	fuzzy	fuzzy	JJ
cord-002542-f7l4ty2j	133	64	site	site	NN
cord-002542-f7l4ty2j	133	65	contained	contain	VBD
cord-002542-f7l4ty2j	133	66	an	an	DT
cord-002542-f7l4ty2j	133	67	even	even	JJ
cord-002542-f7l4ty2j	133	68	number	number	NN
cord-002542-f7l4ty2j	133	69	of	of	IN
cord-002542-f7l4ty2j	133	70	residues	residue	NNS
cord-002542-f7l4ty2j	133	71	.	.	.
cord-002542-f7l4ty2j	134	1	This	this	DT
cord-002542-f7l4ty2j	134	2	is	be	VBZ
cord-002542-f7l4ty2j	134	3	the	the	DT
cord-002542-f7l4ty2j	134	4	same	same	JJ
cord-002542-f7l4ty2j	134	5	methodology	methodology	NN
cord-002542-f7l4ty2j	134	6	as	as	IN
cord-002542-f7l4ty2j	134	7	employed	employ	VBN
cord-002542-f7l4ty2j	134	8	in	in	IN
cord-002542-f7l4ty2j	134	9	the	the	DT
cord-002542-f7l4ty2j	134	10	ViReMa	virema	NN
cord-002542-f7l4ty2j	134	11	script	script	NN
cord-002542-f7l4ty2j	134	12	[	[	-LRB-
cord-002542-f7l4ty2j	134	13	32	32	CD
cord-002542-f7l4ty2j	134	14	]	]	-RRB-
cord-002542-f7l4ty2j	134	15	used	use	VBN
cord-002542-f7l4ty2j	134	16	to	to	TO
cord-002542-f7l4ty2j	134	17	map	map	VB
cord-002542-f7l4ty2j	134	18	recombination	recombination	NN
cord-002542-f7l4ty2j	134	19	event	event	NN
cord-002542-f7l4ty2j	134	20	in	in	IN
cord-002542-f7l4ty2j	134	21	the	the	DT
cord-002542-f7l4ty2j	134	22	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	134	23	data	datum	NNS
cord-002542-f7l4ty2j	134	24	.	.	.
cord-002542-f7l4ty2j	135	1	Insertion	insertion	NN
cord-002542-f7l4ty2j	135	2	events	event	NNS
cord-002542-f7l4ty2j	135	3	and	and	CC
cord-002542-f7l4ty2j	135	4	soft	soft	JJ
cord-002542-f7l4ty2j	135	5	-	-	HYPH
cord-002542-f7l4ty2j	135	6	pads	pad	NNS
cord-002542-f7l4ty2j	135	7	longer	long	RBR
cord-002542-f7l4ty2j	135	8	than	than	IN
cord-002542-f7l4ty2j	135	9	100	100	CD
cord-002542-f7l4ty2j	135	10	nts	nt	NNS
cord-002542-f7l4ty2j	135	11	were	be	VBD
cord-002542-f7l4ty2j	135	12	extracted	extract	VBN
cord-002542-f7l4ty2j	135	13	and	and	CC
cord-002542-f7l4ty2j	135	14	their	-PRON-	PRP$
cord-002542-f7l4ty2j	135	15	nucleotide	nucleotide	JJ
cord-002542-f7l4ty2j	135	16	sequence	sequence	NN
cord-002542-f7l4ty2j	135	17	was	be	VBD
cord-002542-f7l4ty2j	135	18	analyzed	analyze	VBN
cord-002542-f7l4ty2j	135	19	using	use	VBG
cord-002542-f7l4ty2j	135	20	an	an	DT
cord-002542-f7l4ty2j	135	21	online	online	JJ
cord-002542-f7l4ty2j	135	22	BLASTn	BLASTn	NNS
cord-002542-f7l4ty2j	135	23	search	search	NN
cord-002542-f7l4ty2j	135	24	to	to	TO
cord-002542-f7l4ty2j	135	25	determine	determine	VB
cord-002542-f7l4ty2j	135	26	their	-PRON-	PRP$
cord-002542-f7l4ty2j	135	27	identity	identity	NN
cord-002542-f7l4ty2j	135	28	.	.	.
cord-002542-f7l4ty2j	136	1	To	to	TO
cord-002542-f7l4ty2j	136	2	annotate	annotate	VB
cord-002542-f7l4ty2j	136	3	the	the	DT
cord-002542-f7l4ty2j	136	4	defective	defective	JJ
cord-002542-f7l4ty2j	136	5	genomes	genome	NNS
cord-002542-f7l4ty2j	136	6	detected	detect	VBN
cord-002542-f7l4ty2j	136	7	by	by	IN
cord-002542-f7l4ty2j	136	8	MinION	MinION	VBG
cord-002542-f7l4ty2j	136	9	nanopore	nanopore	JJ
cord-002542-f7l4ty2j	136	10	sequencing	sequencing	NN
cord-002542-f7l4ty2j	136	11	or	or	CC
cord-002542-f7l4ty2j	136	12	recombination	recombination	NN
cord-002542-f7l4ty2j	136	13	events	event	NNS
cord-002542-f7l4ty2j	136	14	detected	detect	VBN
cord-002542-f7l4ty2j	136	15	by	by	IN
cord-002542-f7l4ty2j	136	16	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	136	17	,	,	,
cord-002542-f7l4ty2j	136	18	we	-PRON-	PRP
cord-002542-f7l4ty2j	136	19	use	use	VBP
cord-002542-f7l4ty2j	136	20	underscores	underscore	VBZ
cord-002542-f7l4ty2j	136	21	'	'	``
cord-002542-f7l4ty2j	136	22	_	_	NN
cord-002542-f7l4ty2j	136	23	'	'	''
cord-002542-f7l4ty2j	136	24	to	to	TO
cord-002542-f7l4ty2j	136	25	denote	denote	VB
cord-002542-f7l4ty2j	136	26	continued	continued	JJ
cord-002542-f7l4ty2j	136	27	mapping	mapping	NN
cord-002542-f7l4ty2j	136	28	,	,	,
cord-002542-f7l4ty2j	136	29	and	and	CC
cord-002542-f7l4ty2j	136	30	carets	caret	NNS
cord-002542-f7l4ty2j	136	31	'	'	''
cord-002542-f7l4ty2j	136	32	^	^	SYM
cord-002542-f7l4ty2j	136	33	'	'	''
cord-002542-f7l4ty2j	136	34	to	to	TO
cord-002542-f7l4ty2j	136	35	denote	denote	VB
cord-002542-f7l4ty2j	136	36	a	a	DT
cord-002542-f7l4ty2j	136	37	recombination	recombination	NN
cord-002542-f7l4ty2j	136	38	events	event	NNS
cord-002542-f7l4ty2j	136	39	.	.	.
cord-002542-f7l4ty2j	137	1	For	for	IN
cord-002542-f7l4ty2j	137	2	example	example	NN
cord-002542-f7l4ty2j	137	3	,	,	,
cord-002542-f7l4ty2j	137	4	"	"	''
cord-002542-f7l4ty2j	137	5	1_317	1_317	CD
cord-002542-f7l4ty2j	137	6	^	^	:
cord-002542-f7l4ty2j	137	7	1091_1242	1091_1242	CD
cord-002542-f7l4ty2j	137	8	^	^	:
cord-002542-f7l4ty2j	137	9	2301_3107	2301_3107	CD
cord-002542-f7l4ty2j	137	10	"	"	''
cord-002542-f7l4ty2j	137	11	indicates	indicate	VBZ
cord-002542-f7l4ty2j	137	12	an	an	DT
cord-002542-f7l4ty2j	137	13	authentic	authentic	JJ
cord-002542-f7l4ty2j	137	14	mapping	mapping	NN
cord-002542-f7l4ty2j	137	15	from	from	IN
cord-002542-f7l4ty2j	137	16	nt	nt	RB
cord-002542-f7l4ty2j	137	17	1	1	CD
cord-002542-f7l4ty2j	137	18	to	to	IN
cord-002542-f7l4ty2j	137	19	317	317	CD
cord-002542-f7l4ty2j	137	20	,	,	,
cord-002542-f7l4ty2j	137	21	then	then	RB
cord-002542-f7l4ty2j	137	22	a	a	DT
cord-002542-f7l4ty2j	137	23	deletion	deletion	NN
cord-002542-f7l4ty2j	137	24	event	event	NN
cord-002542-f7l4ty2j	137	25	removing	remove	VBG
cord-002542-f7l4ty2j	137	26	nts	nts	NNPS
cord-002542-f7l4ty2j	137	27	318	318	CD
cord-002542-f7l4ty2j	137	28	through	through	IN
cord-002542-f7l4ty2j	137	29	1090	1090	CD
cord-002542-f7l4ty2j	137	30	,	,	,
cord-002542-f7l4ty2j	137	31	then	then	RB
cord-002542-f7l4ty2j	137	32	another	another	DT
cord-002542-f7l4ty2j	137	33	authentic	authentic	JJ
cord-002542-f7l4ty2j	137	34	mapping	mapping	NN
cord-002542-f7l4ty2j	137	35	from	from	IN
cord-002542-f7l4ty2j	137	36	1091	1091	CD
cord-002542-f7l4ty2j	137	37	to	to	IN
cord-002542-f7l4ty2j	137	38	1242	1242	CD
cord-002542-f7l4ty2j	137	39	,	,	,
cord-002542-f7l4ty2j	137	40	followed	follow	VBN
cord-002542-f7l4ty2j	137	41	by	by	IN
cord-002542-f7l4ty2j	137	42	another	another	DT
cord-002542-f7l4ty2j	137	43	deletion	deletion	NN
cord-002542-f7l4ty2j	137	44	removing	remove	VBG
cord-002542-f7l4ty2j	137	45	nts	nts	NNPS
cord-002542-f7l4ty2j	137	46	1243	1243	CD
cord-002542-f7l4ty2j	137	47	through	through	IN
cord-002542-f7l4ty2j	137	48	2300	2300	CD
cord-002542-f7l4ty2j	137	49	,	,	,
cord-002542-f7l4ty2j	137	50	and	and	CC
cord-002542-f7l4ty2j	137	51	finally	finally	RB
cord-002542-f7l4ty2j	137	52	an	an	DT
cord-002542-f7l4ty2j	137	53	authentic	authentic	JJ
cord-002542-f7l4ty2j	137	54	mapping	mapping	NN
cord-002542-f7l4ty2j	137	55	from	from	IN
cord-002542-f7l4ty2j	137	56	nt	nt	RB
cord-002542-f7l4ty2j	137	57	2301	2301	CD
cord-002542-f7l4ty2j	137	58	to	to	IN
cord-002542-f7l4ty2j	137	59	3107	3107	CD
cord-002542-f7l4ty2j	137	60	.	.	.
cord-002542-f7l4ty2j	138	1	The	the	DT
cord-002542-f7l4ty2j	138	2	Shannon	Shannon	NNP
cord-002542-f7l4ty2j	138	3	Entropy	Entropy	NNP
cord-002542-f7l4ty2j	138	4	Index	Index	NNP
cord-002542-f7l4ty2j	138	5	is	be	VBZ
cord-002542-f7l4ty2j	138	6	given	give	VBN
cord-002542-f7l4ty2j	138	7	by	by	IN
cord-002542-f7l4ty2j	138	8	:	:	:
cord-002542-f7l4ty2j	139	1	HðXÞ	HðXÞ	NNP
cord-002542-f7l4ty2j	139	2	¼	¼	NNP
cord-002542-f7l4ty2j	139	3	À	à	NN
cord-002542-f7l4ty2j	139	4	P	p	NN
cord-002542-f7l4ty2j	139	5	NÀ	NÀ	NNP
cord-002542-f7l4ty2j	139	6	1	1	CD
cord-002542-f7l4ty2j	139	7	i¼0	i¼0	NN
cord-002542-f7l4ty2j	140	1	p	p	NNP
cord-002542-f7l4ty2j	140	2	i	i	PRP
cord-002542-f7l4ty2j	140	3	ln	ln	NN
cord-002542-f7l4ty2j	140	4	p	p	NN
cord-002542-f7l4ty2j	140	5	i	i	PRP
cord-002542-f7l4ty2j	140	6	For	for	IN
cord-002542-f7l4ty2j	140	7	the	the	DT
cord-002542-f7l4ty2j	140	8	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	140	9	data	datum	NNS
cord-002542-f7l4ty2j	141	1	,	,	,
cord-002542-f7l4ty2j	141	2	each	each	DT
cord-002542-f7l4ty2j	141	3	recombination	recombination	NN
cord-002542-f7l4ty2j	141	4	event	event	NN
cord-002542-f7l4ty2j	141	5	is	be	VBZ
cord-002542-f7l4ty2j	141	6	treated	treat	VBN
cord-002542-f7l4ty2j	141	7	as	as	IN
cord-002542-f7l4ty2j	141	8	independent	independent	JJ
cord-002542-f7l4ty2j	141	9	with	with	IN
cord-002542-f7l4ty2j	141	10	its	-PRON-	PRP$
cord-002542-f7l4ty2j	141	11	probability	probability	NN
cord-002542-f7l4ty2j	141	12	determined	determine	VBN
cord-002542-f7l4ty2j	141	13	by	by	IN
cord-002542-f7l4ty2j	141	14	dividing	divide	VBG
cord-002542-f7l4ty2j	141	15	the	the	DT
cord-002542-f7l4ty2j	141	16	number	number	NN
cord-002542-f7l4ty2j	141	17	of	of	IN
cord-002542-f7l4ty2j	141	18	reads	read	NNS
cord-002542-f7l4ty2j	141	19	mapping	mapping	NN
cord-002542-f7l4ty2j	141	20	to	to	IN
cord-002542-f7l4ty2j	141	21	the	the	DT
cord-002542-f7l4ty2j	141	22	present	present	JJ
cord-002542-f7l4ty2j	141	23	recombination	recombination	NN
cord-002542-f7l4ty2j	141	24	event	event	NN
cord-002542-f7l4ty2j	141	25	divided	divide	VBN
cord-002542-f7l4ty2j	141	26	by	by	IN
cord-002542-f7l4ty2j	141	27	the	the	DT
cord-002542-f7l4ty2j	141	28	average	average	JJ
cord-002542-f7l4ty2j	141	29	coverage	coverage	NN
cord-002542-f7l4ty2j	141	30	over	over	IN
cord-002542-f7l4ty2j	141	31	the	the	DT
cord-002542-f7l4ty2j	141	32	whole	whole	JJ
cord-002542-f7l4ty2j	141	33	viral	viral	JJ
cord-002542-f7l4ty2j	141	34	RNA	RNA	NNP
cord-002542-f7l4ty2j	141	35	.	.	.
cord-002542-f7l4ty2j	142	1	For	for	IN
cord-002542-f7l4ty2j	142	2	the	the	DT
cord-002542-f7l4ty2j	142	3	MinION	MinION	NNP
cord-002542-f7l4ty2j	142	4	data	datum	NNS
cord-002542-f7l4ty2j	142	5	,	,	,
cord-002542-f7l4ty2j	142	6	each	each	DT
cord-002542-f7l4ty2j	142	7	individual	individual	JJ
cord-002542-f7l4ty2j	142	8	read	read	VBD
cord-002542-f7l4ty2j	142	9	mapping	mapping	NN
cord-002542-f7l4ty2j	142	10	is	be	VBZ
cord-002542-f7l4ty2j	142	11	treated	treat	VBN
cord-002542-f7l4ty2j	142	12	as	as	IN
cord-002542-f7l4ty2j	142	13	an	an	DT
cord-002542-f7l4ty2j	142	14	individual	individual	JJ
cord-002542-f7l4ty2j	142	15	event	event	NN
cord-002542-f7l4ty2j	142	16	with	with	IN
cord-002542-f7l4ty2j	142	17	the	the	DT
cord-002542-f7l4ty2j	142	18	frequency	frequency	NN
cord-002542-f7l4ty2j	142	19	determined	determine	VBN
cord-002542-f7l4ty2j	142	20	by	by	IN
cord-002542-f7l4ty2j	142	21	dividing	divide	VBG
cord-002542-f7l4ty2j	142	22	the	the	DT
cord-002542-f7l4ty2j	142	23	number	number	NN
cord-002542-f7l4ty2j	142	24	of	of	IN
cord-002542-f7l4ty2j	142	25	identically	identically	RB
cord-002542-f7l4ty2j	142	26	mapping	mapping	NN
cord-002542-f7l4ty2j	142	27	reads	read	NNS
cord-002542-f7l4ty2j	142	28	divided	divide	VBN
cord-002542-f7l4ty2j	142	29	by	by	IN
cord-002542-f7l4ty2j	142	30	total	total	JJ
cord-002542-f7l4ty2j	142	31	mapped	map	VBN
cord-002542-f7l4ty2j	142	32	reads	read	NNS
cord-002542-f7l4ty2j	142	33	.	.	.
cord-002542-f7l4ty2j	143	1	Tissue	tissue	NN
cord-002542-f7l4ty2j	143	2	culture	culture	NN
cord-002542-f7l4ty2j	143	3	infective	infective	JJ
cord-002542-f7l4ty2j	143	4	dose	dose	NN
cord-002542-f7l4ty2j	143	5	50	50	CD
cord-002542-f7l4ty2j	144	1	(	(	-LRB-
cord-002542-f7l4ty2j	144	2	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	144	3	)	)	-RRB-
cord-002542-f7l4ty2j	144	4	analyses	analysis	NNS
cord-002542-f7l4ty2j	144	5	of	of	IN
cord-002542-f7l4ty2j	144	6	the	the	DT
cord-002542-f7l4ty2j	144	7	supernatants	supernatant	NNS
cord-002542-f7l4ty2j	144	8	from	from	IN
cord-002542-f7l4ty2j	144	9	each	each	DT
cord-002542-f7l4ty2j	144	10	passage	passage	NN
cord-002542-f7l4ty2j	144	11	were	be	VBD
cord-002542-f7l4ty2j	144	12	performed	perform	VBN
cord-002542-f7l4ty2j	144	13	using	use	VBG
cord-002542-f7l4ty2j	144	14	standard	standard	JJ
cord-002542-f7l4ty2j	144	15	protocols	protocol	NNS
cord-002542-f7l4ty2j	144	16	[	[	-LRB-
cord-002542-f7l4ty2j	144	17	51	51	CD
cord-002542-f7l4ty2j	144	18	]	]	-RRB-
cord-002542-f7l4ty2j	144	19	.	.	.
cord-002542-f7l4ty2j	145	1	For	for	IN
cord-002542-f7l4ty2j	145	2	purified	purify	VBN
cord-002542-f7l4ty2j	145	3	particles	particle	NNS
cord-002542-f7l4ty2j	145	4	of	of	IN
cord-002542-f7l4ty2j	145	5	each	each	DT
cord-002542-f7l4ty2j	145	6	passage	passage	NN
cord-002542-f7l4ty2j	145	7	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	145	8	was	be	VBD
cord-002542-f7l4ty2j	145	9	calculated	calculate	VBN
cord-002542-f7l4ty2j	145	10	with	with	IN
cord-002542-f7l4ty2j	145	11	slight	slight	JJ
cord-002542-f7l4ty2j	145	12	modifications	modification	NNS
cord-002542-f7l4ty2j	145	13	.	.	.
cord-002542-f7l4ty2j	146	1	Specifically	specifically	RB
cord-002542-f7l4ty2j	146	2	,	,	,
cord-002542-f7l4ty2j	146	3	1	1	CD
cord-002542-f7l4ty2j	146	4	x	x	SYM
cord-002542-f7l4ty2j	146	5	10	10	CD
cord-002542-f7l4ty2j	146	6	5	5	CD
cord-002542-f7l4ty2j	146	7	cells	cell	NNS
cord-002542-f7l4ty2j	146	8	(	(	-LRB-
cord-002542-f7l4ty2j	146	9	S2	s2	NN
cord-002542-f7l4ty2j	146	10	)	)	-RRB-
cord-002542-f7l4ty2j	146	11	per	per	FW
cord-002542-f7l4ty2j	146	12	well	well	RB
cord-002542-f7l4ty2j	146	13	were	be	VBD
cord-002542-f7l4ty2j	146	14	plated	plate	VBN
cord-002542-f7l4ty2j	146	15	in	in	IN
cord-002542-f7l4ty2j	146	16	96	96	CD
cord-002542-f7l4ty2j	146	17	well	well	JJ
cord-002542-f7l4ty2j	146	18	format	format	NN
cord-002542-f7l4ty2j	146	19	.	.	.
cord-002542-f7l4ty2j	147	1	Virus	virus	NN
cord-002542-f7l4ty2j	147	2	samples	sample	NNS
cord-002542-f7l4ty2j	147	3	were	be	VBD
cord-002542-f7l4ty2j	147	4	quantified	quantify	VBN
cord-002542-f7l4ty2j	147	5	by	by	IN
cord-002542-f7l4ty2j	147	6	measuring	measure	VBG
cord-002542-f7l4ty2j	147	7	the	the	DT
cord-002542-f7l4ty2j	147	8	OD	OD	NNP
cord-002542-f7l4ty2j	147	9	260	260	CD
cord-002542-f7l4ty2j	147	10	nm	nm	NN
cord-002542-f7l4ty2j	147	11	.	.	.
cord-002542-f7l4ty2j	148	1	An	an	DT
cord-002542-f7l4ty2j	148	2	OD	OD	NNP
cord-002542-f7l4ty2j	148	3	of	of	IN
cord-002542-f7l4ty2j	148	4	4.15	4.15	CD
cord-002542-f7l4ty2j	148	5	corresponds	correspond	VBZ
cord-002542-f7l4ty2j	148	6	to	to	IN
cord-002542-f7l4ty2j	148	7	1	1	CD
cord-002542-f7l4ty2j	148	8	mg	mg	NN
cord-002542-f7l4ty2j	148	9	virus	virus	NN
cord-002542-f7l4ty2j	148	10	[	[	-LRB-
cord-002542-f7l4ty2j	148	11	52	52	CD
cord-002542-f7l4ty2j	148	12	]	]	-RRB-
cord-002542-f7l4ty2j	148	13	,	,	,
cord-002542-f7l4ty2j	148	14	which	which	WDT
cord-002542-f7l4ty2j	148	15	in	in	IN
cord-002542-f7l4ty2j	148	16	turn	turn	NN
cord-002542-f7l4ty2j	148	17	corresponds	correspond	VBZ
cord-002542-f7l4ty2j	148	18	to	to	IN
cord-002542-f7l4ty2j	148	19	6.4	6.4	CD
cord-002542-f7l4ty2j	148	20	x	x	SYM
cord-002542-f7l4ty2j	148	21	10	10	CD
cord-002542-f7l4ty2j	148	22	13	13	CD
cord-002542-f7l4ty2j	148	23	virus	virus	NN
cord-002542-f7l4ty2j	148	24	particles	particle	NNS
cord-002542-f7l4ty2j	148	25	assuming	assume	VBG
cord-002542-f7l4ty2j	148	26	a	a	DT
cord-002542-f7l4ty2j	148	27	virion	virion	NN
cord-002542-f7l4ty2j	148	28	mass	mass	NN
cord-002542-f7l4ty2j	148	29	of	of	IN
cord-002542-f7l4ty2j	148	30	9.4MDa	9.4mda	CD
cord-002542-f7l4ty2j	148	31	[	[	-LRB-
cord-002542-f7l4ty2j	148	32	53	53	CD
cord-002542-f7l4ty2j	148	33	]	]	-RRB-
cord-002542-f7l4ty2j	148	34	.	.	.
cord-002542-f7l4ty2j	149	1	Purified	purify	VBN
cord-002542-f7l4ty2j	149	2	virus	virus	NN
cord-002542-f7l4ty2j	149	3	samples	sample	NNS
cord-002542-f7l4ty2j	149	4	were	be	VBD
cord-002542-f7l4ty2j	149	5	diluted	dilute	VBN
cord-002542-f7l4ty2j	149	6	to	to	IN
cord-002542-f7l4ty2j	149	7	a	a	DT
cord-002542-f7l4ty2j	149	8	starting	start	VBG
cord-002542-f7l4ty2j	149	9	concentration	concentration	NN
cord-002542-f7l4ty2j	149	10	of	of	IN
cord-002542-f7l4ty2j	149	11	47ng	47ng	NN
cord-002542-f7l4ty2j	149	12	/	/	SYM
cord-002542-f7l4ty2j	149	13	μL	μL	NNP
cord-002542-f7l4ty2j	149	14	,	,	,
cord-002542-f7l4ty2j	149	15	which	which	WDT
cord-002542-f7l4ty2j	149	16	corresponds	correspond	VBZ
cord-002542-f7l4ty2j	149	17	to	to	IN
cord-002542-f7l4ty2j	149	18	3	3	CD
cord-002542-f7l4ty2j	149	19	x	x	SYM
cord-002542-f7l4ty2j	149	20	10	10	CD
cord-002542-f7l4ty2j	149	21	10	10	CD
cord-002542-f7l4ty2j	149	22	virus	virus	NN
cord-002542-f7l4ty2j	149	23	particles	particle	NNS
cord-002542-f7l4ty2j	149	24	per	per	IN
cord-002542-f7l4ty2j	149	25	10μL.	10μl.	CD
cord-002542-f7l4ty2j	149	26	These	these	DT
cord-002542-f7l4ty2j	149	27	quantities	quantity	NNS
cord-002542-f7l4ty2j	149	28	were	be	VBD
cord-002542-f7l4ty2j	149	29	chosen	choose	VBN
cord-002542-f7l4ty2j	149	30	as	as	IN
cord-002542-f7l4ty2j	149	31	particle	particle	NN
cord-002542-f7l4ty2j	149	32	-	-	HYPH
cord-002542-f7l4ty2j	149	33	to	to	IN
cord-002542-f7l4ty2j	149	34	-	-	HYPH
cord-002542-f7l4ty2j	149	35	PFU	pfu	NN
cord-002542-f7l4ty2j	149	36	ratios	ratio	NNS
cord-002542-f7l4ty2j	149	37	for	for	IN
cord-002542-f7l4ty2j	149	38	rescued	rescue	VBN
cord-002542-f7l4ty2j	149	39	FHV	FHV	NNP
cord-002542-f7l4ty2j	149	40	has	have	VBZ
cord-002542-f7l4ty2j	149	41	previously	previously	RB
cord-002542-f7l4ty2j	149	42	been	be	VBN
cord-002542-f7l4ty2j	149	43	reported	report	VBN
cord-002542-f7l4ty2j	149	44	to	to	TO
cord-002542-f7l4ty2j	149	45	be	be	VB
cord-002542-f7l4ty2j	149	46	300	300	CD
cord-002542-f7l4ty2j	149	47	-	-	SYM
cord-002542-f7l4ty2j	149	48	400	400	CD
cord-002542-f7l4ty2j	149	49	particles	particle	NNS
cord-002542-f7l4ty2j	149	50	[	[	-LRB-
cord-002542-f7l4ty2j	149	51	26	26	CD
cord-002542-f7l4ty2j	149	52	,	,	,
cord-002542-f7l4ty2j	149	53	52	52	CD
cord-002542-f7l4ty2j	149	54	]	]	-RRB-
cord-002542-f7l4ty2j	149	55	.	.	.
cord-002542-f7l4ty2j	150	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	150	2	3	3	CD
cord-002542-f7l4ty2j	150	3	x	x	SYM
cord-002542-f7l4ty2j	150	4	10	10	CD
cord-002542-f7l4ty2j	150	5	10	10	CD
cord-002542-f7l4ty2j	150	6	particles	particle	NNS
cord-002542-f7l4ty2j	150	7	per	per	IN
cord-002542-f7l4ty2j	150	8	10	10	CD
cord-002542-f7l4ty2j	150	9	5	5	CD
cord-002542-f7l4ty2j	150	10	cells	cell	NNS
cord-002542-f7l4ty2j	150	11	corresponds	correspond	VBZ
cord-002542-f7l4ty2j	150	12	to	to	IN
cord-002542-f7l4ty2j	150	13	approximately	approximately	RB
cord-002542-f7l4ty2j	150	14	1000	1000	CD
cord-002542-f7l4ty2j	150	15	PFUs	pfus	NN
cord-002542-f7l4ty2j	150	16	per	per	IN
cord-002542-f7l4ty2j	150	17	cell	cell	NN
cord-002542-f7l4ty2j	150	18	.	.	.
cord-002542-f7l4ty2j	151	1	Eight	eight	CD
cord-002542-f7l4ty2j	151	2	serial	serial	JJ
cord-002542-f7l4ty2j	151	3	10-fold	10-fold	JJ
cord-002542-f7l4ty2j	151	4	dilutions	dilution	NNS
cord-002542-f7l4ty2j	151	5	were	be	VBD
cord-002542-f7l4ty2j	151	6	subsequently	subsequently	RB
cord-002542-f7l4ty2j	151	7	made	make	VBN
cord-002542-f7l4ty2j	151	8	and	and	CC
cord-002542-f7l4ty2j	151	9	added	add	VBN
cord-002542-f7l4ty2j	151	10	to	to	IN
cord-002542-f7l4ty2j	151	11	each	each	DT
cord-002542-f7l4ty2j	151	12	column	column	NN
cord-002542-f7l4ty2j	151	13	of	of	IN
cord-002542-f7l4ty2j	151	14	the	the	DT
cord-002542-f7l4ty2j	151	15	96-well	96-well	CD
cord-002542-f7l4ty2j	151	16	plate	plate	NN
cord-002542-f7l4ty2j	151	17	(	(	-LRB-
cord-002542-f7l4ty2j	151	18	8	8	CD
cord-002542-f7l4ty2j	151	19	replicate	replicate	VB
cord-002542-f7l4ty2j	151	20	wells	well	NNS
cord-002542-f7l4ty2j	151	21	per	per	IN
cord-002542-f7l4ty2j	151	22	dilution	dilution	NN
cord-002542-f7l4ty2j	151	23	)	)	-RRB-
cord-002542-f7l4ty2j	151	24	,	,	,
cord-002542-f7l4ty2j	151	25	as	as	IN
cord-002542-f7l4ty2j	151	26	per	per	IN
cord-002542-f7l4ty2j	151	27	standard	standard	JJ
cord-002542-f7l4ty2j	151	28	TCID50	tcid50	CD
cord-002542-f7l4ty2j	151	29	protocols	protocol	NNS
cord-002542-f7l4ty2j	151	30	.	.	.
cord-002542-f7l4ty2j	152	1	Virus	virus	NN
cord-002542-f7l4ty2j	152	2	was	be	VBD
cord-002542-f7l4ty2j	152	3	allowed	allow	VBN
cord-002542-f7l4ty2j	152	4	to	to	TO
cord-002542-f7l4ty2j	152	5	grow	grow	VB
cord-002542-f7l4ty2j	152	6	for	for	IN
cord-002542-f7l4ty2j	152	7	4	4	CD
cord-002542-f7l4ty2j	152	8	days	day	NNS
cord-002542-f7l4ty2j	152	9	after	after	IN
cord-002542-f7l4ty2j	152	10	which	which	WDT
cord-002542-f7l4ty2j	152	11	the	the	DT
cord-002542-f7l4ty2j	152	12	number	number	NN
cord-002542-f7l4ty2j	152	13	of	of	IN
cord-002542-f7l4ty2j	152	14	positive	positive	JJ
cord-002542-f7l4ty2j	152	15	wells	well	NNS
cord-002542-f7l4ty2j	152	16	exhibiting	exhibit	VBG
cord-002542-f7l4ty2j	152	17	cytopathic	cytopathic	JJ
cord-002542-f7l4ty2j	152	18	effect	effect	NN
cord-002542-f7l4ty2j	152	19	(	(	-LRB-
cord-002542-f7l4ty2j	152	20	CPE	CPE	NNP
cord-002542-f7l4ty2j	152	21	)	)	-RRB-
cord-002542-f7l4ty2j	152	22	were	be	VBD
cord-002542-f7l4ty2j	152	23	counted	count	VBN
cord-002542-f7l4ty2j	152	24	.	.	.
cord-002542-f7l4ty2j	153	1	The	the	DT
cord-002542-f7l4ty2j	153	2	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	153	3	values	value	NNS
cord-002542-f7l4ty2j	153	4	and	and	CC
cord-002542-f7l4ty2j	153	5	effective	effective	JJ
cord-002542-f7l4ty2j	153	6	MOI	MOI	NNP
cord-002542-f7l4ty2j	153	7	were	be	VBD
cord-002542-f7l4ty2j	153	8	calculated	calculate	VBN
cord-002542-f7l4ty2j	153	9	using	use	VBG
cord-002542-f7l4ty2j	153	10	the	the	DT
cord-002542-f7l4ty2j	153	11	Reed	Reed	NNP
cord-002542-f7l4ty2j	153	12	and	and	CC
cord-002542-f7l4ty2j	153	13	Muench	Muench	NNP
cord-002542-f7l4ty2j	153	14	Calculator	Calculator	NNP
cord-002542-f7l4ty2j	153	15	[	[	-LRB-
cord-002542-f7l4ty2j	153	16	51	51	CD
cord-002542-f7l4ty2j	153	17	]	]	-RRB-
cord-002542-f7l4ty2j	153	18	.	.	.
cord-002542-f7l4ty2j	154	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	154	2	further	further	RB
cord-002542-f7l4ty2j	154	3	counted	count	VBD
cord-002542-f7l4ty2j	154	4	the	the	DT
cord-002542-f7l4ty2j	154	5	total	total	JJ
cord-002542-f7l4ty2j	154	6	number	number	NN
cord-002542-f7l4ty2j	154	7	of	of	IN
cord-002542-f7l4ty2j	154	8	cells	cell	NNS
cord-002542-f7l4ty2j	154	9	that	that	WDT
cord-002542-f7l4ty2j	154	10	were	be	VBD
cord-002542-f7l4ty2j	154	11	present	present	JJ
cord-002542-f7l4ty2j	154	12	in	in	IN
cord-002542-f7l4ty2j	154	13	each	each	DT
cord-002542-f7l4ty2j	154	14	well	well	RB
cord-002542-f7l4ty2j	154	15	after	after	IN
cord-002542-f7l4ty2j	154	16	infection	infection	NN
cord-002542-f7l4ty2j	154	17	using	use	VBG
cord-002542-f7l4ty2j	154	18	a	a	DT
cord-002542-f7l4ty2j	154	19	Guava	Guava	NNP
cord-002542-f7l4ty2j	154	20	easyCyte	easycyte	JJ
cord-002542-f7l4ty2j	154	21	HT	HT	NNP
cord-002542-f7l4ty2j	154	22	(	(	-LRB-
cord-002542-f7l4ty2j	154	23	Millipore	Millipore	NNP
cord-002542-f7l4ty2j	154	24	)	)	-RRB-
cord-002542-f7l4ty2j	154	25	flow	flow	VBP
cord-002542-f7l4ty2j	154	26	cytometer	cytometer	NN
cord-002542-f7l4ty2j	154	27	to	to	TO
cord-002542-f7l4ty2j	154	28	provide	provide	VB
cord-002542-f7l4ty2j	154	29	us	-PRON-	PRP
cord-002542-f7l4ty2j	154	30	with	with	IN
cord-002542-f7l4ty2j	154	31	quantifiable	quantifiable	JJ
cord-002542-f7l4ty2j	154	32	amount	amount	NN
cord-002542-f7l4ty2j	154	33	of	of	IN
cord-002542-f7l4ty2j	154	34	cell	cell	NN
cord-002542-f7l4ty2j	154	35	death	death	NN
cord-002542-f7l4ty2j	154	36	.	.	.
cord-002542-f7l4ty2j	155	1	50μL	50μl	CD
cord-002542-f7l4ty2j	155	2	from	from	IN
cord-002542-f7l4ty2j	155	3	each	each	DT
cord-002542-f7l4ty2j	155	4	well	well	NN
cord-002542-f7l4ty2j	155	5	was	be	VBD
cord-002542-f7l4ty2j	155	6	diluted	dilute	VBN
cord-002542-f7l4ty2j	155	7	in	in	IN
cord-002542-f7l4ty2j	155	8	150μL	150μl	CD
cord-002542-f7l4ty2j	155	9	PBS	PBS	NNP
cord-002542-f7l4ty2j	155	10	and	and	CC
cord-002542-f7l4ty2j	155	11	injected	inject	VBD
cord-002542-f7l4ty2j	155	12	using	use	VBG
cord-002542-f7l4ty2j	155	13	manufactures	manufacture	NNS
cord-002542-f7l4ty2j	155	14	'	'	POS
cord-002542-f7l4ty2j	155	15	protocols	protocol	NNS
cord-002542-f7l4ty2j	155	16	.	.	.
cord-002542-f7l4ty2j	156	1	The	the	DT
cord-002542-f7l4ty2j	156	2	InCyt	InCyt	NNP
cord-002542-f7l4ty2j	156	3	v3.1	v3.1	NN
cord-002542-f7l4ty2j	156	4	software	software	NN
cord-002542-f7l4ty2j	156	5	was	be	VBD
cord-002542-f7l4ty2j	156	6	used	use	VBN
cord-002542-f7l4ty2j	156	7	to	to	TO
cord-002542-f7l4ty2j	156	8	collect	collect	VB
cord-002542-f7l4ty2j	156	9	data	datum	NNS
cord-002542-f7l4ty2j	156	10	with	with	IN
cord-002542-f7l4ty2j	156	11	the	the	DT
cord-002542-f7l4ty2j	156	12	following	follow	VBG
cord-002542-f7l4ty2j	156	13	parameters	parameter	NNS
cord-002542-f7l4ty2j	156	14	:	:	:
cord-002542-f7l4ty2j	156	15	collection	collection	NN
cord-002542-f7l4ty2j	156	16	time	time	NN
cord-002542-f7l4ty2j	156	17	:	:	:
cord-002542-f7l4ty2j	156	18	30sec	30sec	JJ
cord-002542-f7l4ty2j	156	19	;	;	:
cord-002542-f7l4ty2j	156	20	flow	flow	NN
cord-002542-f7l4ty2j	156	21	rate	rate	NN
cord-002542-f7l4ty2j	156	22	:	:	:
cord-002542-f7l4ty2j	156	23	0.59μL	0.59μl	CD
cord-002542-f7l4ty2j	156	24	/	/	SYM
cord-002542-f7l4ty2j	156	25	sec	sec	NNP
cord-002542-f7l4ty2j	156	26	;	;	:
cord-002542-f7l4ty2j	156	27	FSC	FSC	NNP
cord-002542-f7l4ty2j	156	28	:	:	:
cord-002542-f7l4ty2j	156	29	16	16	CD
cord-002542-f7l4ty2j	157	1	;	;	:
cord-002542-f7l4ty2j	157	2	SSC	SSC	NNP
cord-002542-f7l4ty2j	157	3	:	:	:
cord-002542-f7l4ty2j	157	4	25	25	CD
cord-002542-f7l4ty2j	157	5	;	;	,
cord-002542-f7l4ty2j	157	6	threshold	threshold	NN
cord-002542-f7l4ty2j	157	7	:	:	:
cord-002542-f7l4ty2j	157	8	0	0	NFP
cord-002542-f7l4ty2j	157	9	.	.	.
cord-002542-f7l4ty2j	158	1	The	the	DT
cord-002542-f7l4ty2j	158	2	region	region	NN
cord-002542-f7l4ty2j	158	3	used	use	VBD
cord-002542-f7l4ty2j	158	4	to	to	TO
cord-002542-f7l4ty2j	158	5	determine	determine	VB
cord-002542-f7l4ty2j	158	6	live	live	JJ
cord-002542-f7l4ty2j	158	7	cells	cell	NNS
cord-002542-f7l4ty2j	158	8	was	be	VBD
cord-002542-f7l4ty2j	158	9	based	base	VBN
cord-002542-f7l4ty2j	158	10	on	on	IN
cord-002542-f7l4ty2j	158	11	scattering	scatter	VBG
cord-002542-f7l4ty2j	158	12	features	feature	NNS
cord-002542-f7l4ty2j	158	13	of	of	IN
cord-002542-f7l4ty2j	158	14	the	the	DT
cord-002542-f7l4ty2j	158	15	negative	negative	JJ
cord-002542-f7l4ty2j	158	16	controls	control	NNS
cord-002542-f7l4ty2j	158	17	(	(	-LRB-
cord-002542-f7l4ty2j	158	18	wells	well	NNS
cord-002542-f7l4ty2j	158	19	with	with	IN
cord-002542-f7l4ty2j	158	20	no	no	DT
cord-002542-f7l4ty2j	158	21	viral	viral	JJ
cord-002542-f7l4ty2j	158	22	infection	infection	NN
cord-002542-f7l4ty2j	158	23	)	)	-RRB-
cord-002542-f7l4ty2j	159	1	(	(	-LRB-
cord-002542-f7l4ty2j	159	2	S7	S7	NNP
cord-002542-f7l4ty2j	159	3	Fig	Fig	NNP
cord-002542-f7l4ty2j	159	4	)	)	-RRB-
cord-002542-f7l4ty2j	159	5	.	.	.
cord-002542-f7l4ty2j	160	1	All	all	DT
cord-002542-f7l4ty2j	160	2	raw	raw	JJ
cord-002542-f7l4ty2j	160	3	Illumina	Illumina	NNP
cord-002542-f7l4ty2j	160	4	data	datum	NNS
cord-002542-f7l4ty2j	160	5	and	and	CC
cord-002542-f7l4ty2j	160	6	demultiplexed	demultiplexed	NNP
cord-002542-f7l4ty2j	160	7	MinION	MinION	NNP
cord-002542-f7l4ty2j	160	8	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	160	9	data	datum	NNS
cord-002542-f7l4ty2j	160	10	passing	pass	VBG
cord-002542-f7l4ty2j	160	11	quality	quality	NN
cord-002542-f7l4ty2j	160	12	filters	filter	NNS
cord-002542-f7l4ty2j	160	13	(	(	-LRB-
cord-002542-f7l4ty2j	160	14	comprising	comprise	VBG
cord-002542-f7l4ty2j	160	15	2D	2D	NNP
cord-002542-f7l4ty2j	160	16	,	,	,
cord-002542-f7l4ty2j	160	17	template	template	NN
cord-002542-f7l4ty2j	160	18	and	and	CC
cord-002542-f7l4ty2j	160	19	complement	complement	JJ
cord-002542-f7l4ty2j	160	20	strands	strand	NNS
cord-002542-f7l4ty2j	160	21	)	)	-RRB-
cord-002542-f7l4ty2j	160	22	associated	associate	VBN
cord-002542-f7l4ty2j	160	23	with	with	IN
cord-002542-f7l4ty2j	160	24	this	this	DT
cord-002542-f7l4ty2j	160	25	manuscript	manuscript	NN
cord-002542-f7l4ty2j	160	26	are	be	VBP
cord-002542-f7l4ty2j	160	27	available	available	JJ
cord-002542-f7l4ty2j	160	28	on	on	IN
cord-002542-f7l4ty2j	160	29	the	the	DT
cord-002542-f7l4ty2j	160	30	SRA	SRA	NNP
cord-002542-f7l4ty2j	160	31	NCBI	NCBI	NNP
cord-002542-f7l4ty2j	160	32	archive	archive	NN
cord-002542-f7l4ty2j	160	33	with	with	IN
cord-002542-f7l4ty2j	160	34	study	study	NN
cord-002542-f7l4ty2j	160	35	number	number	NN
cord-002542-f7l4ty2j	160	36	SRP094723	srp094723	NN
cord-002542-f7l4ty2j	160	37	and	and	CC
cord-002542-f7l4ty2j	161	1	BioProject	BioProject	NNP
cord-002542-f7l4ty2j	161	2	number	number	NN
cord-002542-f7l4ty2j	161	3	PRJNA352872	PRJNA352872	NNP
cord-002542-f7l4ty2j	161	4	.	.	.
cord-002542-f7l4ty2j	162	1	D.	D.	NNP
cord-002542-f7l4ty2j	162	2	melanogaster	melanogaster	NNP
cord-002542-f7l4ty2j	162	3	(	(	-LRB-
cord-002542-f7l4ty2j	162	4	S2	S2	NNP
cord-002542-f7l4ty2j	162	5	)	)	-RRB-
cord-002542-f7l4ty2j	162	6	cells	cell	NNS
cord-002542-f7l4ty2j	162	7	in	in	IN
cord-002542-f7l4ty2j	162	8	culture	culture	NN
cord-002542-f7l4ty2j	162	9	were	be	VBD
cord-002542-f7l4ty2j	162	10	transfected	transfecte	VBN
cord-002542-f7l4ty2j	162	11	with	with	IN
cord-002542-f7l4ty2j	162	12	cDNA	cdna	NN
cord-002542-f7l4ty2j	162	13	plasmids	plasmid	NNS
cord-002542-f7l4ty2j	162	14	containing	contain	VBG
cord-002542-f7l4ty2j	162	15	each	each	DT
cord-002542-f7l4ty2j	162	16	of	of	IN
cord-002542-f7l4ty2j	162	17	the	the	DT
cord-002542-f7l4ty2j	162	18	Flock	Flock	NNP
cord-002542-f7l4ty2j	162	19	House	House	NNP
cord-002542-f7l4ty2j	162	20	virus	virus	NN
cord-002542-f7l4ty2j	162	21	genomic	genomic	JJ
cord-002542-f7l4ty2j	162	22	RNAs	rna	NNS
cord-002542-f7l4ty2j	162	23	followed	follow	VBN
cord-002542-f7l4ty2j	162	24	by	by	IN
cord-002542-f7l4ty2j	162	25	a	a	DT
cord-002542-f7l4ty2j	162	26	hepatitis	hepatitis	NN
cord-002542-f7l4ty2j	162	27	D	d	NN
cord-002542-f7l4ty2j	162	28	virus	virus	NN
cord-002542-f7l4ty2j	162	29	(	(	-LRB-
cord-002542-f7l4ty2j	162	30	HDV	HDV	NNP
cord-002542-f7l4ty2j	162	31	)	)	-RRB-
cord-002542-f7l4ty2j	162	32	ribozyme	ribozyme	NN
cord-002542-f7l4ty2j	162	33	sequence	sequence	NN
cord-002542-f7l4ty2j	162	34	.	.	.
cord-002542-f7l4ty2j	163	1	After	after	IN
cord-002542-f7l4ty2j	163	2	induction	induction	NN
cord-002542-f7l4ty2j	163	3	,	,	,
cord-002542-f7l4ty2j	163	4	the	the	DT
cord-002542-f7l4ty2j	163	5	HDV	HDV	NNP
cord-002542-f7l4ty2j	163	6	ribozyme	ribozyme	NN
cord-002542-f7l4ty2j	163	7	regenerates	regenerate	VBZ
cord-002542-f7l4ty2j	163	8	the	the	DT
cord-002542-f7l4ty2j	163	9	authentic	authentic	JJ
cord-002542-f7l4ty2j	163	10	3	3	CD
cord-002542-f7l4ty2j	163	11	'	'	NN
cord-002542-f7l4ty2j	163	12	end	end	NN
cord-002542-f7l4ty2j	163	13	of	of	IN
cord-002542-f7l4ty2j	163	14	the	the	DT
cord-002542-f7l4ty2j	163	15	positive	positive	JJ
cord-002542-f7l4ty2j	163	16	sense	sense	NN
cord-002542-f7l4ty2j	163	17	viral	viral	JJ
cord-002542-f7l4ty2j	163	18	RNA	RNA	NNP
cord-002542-f7l4ty2j	163	19	,	,	,
cord-002542-f7l4ty2j	163	20	which	which	WDT
cord-002542-f7l4ty2j	163	21	is	be	VBZ
cord-002542-f7l4ty2j	163	22	thus	thus	RB
cord-002542-f7l4ty2j	163	23	successfully	successfully	RB
cord-002542-f7l4ty2j	163	24	recognized	recognize	VBN
cord-002542-f7l4ty2j	163	25	by	by	IN
cord-002542-f7l4ty2j	163	26	the	the	DT
cord-002542-f7l4ty2j	163	27	FHV	FHV	NNP
cord-002542-f7l4ty2j	163	28	RdRp	RdRp	NNP
cord-002542-f7l4ty2j	163	29	allowing	allow	VBG
cord-002542-f7l4ty2j	163	30	the	the	DT
cord-002542-f7l4ty2j	163	31	initiation	initiation	NN
cord-002542-f7l4ty2j	163	32	of	of	IN
cord-002542-f7l4ty2j	163	33	viral	viral	JJ
cord-002542-f7l4ty2j	163	34	replication	replication	NN
cord-002542-f7l4ty2j	163	35	[	[	-LRB-
cord-002542-f7l4ty2j	163	36	54	54	CD
cord-002542-f7l4ty2j	163	37	]	]	-RRB-
cord-002542-f7l4ty2j	163	38	.	.	.
cord-002542-f7l4ty2j	164	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	164	2	choose	choose	VBP
cord-002542-f7l4ty2j	164	3	to	to	TO
cord-002542-f7l4ty2j	164	4	initiate	initiate	VB
cord-002542-f7l4ty2j	164	5	replication	replication	NN
cord-002542-f7l4ty2j	164	6	with	with	IN
cord-002542-f7l4ty2j	164	7	this	this	DT
cord-002542-f7l4ty2j	164	8	method	method	NN
cord-002542-f7l4ty2j	164	9	to	to	TO
cord-002542-f7l4ty2j	164	10	ensure	ensure	VB
cord-002542-f7l4ty2j	164	11	that	that	IN
cord-002542-f7l4ty2j	164	12	the	the	DT
cord-002542-f7l4ty2j	164	13	starting	start	VBG
cord-002542-f7l4ty2j	164	14	viral	viral	JJ
cord-002542-f7l4ty2j	164	15	population	population	NN
cord-002542-f7l4ty2j	164	16	would	would	MD
cord-002542-f7l4ty2j	164	17	be	be	VB
cord-002542-f7l4ty2j	164	18	homogeneous	homogeneous	JJ
cord-002542-f7l4ty2j	164	19	containing	contain	VBG
cord-002542-f7l4ty2j	164	20	only	only	RB
cord-002542-f7l4ty2j	164	21	the	the	DT
cord-002542-f7l4ty2j	164	22	full	full	JJ
cord-002542-f7l4ty2j	164	23	-	-	HYPH
cord-002542-f7l4ty2j	164	24	length	length	NN
cord-002542-f7l4ty2j	164	25	RNAs	rna	NNS
cord-002542-f7l4ty2j	164	26	derived	derive	VBN
cord-002542-f7l4ty2j	164	27	from	from	IN
cord-002542-f7l4ty2j	164	28	the	the	DT
cord-002542-f7l4ty2j	164	29	plasmid	plasmid	NN
cord-002542-f7l4ty2j	164	30	cDNA	cdna	NN
cord-002542-f7l4ty2j	164	31	.	.	.
cord-002542-f7l4ty2j	165	1	After	after	IN
cord-002542-f7l4ty2j	165	2	transfection	transfection	NN
cord-002542-f7l4ty2j	165	3	,	,	,
cord-002542-f7l4ty2j	165	4	the	the	DT
cord-002542-f7l4ty2j	165	5	viral	viral	JJ
cord-002542-f7l4ty2j	165	6	inoculum	inoculum	NN
cord-002542-f7l4ty2j	165	7	was	be	VBD
cord-002542-f7l4ty2j	165	8	allowed	allow	VBN
cord-002542-f7l4ty2j	165	9	to	to	TO
cord-002542-f7l4ty2j	165	10	amplify	amplify	VB
cord-002542-f7l4ty2j	165	11	for	for	IN
cord-002542-f7l4ty2j	165	12	3	3	CD
cord-002542-f7l4ty2j	165	13	days	day	NNS
cord-002542-f7l4ty2j	165	14	(	(	-LRB-
cord-002542-f7l4ty2j	165	15	Passage	passage	NN
cord-002542-f7l4ty2j	165	16	number	number	NN
cord-002542-f7l4ty2j	165	17	=	=	SYM
cord-002542-f7l4ty2j	165	18	P0	p0	NN
cord-002542-f7l4ty2j	165	19	)	)	-RRB-
cord-002542-f7l4ty2j	165	20	,	,	,
cord-002542-f7l4ty2j	165	21	after	after	IN
cord-002542-f7l4ty2j	165	22	which	which	WDT
cord-002542-f7l4ty2j	165	23	most	most	JJS
cord-002542-f7l4ty2j	165	24	cells	cell	NNS
cord-002542-f7l4ty2j	165	25	exhibited	exhibit	VBD
cord-002542-f7l4ty2j	165	26	cytopathic	cytopathic	JJ
cord-002542-f7l4ty2j	165	27	effect	effect	NN
cord-002542-f7l4ty2j	165	28	.	.	.
cord-002542-f7l4ty2j	166	1	Subsequently	subsequently	RB
cord-002542-f7l4ty2j	166	2	,	,	,
cord-002542-f7l4ty2j	166	3	the	the	DT
cord-002542-f7l4ty2j	166	4	supernatant	supernatant	NN
cord-002542-f7l4ty2j	166	5	from	from	IN
cord-002542-f7l4ty2j	166	6	infected	infected	JJ
cord-002542-f7l4ty2j	166	7	cells	cell	NNS
cord-002542-f7l4ty2j	166	8	was	be	VBD
cord-002542-f7l4ty2j	166	9	collected	collect	VBN
cord-002542-f7l4ty2j	166	10	and	and	CC
cord-002542-f7l4ty2j	166	11	a	a	DT
cord-002542-f7l4ty2j	166	12	1mL	1ml	CD
cord-002542-f7l4ty2j	166	13	fraction	fraction	NN
cord-002542-f7l4ty2j	166	14	(	(	-LRB-
cord-002542-f7l4ty2j	166	15	10	10	CD
cord-002542-f7l4ty2j	166	16	%	%	NN
cord-002542-f7l4ty2j	166	17	of	of	IN
cord-002542-f7l4ty2j	166	18	the	the	DT
cord-002542-f7l4ty2j	166	19	total	total	JJ
cord-002542-f7l4ty2j	166	20	volume	volume	NN
cord-002542-f7l4ty2j	166	21	)	)	-RRB-
cord-002542-f7l4ty2j	166	22	was	be	VBD
cord-002542-f7l4ty2j	166	23	used	use	VBN
cord-002542-f7l4ty2j	166	24	to	to	TO
cord-002542-f7l4ty2j	166	25	infect	infect	VB
cord-002542-f7l4ty2j	166	26	10mL	10ml	CD
cord-002542-f7l4ty2j	166	27	of	of	IN
cord-002542-f7l4ty2j	166	28	fresh	fresh	JJ
cord-002542-f7l4ty2j	166	29	S2	s2	NN
cord-002542-f7l4ty2j	166	30	cells	cell	NNS
cord-002542-f7l4ty2j	166	31	in	in	IN
cord-002542-f7l4ty2j	166	32	triplicate	triplicate	NN
cord-002542-f7l4ty2j	166	33	(	(	-LRB-
cord-002542-f7l4ty2j	166	34	Replicates	replicate	VBZ
cord-002542-f7l4ty2j	166	35	R1	R1	NNP
cord-002542-f7l4ty2j	166	36	,	,	,
cord-002542-f7l4ty2j	166	37	R2	R2	NNP
cord-002542-f7l4ty2j	166	38	,	,	,
cord-002542-f7l4ty2j	166	39	and	and	CC
cord-002542-f7l4ty2j	166	40	R3	R3	NNP
cord-002542-f7l4ty2j	166	41	)	)	-RRB-
cord-002542-f7l4ty2j	166	42	.	.	.
cord-002542-f7l4ty2j	167	1	Again	again	RB
cord-002542-f7l4ty2j	167	2	,	,	,
cord-002542-f7l4ty2j	167	3	after	after	IN
cord-002542-f7l4ty2j	167	4	three	three	CD
cord-002542-f7l4ty2j	167	5	days	day	NNS
cord-002542-f7l4ty2j	167	6	,	,	,
cord-002542-f7l4ty2j	167	7	1mL	1ml	CD
cord-002542-f7l4ty2j	167	8	of	of	IN
cord-002542-f7l4ty2j	167	9	the	the	DT
cord-002542-f7l4ty2j	167	10	supernatant	supernatant	NN
cord-002542-f7l4ty2j	167	11	was	be	VBD
cord-002542-f7l4ty2j	167	12	harvested	harvest	VBN
cord-002542-f7l4ty2j	167	13	and	and	CC
cord-002542-f7l4ty2j	167	14	used	use	VBN
cord-002542-f7l4ty2j	167	15	to	to	TO
cord-002542-f7l4ty2j	167	16	infect	infect	VB
cord-002542-f7l4ty2j	167	17	fresh	fresh	JJ
cord-002542-f7l4ty2j	167	18	S2	s2	NN
cord-002542-f7l4ty2j	167	19	cells	cell	NNS
cord-002542-f7l4ty2j	167	20	in	in	IN
cord-002542-f7l4ty2j	167	21	series	series	NN
cord-002542-f7l4ty2j	167	22	for	for	IN
cord-002542-f7l4ty2j	167	23	a	a	DT
cord-002542-f7l4ty2j	167	24	total	total	NN
cord-002542-f7l4ty2j	167	25	of	of	IN
cord-002542-f7l4ty2j	167	26	nine	nine	CD
cord-002542-f7l4ty2j	167	27	3-day	3-day	JJ
cord-002542-f7l4ty2j	167	28	passages	passage	NNS
cord-002542-f7l4ty2j	167	29	(	(	-LRB-
cord-002542-f7l4ty2j	167	30	Passage	passage	NN
cord-002542-f7l4ty2j	167	31	numbers	number	NNS
cord-002542-f7l4ty2j	167	32	=	=	SYM
cord-002542-f7l4ty2j	167	33	P1	P1	NNP
cord-002542-f7l4ty2j	167	34	-P9	-p9	NN
cord-002542-f7l4ty2j	167	35	)	)	-RRB-
cord-002542-f7l4ty2j	167	36	.	.	.
cord-002542-f7l4ty2j	168	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	168	2	,	,	,
cord-002542-f7l4ty2j	168	3	one	one	CD
cord-002542-f7l4ty2j	168	4	single	single	JJ
cord-002542-f7l4ty2j	168	5	inoculum	inoculum	NN
cord-002542-f7l4ty2j	168	6	was	be	VBD
cord-002542-f7l4ty2j	168	7	used	use	VBN
cord-002542-f7l4ty2j	168	8	to	to	TO
cord-002542-f7l4ty2j	168	9	generate	generate	VB
cord-002542-f7l4ty2j	168	10	three	three	CD
cord-002542-f7l4ty2j	168	11	distinct	distinct	JJ
cord-002542-f7l4ty2j	168	12	lineages	lineage	NNS
cord-002542-f7l4ty2j	168	13	as	as	IN
cord-002542-f7l4ty2j	168	14	shown	show	VBN
cord-002542-f7l4ty2j	168	15	in	in	IN
cord-002542-f7l4ty2j	168	16	Fig	Fig	NNP
cord-002542-f7l4ty2j	168	17	1	1	CD
cord-002542-f7l4ty2j	168	18	.	.	.
cord-002542-f7l4ty2j	169	1	For	for	IN
cord-002542-f7l4ty2j	169	2	each	each	DT
cord-002542-f7l4ty2j	169	3	passage	passage	NN
cord-002542-f7l4ty2j	169	4	and	and	CC
cord-002542-f7l4ty2j	169	5	replicate	replicate	VB
cord-002542-f7l4ty2j	169	6	,	,	,
cord-002542-f7l4ty2j	169	7	including	include	VBG
cord-002542-f7l4ty2j	169	8	the	the	DT
cord-002542-f7l4ty2j	169	9	original	original	JJ
cord-002542-f7l4ty2j	169	10	inoculum	inoculum	NN
cord-002542-f7l4ty2j	169	11	,	,	,
cord-002542-f7l4ty2j	169	12	viral	viral	JJ
cord-002542-f7l4ty2j	169	13	particles	particle	NNS
cord-002542-f7l4ty2j	169	14	were	be	VBD
cord-002542-f7l4ty2j	169	15	purified	purify	VBN
cord-002542-f7l4ty2j	169	16	over	over	IN
cord-002542-f7l4ty2j	169	17	a	a	DT
cord-002542-f7l4ty2j	169	18	sucrose	sucrose	NN
cord-002542-f7l4ty2j	169	19	cushion	cushion	NN
cord-002542-f7l4ty2j	169	20	and	and	CC
cord-002542-f7l4ty2j	169	21	non	non	JJ
cord-002542-f7l4ty2j	169	22	-	-	JJ
cord-002542-f7l4ty2j	169	23	encapsidated	encapsidated	JJ
cord-002542-f7l4ty2j	169	24	genetic	genetic	JJ
cord-002542-f7l4ty2j	169	25	material	material	NN
cord-002542-f7l4ty2j	169	26	was	be	VBD
cord-002542-f7l4ty2j	169	27	degraded	degrade	VBN
cord-002542-f7l4ty2j	169	28	to	to	TO
cord-002542-f7l4ty2j	169	29	ensure	ensure	VB
cord-002542-f7l4ty2j	169	30	that	that	IN
cord-002542-f7l4ty2j	169	31	the	the	DT
cord-002542-f7l4ty2j	169	32	genetic	genetic	JJ
cord-002542-f7l4ty2j	169	33	material	material	NN
cord-002542-f7l4ty2j	169	34	subsequently	subsequently	RB
cord-002542-f7l4ty2j	169	35	analyzed	analyze	VBN
cord-002542-f7l4ty2j	169	36	was	be	VBD
cord-002542-f7l4ty2j	169	37	packaged	package	VBN
cord-002542-f7l4ty2j	169	38	within	within	IN
cord-002542-f7l4ty2j	169	39	the	the	DT
cord-002542-f7l4ty2j	169	40	viral	viral	JJ
cord-002542-f7l4ty2j	169	41	capsid	capsid	NN
cord-002542-f7l4ty2j	169	42	.	.	.
cord-002542-f7l4ty2j	170	1	RNA	RNA	NNP
cord-002542-f7l4ty2j	170	2	was	be	VBD
cord-002542-f7l4ty2j	170	3	extracted	extract	VBN
cord-002542-f7l4ty2j	170	4	from	from	IN
cord-002542-f7l4ty2j	170	5	the	the	DT
cord-002542-f7l4ty2j	170	6	purified	purify	VBN
cord-002542-f7l4ty2j	170	7	viral	viral	JJ
cord-002542-f7l4ty2j	170	8	particles	particle	NNS
cord-002542-f7l4ty2j	170	9	using	use	VBG
cord-002542-f7l4ty2j	170	10	standard	standard	JJ
cord-002542-f7l4ty2j	170	11	silica	silica	NN
cord-002542-f7l4ty2j	170	12	-	-	HYPH
cord-002542-f7l4ty2j	170	13	based	base	VBN
cord-002542-f7l4ty2j	170	14	spin	spin	NN
cord-002542-f7l4ty2j	170	15	columns	column	NNS
cord-002542-f7l4ty2j	170	16	.	.	.
cord-002542-f7l4ty2j	171	1	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	171	2	libraries	library	NNS
cord-002542-f7l4ty2j	171	3	[	[	-LRB-
cord-002542-f7l4ty2j	171	4	35	35	CD
cord-002542-f7l4ty2j	171	5	]	]	-RRB-
cord-002542-f7l4ty2j	171	6	were	be	VBD
cord-002542-f7l4ty2j	171	7	synthesized	synthesize	VBN
cord-002542-f7l4ty2j	171	8	from	from	IN
cord-002542-f7l4ty2j	171	9	the	the	DT
cord-002542-f7l4ty2j	171	10	purified	purify	VBN
cord-002542-f7l4ty2j	171	11	viral	viral	JJ
cord-002542-f7l4ty2j	171	12	genomic	genomic	NN
cord-002542-f7l4ty2j	171	13	RNA	RNA	NNP
cord-002542-f7l4ty2j	171	14	and	and	CC
cord-002542-f7l4ty2j	171	15	sequenced	sequence	VBN
cord-002542-f7l4ty2j	171	16	on	on	IN
cord-002542-f7l4ty2j	171	17	an	an	DT
cord-002542-f7l4ty2j	171	18	Illumina	Illumina	NNP
cord-002542-f7l4ty2j	171	19	HiSeq	HiSeq	NNP
cord-002542-f7l4ty2j	171	20	1500	1500	CD
cord-002542-f7l4ty2j	171	21	for	for	IN
cord-002542-f7l4ty2j	171	22	1x150	1x150	CD
cord-002542-f7l4ty2j	171	23	single	single	JJ
cord-002542-f7l4ty2j	171	24	-	-	HYPH
cord-002542-f7l4ty2j	171	25	end	end	NN
cord-002542-f7l4ty2j	171	26	reads	read	NNS
cord-002542-f7l4ty2j	171	27	.	.	.
cord-002542-f7l4ty2j	172	1	The	the	DT
cord-002542-f7l4ty2j	172	2	inoculum	inoculum	NN
cord-002542-f7l4ty2j	172	3	sample	sample	NN
cord-002542-f7l4ty2j	172	4	was	be	VBD
cord-002542-f7l4ty2j	172	5	sequenced	sequence	VBN
cord-002542-f7l4ty2j	172	6	on	on	IN
cord-002542-f7l4ty2j	172	7	a	a	DT
cord-002542-f7l4ty2j	172	8	separate	separate	JJ
cord-002542-f7l4ty2j	172	9	flowcell	flowcell	NN
cord-002542-f7l4ty2j	172	10	to	to	IN
cord-002542-f7l4ty2j	172	11	all	all	DT
cord-002542-f7l4ty2j	172	12	other	other	JJ
cord-002542-f7l4ty2j	172	13	samples	sample	NNS
cord-002542-f7l4ty2j	172	14	to	to	TO
cord-002542-f7l4ty2j	172	15	prevent	prevent	VB
cord-002542-f7l4ty2j	172	16	any	any	DT
cord-002542-f7l4ty2j	172	17	cross	cross	NN
cord-002542-f7l4ty2j	172	18	-	-	NN
cord-002542-f7l4ty2j	172	19	contamination	contamination	NN
cord-002542-f7l4ty2j	172	20	from	from	IN
cord-002542-f7l4ty2j	172	21	incorrect	incorrect	JJ
cord-002542-f7l4ty2j	172	22	demultiplexing	demultiplexing	NN
cord-002542-f7l4ty2j	172	23	.	.	.
cord-002542-f7l4ty2j	173	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	173	2	obtained	obtain	VBD
cord-002542-f7l4ty2j	173	3	1.2	1.2	CD
cord-002542-f7l4ty2j	173	4	-	-	SYM
cord-002542-f7l4ty2j	173	5	30.6	30.6	CD
cord-002542-f7l4ty2j	173	6	million	million	CD
cord-002542-f7l4ty2j	173	7	reads	read	VBZ
cord-002542-f7l4ty2j	173	8	after	after	IN
cord-002542-f7l4ty2j	173	9	trimming	trim	VBG
cord-002542-f7l4ty2j	173	10	and	and	CC
cord-002542-f7l4ty2j	173	11	quality	quality	NN
cord-002542-f7l4ty2j	173	12	filtering	filter	VBG
cord-002542-f7l4ty2j	173	13	for	for	IN
cord-002542-f7l4ty2j	173	14	each	each	DT
cord-002542-f7l4ty2j	173	15	passaged	passage	VBN
cord-002542-f7l4ty2j	173	16	sample	sample	NN
cord-002542-f7l4ty2j	173	17	,	,	,
cord-002542-f7l4ty2j	173	18	and	and	CC
cord-002542-f7l4ty2j	173	19	41.6	41.6	CD
cord-002542-f7l4ty2j	173	20	million	million	CD
cord-002542-f7l4ty2j	173	21	reads	read	VBZ
cord-002542-f7l4ty2j	173	22	for	for	IN
cord-002542-f7l4ty2j	173	23	the	the	DT
cord-002542-f7l4ty2j	173	24	original	original	JJ
cord-002542-f7l4ty2j	173	25	inoculum	inoculum	NN
cord-002542-f7l4ty2j	173	26	(	(	-LRB-
cord-002542-f7l4ty2j	173	27	Table	table	NN
cord-002542-f7l4ty2j	173	28	1	1	CD
cord-002542-f7l4ty2j	173	29	and	and	CC
cord-002542-f7l4ty2j	173	30	S1	S1	NNP
cord-002542-f7l4ty2j	173	31	Table	Table	NNP
cord-002542-f7l4ty2j	173	32	)	)	-RRB-
cord-002542-f7l4ty2j	173	33	.	.	.
cord-002542-f7l4ty2j	174	1	1	1	CD
cord-002542-f7l4ty2j	174	2	million	million	CD
cord-002542-f7l4ty2j	174	3	reads	read	NNS
cord-002542-f7l4ty2j	174	4	corresponds	correspond	VBZ
cord-002542-f7l4ty2j	174	5	to	to	IN
cord-002542-f7l4ty2j	174	6	an	an	DT
cord-002542-f7l4ty2j	174	7	average	average	JJ
cord-002542-f7l4ty2j	174	8	coverage	coverage	NN
cord-002542-f7l4ty2j	174	9	of	of	IN
cord-002542-f7l4ty2j	174	10	greater	great	JJR
cord-002542-f7l4ty2j	174	11	than	than	IN
cord-002542-f7l4ty2j	174	12	33'000X	33'000X	NNP
cord-002542-f7l4ty2j	174	13	across	across	IN
cord-002542-f7l4ty2j	174	14	the	the	DT
cord-002542-f7l4ty2j	174	15	FHV	FHV	NNP
cord-002542-f7l4ty2j	174	16	genome	genome	NN
cord-002542-f7l4ty2j	174	17	.	.	.
cord-002542-f7l4ty2j	175	1	Reads	read	NNS
cord-002542-f7l4ty2j	175	2	were	be	VBD
cord-002542-f7l4ty2j	175	3	aligned	align	VBN
cord-002542-f7l4ty2j	175	4	to	to	IN
cord-002542-f7l4ty2j	175	5	the	the	DT
cord-002542-f7l4ty2j	175	6	FHV	FHV	NNP
cord-002542-f7l4ty2j	175	7	genome	genome	NN
cord-002542-f7l4ty2j	175	8	and	and	CC
cord-002542-f7l4ty2j	175	9	the	the	DT
cord-002542-f7l4ty2j	175	10	host	host	NN
cord-002542-f7l4ty2j	175	11	genome	genome	NN
cord-002542-f7l4ty2j	175	12	(	(	-LRB-
cord-002542-f7l4ty2j	175	13	D.	D.	NNP
cord-002542-f7l4ty2j	175	14	melanogaster	melanogaster	NN
cord-002542-f7l4ty2j	175	15	,	,	,
cord-002542-f7l4ty2j	175	16	fb5_22	fb5_22	NN
cord-002542-f7l4ty2j	175	17	)	)	-RRB-
cord-002542-f7l4ty2j	175	18	using	use	VBG
cord-002542-f7l4ty2j	175	19	Bowtie	Bowtie	NNP
cord-002542-f7l4ty2j	175	20	end	end	NN
cord-002542-f7l4ty2j	175	21	-	-	HYPH
cord-002542-f7l4ty2j	175	22	to	to	IN
cord-002542-f7l4ty2j	175	23	-	-	HYPH
cord-002542-f7l4ty2j	175	24	end	end	NN
cord-002542-f7l4ty2j	175	25	mapping	mapping	NN
cord-002542-f7l4ty2j	175	26	[	[	-LRB-
cord-002542-f7l4ty2j	175	27	47	47	CD
cord-002542-f7l4ty2j	175	28	]	]	-RRB-
cord-002542-f7l4ty2j	175	29	.	.	.
cord-002542-f7l4ty2j	176	1	As	as	IN
cord-002542-f7l4ty2j	176	2	expected	expect	VBN
cord-002542-f7l4ty2j	176	3	,	,	,
cord-002542-f7l4ty2j	176	4	the	the	DT
cord-002542-f7l4ty2j	176	5	majority	majority	NN
cord-002542-f7l4ty2j	176	6	of	of	IN
cord-002542-f7l4ty2j	176	7	the	the	DT
cord-002542-f7l4ty2j	176	8	reads	read	NNS
cord-002542-f7l4ty2j	176	9	aligned	align	VBN
cord-002542-f7l4ty2j	176	10	to	to	IN
cord-002542-f7l4ty2j	176	11	FHV	FHV	NNP
cord-002542-f7l4ty2j	176	12	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	176	13	(	(	-LRB-
cord-002542-f7l4ty2j	176	14	3107	3107	CD
cord-002542-f7l4ty2j	176	15	nts	nts	NNPS
cord-002542-f7l4ty2j	176	16	)	)	-RRB-
cord-002542-f7l4ty2j	176	17	and	and	CC
cord-002542-f7l4ty2j	176	18	FHV	FHV	NNP
cord-002542-f7l4ty2j	176	19	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	177	1	(	(	-LRB-
cord-002542-f7l4ty2j	177	2	1400	1400	CD
cord-002542-f7l4ty2j	177	3	nts	nts	NNPS
cord-002542-f7l4ty2j	177	4	)	)	-RRB-
cord-002542-f7l4ty2j	177	5	in	in	IN
cord-002542-f7l4ty2j	177	6	a	a	DT
cord-002542-f7l4ty2j	177	7	ratio	ratio	NN
cord-002542-f7l4ty2j	177	8	reflecting	reflect	VBG
cord-002542-f7l4ty2j	177	9	the	the	DT
cord-002542-f7l4ty2j	177	10	longer	long	JJR
cord-002542-f7l4ty2j	177	11	length	length	NN
cord-002542-f7l4ty2j	177	12	of	of	IN
cord-002542-f7l4ty2j	177	13	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	177	14	.	.	.
cord-002542-f7l4ty2j	178	1	As	as	IN
cord-002542-f7l4ty2j	178	2	we	-PRON-	PRP
cord-002542-f7l4ty2j	178	3	have	have	VBP
cord-002542-f7l4ty2j	178	4	observed	observe	VBN
cord-002542-f7l4ty2j	178	5	previously	previously	RB
cord-002542-f7l4ty2j	178	6	[	[	-LRB-
cord-002542-f7l4ty2j	178	7	34	34	CD
cord-002542-f7l4ty2j	178	8	,	,	,
cord-002542-f7l4ty2j	178	9	55	55	CD
cord-002542-f7l4ty2j	178	10	]	]	-RRB-
cord-002542-f7l4ty2j	178	11	,	,	,
cord-002542-f7l4ty2j	178	12	0.3	0.3	CD
cord-002542-f7l4ty2j	178	13	-	-	SYM
cord-002542-f7l4ty2j	178	14	8.4	8.4	CD
cord-002542-f7l4ty2j	178	15	%	%	NN
cord-002542-f7l4ty2j	178	16	of	of	IN
cord-002542-f7l4ty2j	178	17	reads	read	NNS
cord-002542-f7l4ty2j	178	18	correspond	correspond	VBP
cord-002542-f7l4ty2j	178	19	to	to	TO
cord-002542-f7l4ty2j	178	20	host	host	VB
cord-002542-f7l4ty2j	178	21	RNAs	rna	NNS
cord-002542-f7l4ty2j	178	22	that	that	WDT
cord-002542-f7l4ty2j	178	23	are	be	VBP
cord-002542-f7l4ty2j	178	24	encapsidated	encapsidate	VBN
cord-002542-f7l4ty2j	178	25	within	within	IN
cord-002542-f7l4ty2j	178	26	the	the	DT
cord-002542-f7l4ty2j	178	27	viral	viral	JJ
cord-002542-f7l4ty2j	178	28	particles	particle	NNS
cord-002542-f7l4ty2j	178	29	including	include	VBG
cord-002542-f7l4ty2j	178	30	mRNAs	mrnas	ADD
cord-002542-f7l4ty2j	178	31	,	,	,
cord-002542-f7l4ty2j	178	32	ribosomal	ribosomal	JJ
cord-002542-f7l4ty2j	178	33	RNAs	rna	NNS
cord-002542-f7l4ty2j	178	34	and	and	CC
cord-002542-f7l4ty2j	178	35	retrotransposons	retrotransposon	NNS
cord-002542-f7l4ty2j	178	36	.	.	.
cord-002542-f7l4ty2j	179	1	Interestingly	interestingly	RB
cord-002542-f7l4ty2j	179	2	,	,	,
cord-002542-f7l4ty2j	179	3	the	the	DT
cord-002542-f7l4ty2j	179	4	amount	amount	NN
cord-002542-f7l4ty2j	179	5	of	of	IN
cord-002542-f7l4ty2j	179	6	encapsidated	encapsidated	JJ
cord-002542-f7l4ty2j	179	7	host	host	NN
cord-002542-f7l4ty2j	179	8	RNA	RNA	NNP
cord-002542-f7l4ty2j	179	9	increases	increase	VBZ
cord-002542-f7l4ty2j	179	10	modestly	modestly	RB
cord-002542-f7l4ty2j	179	11	through	through	IN
cord-002542-f7l4ty2j	179	12	later	later	JJ
cord-002542-f7l4ty2j	179	13	passages	passage	NNS
cord-002542-f7l4ty2j	179	14	(	(	-LRB-
cord-002542-f7l4ty2j	179	15	S1	S1	NNP
cord-002542-f7l4ty2j	179	16	Fig	Fig	NNP
cord-002542-f7l4ty2j	179	17	)	)	-RRB-
cord-002542-f7l4ty2j	179	18	.	.	.
cord-002542-f7l4ty2j	180	1	Subsequently	subsequently	RB
cord-002542-f7l4ty2j	180	2	,	,	,
cord-002542-f7l4ty2j	180	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	180	4	further	further	RB
cord-002542-f7l4ty2j	180	5	characterized	characterize	VBD
cord-002542-f7l4ty2j	180	6	the	the	DT
cord-002542-f7l4ty2j	180	7	unmapped	unmapped	JJ
cord-002542-f7l4ty2j	180	8	reads	read	NNS
cord-002542-f7l4ty2j	180	9	with	with	IN
cord-002542-f7l4ty2j	180	10	the	the	DT
cord-002542-f7l4ty2j	180	11	Python	Python	NNP
cord-002542-f7l4ty2j	180	12	script	script	NN
cord-002542-f7l4ty2j	180	13	ViReMa	virema	NN
cord-002542-f7l4ty2j	180	14	(	(	-LRB-
cord-002542-f7l4ty2j	180	15	"	"	``
cord-002542-f7l4ty2j	180	16	Virus	Virus	NNP
cord-002542-f7l4ty2j	180	17	Recombination	Recombination	NNP
cord-002542-f7l4ty2j	180	18	Mapper	Mapper	NNP
cord-002542-f7l4ty2j	180	19	"	"	''
cord-002542-f7l4ty2j	180	20	)	)	-RRB-
cord-002542-f7l4ty2j	180	21	[	[	-LRB-
cord-002542-f7l4ty2j	180	22	32	32	CD
cord-002542-f7l4ty2j	180	23	]	]	-RRB-
cord-002542-f7l4ty2j	180	24	.	.	.
cord-002542-f7l4ty2j	181	1	ViReMa	ViReMa	NNP
cord-002542-f7l4ty2j	181	2	is	be	VBZ
cord-002542-f7l4ty2j	181	3	a	a	DT
cord-002542-f7l4ty2j	181	4	computational	computational	JJ
cord-002542-f7l4ty2j	181	5	pipeline	pipeline	NN
cord-002542-f7l4ty2j	181	6	optimized	optimize	VBN
cord-002542-f7l4ty2j	181	7	for	for	IN
cord-002542-f7l4ty2j	181	8	mapping	mapping	NN
cord-002542-f7l4ty2j	181	9	virus	virus	NN
cord-002542-f7l4ty2j	181	10	recombination	recombination	NN
cord-002542-f7l4ty2j	181	11	junctions	junction	NNS
cord-002542-f7l4ty2j	181	12	in	in	IN
cord-002542-f7l4ty2j	181	13	NGS	NGS	NNP
cord-002542-f7l4ty2j	181	14	data	datum	NNS
cord-002542-f7l4ty2j	181	15	with	with	IN
cord-002542-f7l4ty2j	181	16	nucleotide	nucleotide	JJ
cord-002542-f7l4ty2j	181	17	resolution	resolution	NN
cord-002542-f7l4ty2j	181	18	by	by	IN
cord-002542-f7l4ty2j	181	19	dynamically	dynamically	RB
cord-002542-f7l4ty2j	181	20	generating	generate	VBG
cord-002542-f7l4ty2j	181	21	moving	move	VBG
cord-002542-f7l4ty2j	181	22	read	read	NN
cord-002542-f7l4ty2j	181	23	segments	segment	NNS
cord-002542-f7l4ty2j	181	24	.	.	.
cord-002542-f7l4ty2j	182	1	ViReMa	ViReMa	NNP
cord-002542-f7l4ty2j	182	2	is	be	VBZ
cord-002542-f7l4ty2j	182	3	sensitive	sensitive	JJ
cord-002542-f7l4ty2j	182	4	to	to	IN
cord-002542-f7l4ty2j	182	5	many	many	JJ
cord-002542-f7l4ty2j	182	6	types	type	NNS
cord-002542-f7l4ty2j	182	7	of	of	IN
cord-002542-f7l4ty2j	182	8	RNA	RNA	NNP
cord-002542-f7l4ty2j	182	9	recombination	recombination	NN
cord-002542-f7l4ty2j	182	10	events	event	NNS
cord-002542-f7l4ty2j	182	11	.	.	.
cord-002542-f7l4ty2j	183	1	This	this	DT
cord-002542-f7l4ty2j	183	2	includes	include	VBZ
cord-002542-f7l4ty2j	183	3	micro	micro	NNS
cord-002542-f7l4ty2j	183	4	-	-	HYPH
cord-002542-f7l4ty2j	183	5	insertions	insertion	NNS
cord-002542-f7l4ty2j	183	6	and	and	CC
cord-002542-f7l4ty2j	183	7	deletions	deletion	NNS
cord-002542-f7l4ty2j	183	8	(	(	-LRB-
cord-002542-f7l4ty2j	183	9	InDels	indel	NNS
cord-002542-f7l4ty2j	183	10	comprising	comprise	VBG
cord-002542-f7l4ty2j	183	11	5	5	CD
cord-002542-f7l4ty2j	183	12	or	or	CC
cord-002542-f7l4ty2j	183	13	fewer	few	JJR
cord-002542-f7l4ty2j	183	14	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	183	15	)	)	-RRB-
cord-002542-f7l4ty2j	183	16	,	,	,
cord-002542-f7l4ty2j	183	17	duplications	duplication	NNS
cord-002542-f7l4ty2j	183	18	,	,	,
cord-002542-f7l4ty2j	183	19	deletions	deletion	NNS
cord-002542-f7l4ty2j	183	20	,	,	,
cord-002542-f7l4ty2j	183	21	inter	inter	JJ
cord-002542-f7l4ty2j	183	22	-	-	JJ
cord-002542-f7l4ty2j	183	23	RNA	rna	JJ
cord-002542-f7l4ty2j	183	24	recombination	recombination	NN
cord-002542-f7l4ty2j	183	25	(	(	-LRB-
cord-002542-f7l4ty2j	183	26	denoting	denote	VBG
cord-002542-f7l4ty2j	183	27	recombination	recombination	NN
cord-002542-f7l4ty2j	183	28	between	between	IN
cord-002542-f7l4ty2j	183	29	FHV	FHV	NNP
cord-002542-f7l4ty2j	183	30	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	183	31	and	and	CC
cord-002542-f7l4ty2j	183	32	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	183	33	)	)	-RRB-
cord-002542-f7l4ty2j	183	34	and	and	CC
cord-002542-f7l4ty2j	183	35	virus	virus	NN
cord-002542-f7l4ty2j	183	36	-	-	HYPH
cord-002542-f7l4ty2j	183	37	to	to	IN
cord-002542-f7l4ty2j	183	38	-	-	HYPH
cord-002542-f7l4ty2j	183	39	host	host	NN
cord-002542-f7l4ty2j	183	40	recombination	recombination	NN
cord-002542-f7l4ty2j	183	41	events	event	NNS
cord-002542-f7l4ty2j	183	42	,	,	,
cord-002542-f7l4ty2j	183	43	and	and	CC
cord-002542-f7l4ty2j	183	44	reports	report	VBZ
cord-002542-f7l4ty2j	183	45	both	both	CC
cord-002542-f7l4ty2j	183	46	the	the	DT
cord-002542-f7l4ty2j	183	47	identity	identity	NN
cord-002542-f7l4ty2j	183	48	and	and	CC
cord-002542-f7l4ty2j	183	49	frequency	frequency	NN
cord-002542-f7l4ty2j	183	50	of	of	IN
cord-002542-f7l4ty2j	183	51	recombination	recombination	NN
cord-002542-f7l4ty2j	183	52	events	event	NNS
cord-002542-f7l4ty2j	183	53	.	.	.
cord-002542-f7l4ty2j	184	1	Recombination	recombination	NN
cord-002542-f7l4ty2j	184	2	events	event	NNS
cord-002542-f7l4ty2j	184	3	that	that	WDT
cord-002542-f7l4ty2j	184	4	can	can	MD
cord-002542-f7l4ty2j	184	5	not	not	RB
cord-002542-f7l4ty2j	184	6	be	be	VB
cord-002542-f7l4ty2j	184	7	unambiguously	unambiguously	RB
cord-002542-f7l4ty2j	184	8	identified	identify	VBN
cord-002542-f7l4ty2j	184	9	due	due	IN
cord-002542-f7l4ty2j	184	10	to	to	IN
cord-002542-f7l4ty2j	184	11	unmapped	unmapped	JJ
cord-002542-f7l4ty2j	184	12	read	read	NN
cord-002542-f7l4ty2j	184	13	segments	segment	NNS
cord-002542-f7l4ty2j	184	14	,	,	,
cord-002542-f7l4ty2j	185	1	mismatches	mismatch	NNS
cord-002542-f7l4ty2j	185	2	occurring	occur	VBG
cord-002542-f7l4ty2j	185	3	near	near	RB
cord-002542-f7l4ty2j	185	4	to	to	IN
cord-002542-f7l4ty2j	185	5	putative	putative	JJ
cord-002542-f7l4ty2j	185	6	recombination	recombination	NN
cord-002542-f7l4ty2j	185	7	events	event	NNS
cord-002542-f7l4ty2j	185	8	,	,	,
cord-002542-f7l4ty2j	185	9	or	or	CC
cord-002542-f7l4ty2j	185	10	reads	read	VBZ
cord-002542-f7l4ty2j	185	11	containing	contain	VBG
cord-002542-f7l4ty2j	185	12	fragments	fragment	NNS
cord-002542-f7l4ty2j	185	13	of	of	IN
cord-002542-f7l4ty2j	185	14	sequencing	sequencing	NN
cord-002542-f7l4ty2j	185	15	adaptors	adaptor	NNS
cord-002542-f7l4ty2j	185	16	are	be	VBP
cord-002542-f7l4ty2j	185	17	flagged	flag	VBN
cord-002542-f7l4ty2j	185	18	as	as	IN
cord-002542-f7l4ty2j	185	19	'	'	``
cord-002542-f7l4ty2j	185	20	other	other	JJ
cord-002542-f7l4ty2j	185	21	'	'	''
cord-002542-f7l4ty2j	185	22	(	(	-LRB-
cord-002542-f7l4ty2j	185	23	Table	table	NN
cord-002542-f7l4ty2j	185	24	1	1	CD
cord-002542-f7l4ty2j	185	25	)	)	-RRB-
cord-002542-f7l4ty2j	185	26	[	[	-LRB-
cord-002542-f7l4ty2j	185	27	32	32	CD
cord-002542-f7l4ty2j	185	28	]	]	-RRB-
cord-002542-f7l4ty2j	185	29	.	.	.
cord-002542-f7l4ty2j	186	1	In	in	IN
cord-002542-f7l4ty2j	186	2	each	each	DT
cord-002542-f7l4ty2j	186	3	genomic	genomic	JJ
cord-002542-f7l4ty2j	186	4	RNA	RNA	NNP
cord-002542-f7l4ty2j	186	5	we	-PRON-	PRP
cord-002542-f7l4ty2j	186	6	found	find	VBD
cord-002542-f7l4ty2j	186	7	hundreds	hundred	NNS
cord-002542-f7l4ty2j	186	8	of	of	IN
cord-002542-f7l4ty2j	186	9	unique	unique	JJ
cord-002542-f7l4ty2j	186	10	recombination	recombination	NN
cord-002542-f7l4ty2j	186	11	events	event	NNS
cord-002542-f7l4ty2j	186	12	,	,	,
cord-002542-f7l4ty2j	186	13	reflecting	reflect	VBG
cord-002542-f7l4ty2j	186	14	a	a	DT
cord-002542-f7l4ty2j	186	15	diverse	diverse	JJ
cord-002542-f7l4ty2j	186	16	and	and	CC
cord-002542-f7l4ty2j	186	17	complex	complex	JJ
cord-002542-f7l4ty2j	186	18	mutational	mutational	JJ
cord-002542-f7l4ty2j	186	19	landscape	landscape	NN
cord-002542-f7l4ty2j	186	20	(	(	-LRB-
cord-002542-f7l4ty2j	186	21	S1	S1	NNP
cord-002542-f7l4ty2j	186	22	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	186	23	)	)	-RRB-
cord-002542-f7l4ty2j	186	24	.	.	.
cord-002542-f7l4ty2j	187	1	Broadly	broadly	RB
cord-002542-f7l4ty2j	187	2	,	,	,
cord-002542-f7l4ty2j	187	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	187	4	see	see	VBP
cord-002542-f7l4ty2j	187	5	an	an	DT
cord-002542-f7l4ty2j	187	6	increase	increase	NN
cord-002542-f7l4ty2j	187	7	in	in	IN
cord-002542-f7l4ty2j	187	8	the	the	DT
cord-002542-f7l4ty2j	187	9	total	total	JJ
cord-002542-f7l4ty2j	187	10	number	number	NN
cord-002542-f7l4ty2j	187	11	of	of	IN
cord-002542-f7l4ty2j	187	12	recombination	recombination	NN
cord-002542-f7l4ty2j	187	13	events	event	NNS
cord-002542-f7l4ty2j	187	14	during	during	IN
cord-002542-f7l4ty2j	187	15	serial	serial	JJ
cord-002542-f7l4ty2j	187	16	passaging	passaging	NN
cord-002542-f7l4ty2j	187	17	of	of	IN
cord-002542-f7l4ty2j	187	18	FHV	FHV	NNP
cord-002542-f7l4ty2j	187	19	and	and	CC
cord-002542-f7l4ty2j	187	20	a	a	DT
cord-002542-f7l4ty2j	187	21	corresponding	corresponding	JJ
cord-002542-f7l4ty2j	187	22	increase	increase	NN
cord-002542-f7l4ty2j	187	23	in	in	IN
cord-002542-f7l4ty2j	187	24	the	the	DT
cord-002542-f7l4ty2j	187	25	Shannon	Shannon	NNP
cord-002542-f7l4ty2j	187	26	diversity	diversity	NN
cord-002542-f7l4ty2j	187	27	index	index	NN
cord-002542-f7l4ty2j	187	28	(	(	-LRB-
cord-002542-f7l4ty2j	187	29	Fig	Fig	NNP
cord-002542-f7l4ty2j	187	30	2A	2a	CD
cord-002542-f7l4ty2j	187	31	and	and	CC
cord-002542-f7l4ty2j	187	32	2B	2b	CD
cord-002542-f7l4ty2j	187	33	)	)	-RRB-
cord-002542-f7l4ty2j	187	34	.	.	.
cord-002542-f7l4ty2j	188	1	Following	follow	VBG
cord-002542-f7l4ty2j	188	2	these	these	DT
cord-002542-f7l4ty2j	188	3	mapping	mapping	NN
cord-002542-f7l4ty2j	188	4	procedures	procedure	NNS
cord-002542-f7l4ty2j	188	5	,	,	,
cord-002542-f7l4ty2j	188	6	few	few	JJ
cord-002542-f7l4ty2j	188	7	reads	read	NNS
cord-002542-f7l4ty2j	188	8	(	(	-LRB-
cord-002542-f7l4ty2j	188	9	0	0	CD
cord-002542-f7l4ty2j	188	10	-	-	SYM
cord-002542-f7l4ty2j	188	11	1.2	1.2	CD
cord-002542-f7l4ty2j	188	12	%	%	NN
cord-002542-f7l4ty2j	188	13	,	,	,
cord-002542-f7l4ty2j	188	14	Table	table	NN
cord-002542-f7l4ty2j	188	15	1	1	CD
cord-002542-f7l4ty2j	188	16	and	and	CC
cord-002542-f7l4ty2j	188	17	S1	S1	NNP
cord-002542-f7l4ty2j	188	18	Table	Table	NNP
cord-002542-f7l4ty2j	188	19	)	)	-RRB-
cord-002542-f7l4ty2j	188	20	remained	remain	VBD
cord-002542-f7l4ty2j	188	21	uncharacterized	uncharacterized	JJ
cord-002542-f7l4ty2j	188	22	.	.	.
cord-002542-f7l4ty2j	189	1	As	as	IN
cord-002542-f7l4ty2j	189	2	in	in	IN
cord-002542-f7l4ty2j	189	3	previous	previous	JJ
cord-002542-f7l4ty2j	189	4	studies	study	NNS
cord-002542-f7l4ty2j	189	5	,	,	,
cord-002542-f7l4ty2j	189	6	these	these	DT
cord-002542-f7l4ty2j	189	7	were	be	VBD
cord-002542-f7l4ty2j	189	8	found	find	VBN
cord-002542-f7l4ty2j	189	9	to	to	TO
cord-002542-f7l4ty2j	189	10	be	be	VB
cord-002542-f7l4ty2j	189	11	derived	derive	VBN
cord-002542-f7l4ty2j	189	12	from	from	IN
cord-002542-f7l4ty2j	189	13	incorrect	incorrect	JJ
cord-002542-f7l4ty2j	189	14	demultiplexing	demultiplexing	NN
cord-002542-f7l4ty2j	189	15	of	of	IN
cord-002542-f7l4ty2j	189	16	neighboring	neighboring	NN
cord-002542-f7l4ty2j	189	17	samples	sample	NNS
cord-002542-f7l4ty2j	189	18	on	on	IN
cord-002542-f7l4ty2j	189	19	the	the	DT
cord-002542-f7l4ty2j	189	20	HiSeq	HiSeq	NNP
cord-002542-f7l4ty2j	189	21	flow	flow	NN
cord-002542-f7l4ty2j	189	22	-	-	HYPH
cord-002542-f7l4ty2j	189	23	cell	cell	NN
cord-002542-f7l4ty2j	189	24	[	[	-LRB-
cord-002542-f7l4ty2j	189	25	56	56	CD
cord-002542-f7l4ty2j	189	26	]	]	-RRB-
cord-002542-f7l4ty2j	189	27	or	or	CC
cord-002542-f7l4ty2j	189	28	from	from	IN
cord-002542-f7l4ty2j	189	29	contaminants	contaminant	NNS
cord-002542-f7l4ty2j	189	30	in	in	IN
cord-002542-f7l4ty2j	189	31	the	the	DT
cord-002542-f7l4ty2j	189	32	RNAseq	RNAseq	NNP
cord-002542-f7l4ty2j	189	33	library	library	NN
cord-002542-f7l4ty2j	189	34	generation	generation	NN
cord-002542-f7l4ty2j	189	35	[	[	-LRB-
cord-002542-f7l4ty2j	189	36	57	57	CD
cord-002542-f7l4ty2j	189	37	]	]	-RRB-
cord-002542-f7l4ty2j	189	38	.	.	.
cord-002542-f7l4ty2j	190	1	Having	have	VBG
cord-002542-f7l4ty2j	190	2	accounted	account	VBN
cord-002542-f7l4ty2j	190	3	for	for	IN
cord-002542-f7l4ty2j	190	4	almost	almost	RB
cord-002542-f7l4ty2j	190	5	all	all	DT
cord-002542-f7l4ty2j	190	6	of	of	IN
cord-002542-f7l4ty2j	190	7	the	the	DT
cord-002542-f7l4ty2j	190	8	reads	read	NNS
cord-002542-f7l4ty2j	190	9	present	present	JJ
cord-002542-f7l4ty2j	190	10	in	in	IN
cord-002542-f7l4ty2j	190	11	each	each	DT
cord-002542-f7l4ty2j	190	12	dataset	dataset	NN
cord-002542-f7l4ty2j	190	13	,	,	,
cord-002542-f7l4ty2j	190	14	we	-PRON-	PRP
cord-002542-f7l4ty2j	190	15	can	can	MD
cord-002542-f7l4ty2j	190	16	be	be	VB
cord-002542-f7l4ty2j	190	17	confident	confident	JJ
cord-002542-f7l4ty2j	190	18	that	that	IN
cord-002542-f7l4ty2j	190	19	we	-PRON-	PRP
cord-002542-f7l4ty2j	190	20	are	be	VBP
cord-002542-f7l4ty2j	190	21	capturing	capture	VBG
cord-002542-f7l4ty2j	190	22	the	the	DT
cord-002542-f7l4ty2j	190	23	full	full	JJ
cord-002542-f7l4ty2j	190	24	range	range	NN
cord-002542-f7l4ty2j	190	25	of	of	IN
cord-002542-f7l4ty2j	190	26	recombination	recombination	NN
cord-002542-f7l4ty2j	190	27	events	event	NNS
cord-002542-f7l4ty2j	190	28	and/	and/	CD
cord-002542-f7l4ty2j	190	29	or	or	CC
cord-002542-f7l4ty2j	190	30	other	other	JJ
cord-002542-f7l4ty2j	190	31	rearrangements	rearrangement	NNS
cord-002542-f7l4ty2j	190	32	present	present	JJ
cord-002542-f7l4ty2j	190	33	within	within	IN
cord-002542-f7l4ty2j	190	34	each	each	DT
cord-002542-f7l4ty2j	190	35	sample	sample	NN
cord-002542-f7l4ty2j	190	36	and	and	CC
cord-002542-f7l4ty2j	190	37	thus	thus	RB
cord-002542-f7l4ty2j	190	38	are	be	VBP
cord-002542-f7l4ty2j	190	39	not	not	RB
cord-002542-f7l4ty2j	190	40	missing	miss	VBG
cord-002542-f7l4ty2j	190	41	important	important	JJ
cord-002542-f7l4ty2j	190	42	or	or	CC
cord-002542-f7l4ty2j	190	43	significant	significant	JJ
cord-002542-f7l4ty2j	190	44	events	event	NNS
cord-002542-f7l4ty2j	190	45	due	due	IN
cord-002542-f7l4ty2j	190	46	to	to	IN
cord-002542-f7l4ty2j	190	47	computational	computational	JJ
cord-002542-f7l4ty2j	190	48	limitations	limitation	NNS
cord-002542-f7l4ty2j	190	49	.	.	.
cord-002542-f7l4ty2j	191	1	To	to	TO
cord-002542-f7l4ty2j	191	2	demonstrate	demonstrate	VB
cord-002542-f7l4ty2j	191	3	the	the	DT
cord-002542-f7l4ty2j	191	4	reproducibility	reproducibility	NN
cord-002542-f7l4ty2j	191	5	of	of	IN
cord-002542-f7l4ty2j	191	6	the	the	DT
cord-002542-f7l4ty2j	191	7	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	191	8	approach	approach	NN
cord-002542-f7l4ty2j	191	9	and	and	CC
cord-002542-f7l4ty2j	191	10	to	to	TO
cord-002542-f7l4ty2j	191	11	assess	assess	VB
cord-002542-f7l4ty2j	191	12	the	the	DT
cord-002542-f7l4ty2j	191	13	limit	limit	NN
cord-002542-f7l4ty2j	191	14	in	in	IN
cord-002542-f7l4ty2j	191	15	terms	term	NNS
cord-002542-f7l4ty2j	191	16	of	of	IN
cord-002542-f7l4ty2j	191	17	our	-PRON-	PRP$
cord-002542-f7l4ty2j	191	18	ability	ability	NN
cord-002542-f7l4ty2j	191	19	to	to	TO
cord-002542-f7l4ty2j	191	20	successfully	successfully	RB
cord-002542-f7l4ty2j	191	21	detect	detect	VB
cord-002542-f7l4ty2j	191	22	rare	rare	JJ
cord-002542-f7l4ty2j	191	23	recombination	recombination	NN
cord-002542-f7l4ty2j	191	24	events	event	NNS
cord-002542-f7l4ty2j	191	25	,	,	,
cord-002542-f7l4ty2j	191	26	we	-PRON-	PRP
cord-002542-f7l4ty2j	191	27	generated	generate	VBD
cord-002542-f7l4ty2j	191	28	three	three	CD
cord-002542-f7l4ty2j	191	29	Virus	virus	NN
cord-002542-f7l4ty2j	191	30	was	be	VBD
cord-002542-f7l4ty2j	191	31	allowed	allow	VBN
cord-002542-f7l4ty2j	191	32	to	to	TO
cord-002542-f7l4ty2j	191	33	propagate	propagate	VB
cord-002542-f7l4ty2j	191	34	for	for	IN
cord-002542-f7l4ty2j	191	35	three	three	CD
cord-002542-f7l4ty2j	191	36	days	day	NNS
cord-002542-f7l4ty2j	191	37	after	after	IN
cord-002542-f7l4ty2j	191	38	which	which	WDT
cord-002542-f7l4ty2j	191	39	cells	cell	NNS
cord-002542-f7l4ty2j	191	40	and	and	CC
cord-002542-f7l4ty2j	191	41	the	the	DT
cord-002542-f7l4ty2j	191	42	supernatant	supernatant	NN
cord-002542-f7l4ty2j	191	43	were	be	VBD
cord-002542-f7l4ty2j	191	44	collected	collect	VBN
cord-002542-f7l4ty2j	191	45	.	.	.
cord-002542-f7l4ty2j	192	1	A	a	DT
cord-002542-f7l4ty2j	192	2	fraction	fraction	NN
cord-002542-f7l4ty2j	192	3	(	(	-LRB-
cord-002542-f7l4ty2j	192	4	1:10	1:10	CD
cord-002542-f7l4ty2j	192	5	)	)	-RRB-
cord-002542-f7l4ty2j	192	6	was	be	VBD
cord-002542-f7l4ty2j	192	7	used	use	VBN
cord-002542-f7l4ty2j	192	8	to	to	TO
cord-002542-f7l4ty2j	192	9	further	further	RB
cord-002542-f7l4ty2j	192	10	infect	infect	VB
cord-002542-f7l4ty2j	192	11	a	a	DT
cord-002542-f7l4ty2j	192	12	new	new	JJ
cord-002542-f7l4ty2j	192	13	population	population	NN
cord-002542-f7l4ty2j	192	14	of	of	IN
cord-002542-f7l4ty2j	192	15	S2	s2	NN
cord-002542-f7l4ty2j	192	16	cells	cell	NNS
cord-002542-f7l4ty2j	192	17	in	in	IN
cord-002542-f7l4ty2j	192	18	a	a	DT
cord-002542-f7l4ty2j	192	19	series	series	NN
cord-002542-f7l4ty2j	192	20	of	of	IN
cord-002542-f7l4ty2j	192	21	passages	passage	NNS
cord-002542-f7l4ty2j	192	22	.	.	.
cord-002542-f7l4ty2j	193	1	The	the	DT
cord-002542-f7l4ty2j	193	2	remaining	remain	VBG
cord-002542-f7l4ty2j	193	3	fraction	fraction	NN
cord-002542-f7l4ty2j	193	4	was	be	VBD
cord-002542-f7l4ty2j	193	5	collected	collect	VBN
cord-002542-f7l4ty2j	193	6	for	for	IN
cord-002542-f7l4ty2j	193	7	analysis	analysis	NN
cord-002542-f7l4ty2j	193	8	.	.	.
cord-002542-f7l4ty2j	194	1	In	in	IN
cord-002542-f7l4ty2j	194	2	total	total	NN
cord-002542-f7l4ty2j	194	3	,	,	,
cord-002542-f7l4ty2j	194	4	three	three	CD
cord-002542-f7l4ty2j	194	5	replicates	replicate	NNS
cord-002542-f7l4ty2j	194	6	of	of	IN
cord-002542-f7l4ty2j	194	7	nine	nine	CD
cord-002542-f7l4ty2j	194	8	passages	passage	NNS
cord-002542-f7l4ty2j	194	9	were	be	VBD
cord-002542-f7l4ty2j	194	10	collected	collect	VBN
cord-002542-f7l4ty2j	194	11	.	.	.
cord-002542-f7l4ty2j	195	1	replicate	replicate	VB
cord-002542-f7l4ty2j	195	2	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	195	3	libraries	library	NNS
cord-002542-f7l4ty2j	195	4	from	from	IN
cord-002542-f7l4ty2j	195	5	the	the	DT
cord-002542-f7l4ty2j	195	6	RNA	RNA	NNP
cord-002542-f7l4ty2j	195	7	sample	sample	NN
cord-002542-f7l4ty2j	195	8	P7R2	P7R2	NNP
cord-002542-f7l4ty2j	195	9	,	,	,
cord-002542-f7l4ty2j	195	10	obtained	obtain	VBD
cord-002542-f7l4ty2j	195	11	1x150bp	1x150bp	CD
cord-002542-f7l4ty2j	195	12	reads	read	NNS
cord-002542-f7l4ty2j	195	13	and	and	CC
cord-002542-f7l4ty2j	195	14	performed	perform	VBD
cord-002542-f7l4ty2j	195	15	the	the	DT
cord-002542-f7l4ty2j	195	16	same	same	JJ
cord-002542-f7l4ty2j	195	17	computational	computational	JJ
cord-002542-f7l4ty2j	195	18	analyses	analysis	NNS
cord-002542-f7l4ty2j	195	19	as	as	IN
cord-002542-f7l4ty2j	195	20	described	describe	VBN
cord-002542-f7l4ty2j	195	21	above	above	RB
cord-002542-f7l4ty2j	195	22	.	.	.
cord-002542-f7l4ty2j	196	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	196	2	mapped	map	VBD
cord-002542-f7l4ty2j	196	3	0.83	0.83	CD
cord-002542-f7l4ty2j	196	4	M	M	NNP
cord-002542-f7l4ty2j	196	5	,	,	,
cord-002542-f7l4ty2j	196	6	1.45	1.45	CD
cord-002542-f7l4ty2j	196	7	M	M	NNP
cord-002542-f7l4ty2j	196	8	and	and	CC
cord-002542-f7l4ty2j	196	9	1.18	1.18	CD
cord-002542-f7l4ty2j	196	10	M	M	NNP
cord-002542-f7l4ty2j	196	11	reads	read	VBZ
cord-002542-f7l4ty2j	196	12	per	per	IN
cord-002542-f7l4ty2j	196	13	library	library	NN
cord-002542-f7l4ty2j	196	14	,	,	,
cord-002542-f7l4ty2j	196	15	giving	give	VBG
cord-002542-f7l4ty2j	196	16	an	an	DT
cord-002542-f7l4ty2j	196	17	approximate	approximate	JJ
cord-002542-f7l4ty2j	196	18	coverage	coverage	NN
cord-002542-f7l4ty2j	196	19	of~42,000	of~42,000	CD
cord-002542-f7l4ty2j	196	20	-	-	HYPH
cord-002542-f7l4ty2j	196	21	139,000x	139,000x	CD
cord-002542-f7l4ty2j	196	22	coverage	coverage	NN
cord-002542-f7l4ty2j	196	23	over	over	IN
cord-002542-f7l4ty2j	196	24	FHV	FHV	NNP
cord-002542-f7l4ty2j	196	25	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	197	1	and~18,000	and~18,000	LS
cord-002542-f7l4ty2j	197	2	-	-	.
cord-002542-f7l4ty2j	197	3	67,000x	67,000x	.
cord-002542-f7l4ty2j	198	1	over	over	IN
cord-002542-f7l4ty2j	198	2	FHV	FHV	NNP
cord-002542-f7l4ty2j	198	3	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	198	4	(	(	-LRB-
cord-002542-f7l4ty2j	198	5	calculated	calculate	VBN
cord-002542-f7l4ty2j	198	6	from	from	IN
cord-002542-f7l4ty2j	198	7	the	the	DT
cord-002542-f7l4ty2j	198	8	average	average	JJ
cord-002542-f7l4ty2j	198	9	coverage	coverage	NN
cord-002542-f7l4ty2j	198	10	over	over	IN
cord-002542-f7l4ty2j	198	11	the	the	DT
cord-002542-f7l4ty2j	198	12	conserved	conserve	VBN
cord-002542-f7l4ty2j	198	13	5	5	CD
cord-002542-f7l4ty2j	198	14	'	'	''
cord-002542-f7l4ty2j	198	15	and	and	CC
cord-002542-f7l4ty2j	198	16	3	3	CD
cord-002542-f7l4ty2j	198	17	'	'	POS
cord-002542-f7l4ty2j	198	18	ends	end	NNS
cord-002542-f7l4ty2j	198	19	)	)	-RRB-
cord-002542-f7l4ty2j	198	20	.	.	.
cord-002542-f7l4ty2j	199	1	When	when	WRB
cord-002542-f7l4ty2j	199	2	comparing	compare	VBG
cord-002542-f7l4ty2j	199	3	the	the	DT
cord-002542-f7l4ty2j	199	4	frequency	frequency	NN
cord-002542-f7l4ty2j	199	5	of	of	IN
cord-002542-f7l4ty2j	199	6	unique	unique	JJ
cord-002542-f7l4ty2j	199	7	recombination	recombination	NN
cord-002542-f7l4ty2j	199	8	events	event	NNS
cord-002542-f7l4ty2j	199	9	in	in	IN
cord-002542-f7l4ty2j	199	10	either	either	DT
cord-002542-f7l4ty2j	199	11	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	199	12	or	or	CC
cord-002542-f7l4ty2j	199	13	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	199	14	between	between	IN
cord-002542-f7l4ty2j	199	15	any	any	DT
cord-002542-f7l4ty2j	199	16	pair	pair	NN
cord-002542-f7l4ty2j	199	17	of	of	IN
cord-002542-f7l4ty2j	199	18	the	the	DT
cord-002542-f7l4ty2j	199	19	three	three	CD
cord-002542-f7l4ty2j	199	20	replicates	replicate	NNS
cord-002542-f7l4ty2j	199	21	,	,	,
cord-002542-f7l4ty2j	199	22	we	-PRON-	PRP
cord-002542-f7l4ty2j	199	23	find	find	VBP
cord-002542-f7l4ty2j	199	24	excellent	excellent	JJ
cord-002542-f7l4ty2j	199	25	correlation	correlation	NN
cord-002542-f7l4ty2j	199	26	(	(	-LRB-
cord-002542-f7l4ty2j	199	27	Pearson	Pearson	NNP
cord-002542-f7l4ty2j	199	28	>	>	XX
cord-002542-f7l4ty2j	199	29	0.99	0.99	CD
cord-002542-f7l4ty2j	199	30	)	)	-RRB-
cord-002542-f7l4ty2j	199	31	even	even	RB
cord-002542-f7l4ty2j	199	32	for	for	IN
cord-002542-f7l4ty2j	199	33	very	very	RB
cord-002542-f7l4ty2j	199	34	infrequent	infrequent	JJ
cord-002542-f7l4ty2j	199	35	recombination	recombination	NN
cord-002542-f7l4ty2j	199	36	events	event	NNS
cord-002542-f7l4ty2j	199	37	,	,	,
cord-002542-f7l4ty2j	199	38	as	as	IN
cord-002542-f7l4ty2j	199	39	illustrated	illustrate	VBN
cord-002542-f7l4ty2j	199	40	in	in	IN
cord-002542-f7l4ty2j	199	41	the	the	DT
cord-002542-f7l4ty2j	199	42	scatter	scatter	NN
cord-002542-f7l4ty2j	199	43	plots	plot	NNS
cord-002542-f7l4ty2j	199	44	in	in	IN
cord-002542-f7l4ty2j	199	45	S2	S2	NNP
cord-002542-f7l4ty2j	199	46	Fig	Fig	NNP
cord-002542-f7l4ty2j	199	47	.	.	.
cord-002542-f7l4ty2j	200	1	Events	event	NNS
cord-002542-f7l4ty2j	200	2	that	that	WDT
cord-002542-f7l4ty2j	200	3	were	be	VBD
cord-002542-f7l4ty2j	200	4	found	find	VBN
cord-002542-f7l4ty2j	200	5	in	in	IN
cord-002542-f7l4ty2j	200	6	two	two	CD
cord-002542-f7l4ty2j	200	7	replicates	replicate	NNS
cord-002542-f7l4ty2j	200	8	but	but	CC
cord-002542-f7l4ty2j	200	9	not	not	RB
cord-002542-f7l4ty2j	200	10	a	a	DT
cord-002542-f7l4ty2j	200	11	third	third	JJ
cord-002542-f7l4ty2j	200	12	,	,	,
cord-002542-f7l4ty2j	200	13	never	never	RB
cord-002542-f7l4ty2j	200	14	exceeded	exceed	VBD
cord-002542-f7l4ty2j	200	15	more	more	JJR
cord-002542-f7l4ty2j	200	16	than	than	IN
cord-002542-f7l4ty2j	200	17	20	20	CD
cord-002542-f7l4ty2j	200	18	mapped	map	VBN
cord-002542-f7l4ty2j	200	19	reads	read	NNS
cord-002542-f7l4ty2j	200	20	for	for	IN
cord-002542-f7l4ty2j	200	21	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	200	22	and	and	CC
cord-002542-f7l4ty2j	200	23	8	8	CD
cord-002542-f7l4ty2j	200	24	reads	read	NNS
cord-002542-f7l4ty2j	200	25	for	for	IN
cord-002542-f7l4ty2j	200	26	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	200	27	.	.	.
cord-002542-f7l4ty2j	201	1	If	if	IN
cord-002542-f7l4ty2j	201	2	we	-PRON-	PRP
cord-002542-f7l4ty2j	201	3	take	take	VBP
cord-002542-f7l4ty2j	201	4	these	these	DT
cord-002542-f7l4ty2j	201	5	values	value	NNS
cord-002542-f7l4ty2j	201	6	as	as	IN
cord-002542-f7l4ty2j	201	7	a	a	DT
cord-002542-f7l4ty2j	201	8	cut	cut	NN
cord-002542-f7l4ty2j	201	9	-	-	HYPH
cord-002542-f7l4ty2j	201	10	offs	off	NNS
cord-002542-f7l4ty2j	201	11	,	,	,
cord-002542-f7l4ty2j	201	12	below	below	IN
cord-002542-f7l4ty2j	201	13	which	which	WDT
cord-002542-f7l4ty2j	201	14	we	-PRON-	PRP
cord-002542-f7l4ty2j	201	15	begin	begin	VBP
cord-002542-f7l4ty2j	201	16	to	to	TO
cord-002542-f7l4ty2j	201	17	fail	fail	VB
cord-002542-f7l4ty2j	201	18	to	to	TO
cord-002542-f7l4ty2j	201	19	detect	detect	VB
cord-002542-f7l4ty2j	201	20	events	event	NNS
cord-002542-f7l4ty2j	201	21	,	,	,
cord-002542-f7l4ty2j	201	22	then	then	RB
cord-002542-f7l4ty2j	201	23	we	-PRON-	PRP
cord-002542-f7l4ty2j	201	24	can	can	MD
cord-002542-f7l4ty2j	201	25	conservatively	conservatively	RB
cord-002542-f7l4ty2j	201	26	estimate	estimate	VB
cord-002542-f7l4ty2j	201	27	that	that	IN
cord-002542-f7l4ty2j	201	28	we	-PRON-	PRP
cord-002542-f7l4ty2j	201	29	are	be	VBP
cord-002542-f7l4ty2j	201	30	reproducibly	reproducibly	RB
cord-002542-f7l4ty2j	201	31	sensitive	sensitive	JJ
cord-002542-f7l4ty2j	201	32	to	to	IN
cord-002542-f7l4ty2j	201	33	recombinant	recombinant	JJ
cord-002542-f7l4ty2j	201	34	species	specie	NNS
cord-002542-f7l4ty2j	201	35	that	that	WDT
cord-002542-f7l4ty2j	201	36	are	be	VBP
cord-002542-f7l4ty2j	201	37	present	present	JJ
cord-002542-f7l4ty2j	201	38	at	at	IN
cord-002542-f7l4ty2j	201	39	approximately	approximately	RB
cord-002542-f7l4ty2j	201	40	0.048	0.048	CD
cord-002542-f7l4ty2j	201	41	%	%	NN
cord-002542-f7l4ty2j	201	42	(	(	-LRB-
cord-002542-f7l4ty2j	201	43	20/	20/	CD
cord-002542-f7l4ty2j	201	44	42,000	42,000	CD
cord-002542-f7l4ty2j	201	45	)	)	-RRB-
cord-002542-f7l4ty2j	201	46	of	of	IN
cord-002542-f7l4ty2j	201	47	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	201	48	population	population	NN
cord-002542-f7l4ty2j	201	49	and	and	CC
cord-002542-f7l4ty2j	201	50	0.044	0.044	CD
cord-002542-f7l4ty2j	201	51	%	%	NN
cord-002542-f7l4ty2j	201	52	(	(	-LRB-
cord-002542-f7l4ty2j	201	53	8/18,000	8/18,000	CD
cord-002542-f7l4ty2j	201	54	)	)	-RRB-
cord-002542-f7l4ty2j	201	55	of	of	IN
cord-002542-f7l4ty2j	201	56	the	the	DT
cord-002542-f7l4ty2j	201	57	total	total	JJ
cord-002542-f7l4ty2j	201	58	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	201	59	population	population	NN
cord-002542-f7l4ty2j	201	60	when	when	WRB
cord-002542-f7l4ty2j	201	61	obtaining~1	obtaining~1	NNP
cord-002542-f7l4ty2j	201	62	M	M	NNP
cord-002542-f7l4ty2j	201	63	sequence	sequence	NN
cord-002542-f7l4ty2j	201	64	reads	read	VBZ
cord-002542-f7l4ty2j	201	65	.	.	.
cord-002542-f7l4ty2j	202	1	In	in	IN
cord-002542-f7l4ty2j	202	2	the	the	DT
cord-002542-f7l4ty2j	202	3	inoculum	inoculum	NN
cord-002542-f7l4ty2j	202	4	(	(	-LRB-
cord-002542-f7l4ty2j	202	5	P0	p0	NN
cord-002542-f7l4ty2j	202	6	)	)	-RRB-
cord-002542-f7l4ty2j	202	7	,	,	,
cord-002542-f7l4ty2j	202	8	less	less	JJR
cord-002542-f7l4ty2j	202	9	than	than	IN
cord-002542-f7l4ty2j	202	10	0.2	0.2	CD
cord-002542-f7l4ty2j	202	11	%	%	NN
cord-002542-f7l4ty2j	202	12	of	of	IN
cord-002542-f7l4ty2j	202	13	the	the	DT
cord-002542-f7l4ty2j	202	14	all	all	PDT
cord-002542-f7l4ty2j	202	15	the	the	DT
cord-002542-f7l4ty2j	202	16	reads	read	NNS
cord-002542-f7l4ty2j	202	17	mapped	map	VBN
cord-002542-f7l4ty2j	202	18	to	to	IN
cord-002542-f7l4ty2j	202	19	recombination	recombination	NN
cord-002542-f7l4ty2j	202	20	events	event	NNS
cord-002542-f7l4ty2j	202	21	(	(	-LRB-
cord-002542-f7l4ty2j	202	22	Table	table	NN
cord-002542-f7l4ty2j	202	23	1	1	CD
cord-002542-f7l4ty2j	202	24	,	,	,
cord-002542-f7l4ty2j	202	25	Fig	Fig	NNP
cord-002542-f7l4ty2j	202	26	2A	2a	CD
cord-002542-f7l4ty2j	202	27	)	)	-RRB-
cord-002542-f7l4ty2j	202	28	.	.	.
cord-002542-f7l4ty2j	203	1	Inspection	inspection	NN
cord-002542-f7l4ty2j	203	2	of	of	IN
cord-002542-f7l4ty2j	203	3	these	these	DT
cord-002542-f7l4ty2j	203	4	events	event	NNS
cord-002542-f7l4ty2j	203	5	reveals	reveal	VBZ
cord-002542-f7l4ty2j	203	6	that	that	IN
cord-002542-f7l4ty2j	203	7	they	-PRON-	PRP
cord-002542-f7l4ty2j	203	8	are	be	VBP
cord-002542-f7l4ty2j	203	9	dispersed	disperse	VBN
cord-002542-f7l4ty2j	203	10	throughout	throughout	IN
cord-002542-f7l4ty2j	203	11	each	each	DT
cord-002542-f7l4ty2j	203	12	of	of	IN
cord-002542-f7l4ty2j	203	13	the	the	DT
cord-002542-f7l4ty2j	203	14	genomic	genomic	JJ
cord-002542-f7l4ty2j	203	15	RNAs	rna	NNS
cord-002542-f7l4ty2j	203	16	.	.	.
cord-002542-f7l4ty2j	204	1	RNA1	rna1	NN
cord-002542-f7l4ty2j	204	2	recombination	recombination	NN
cord-002542-f7l4ty2j	204	3	events	event	NNS
cord-002542-f7l4ty2j	204	4	are	be	VBP
cord-002542-f7l4ty2j	204	5	the	the	DT
cord-002542-f7l4ty2j	204	6	least	least	RBS
cord-002542-f7l4ty2j	204	7	frequent	frequent	JJ
cord-002542-f7l4ty2j	204	8	,	,	,
cord-002542-f7l4ty2j	204	9	with	with	IN
cord-002542-f7l4ty2j	204	10	only	only	RB
cord-002542-f7l4ty2j	204	11	22	22	CD
cord-002542-f7l4ty2j	204	12	unique	unique	JJ
cord-002542-f7l4ty2j	204	13	events	event	NNS
cord-002542-f7l4ty2j	204	14	detected	detect	VBD
cord-002542-f7l4ty2j	204	15	represented	represent	VBN
cord-002542-f7l4ty2j	204	16	by	by	IN
cord-002542-f7l4ty2j	204	17	2920	2920	CD
cord-002542-f7l4ty2j	204	18	reads	read	NNS
cord-002542-f7l4ty2j	204	19	and	and	CC
cord-002542-f7l4ty2j	204	20	without	without	IN
cord-002542-f7l4ty2j	204	21	an	an	DT
cord-002542-f7l4ty2j	204	22	apparent	apparent	JJ
cord-002542-f7l4ty2j	204	23	bias	bias	NN
cord-002542-f7l4ty2j	204	24	toward	toward	IN
cord-002542-f7l4ty2j	204	25	any	any	DT
cord-002542-f7l4ty2j	204	26	specific	specific	JJ
cord-002542-f7l4ty2j	204	27	location	location	NN
cord-002542-f7l4ty2j	204	28	.	.	.
cord-002542-f7l4ty2j	205	1	The	the	DT
cord-002542-f7l4ty2j	205	2	three	three	CD
cord-002542-f7l4ty2j	205	3	most	most	RBS
cord-002542-f7l4ty2j	205	4	common	common	JJ
cord-002542-f7l4ty2j	205	5	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	205	6	events	event	NNS
cord-002542-f7l4ty2j	205	7	in	in	IN
cord-002542-f7l4ty2j	205	8	the	the	DT
cord-002542-f7l4ty2j	205	9	inoculum	inoculum	NN
cord-002542-f7l4ty2j	205	10	are	be	VBP
cord-002542-f7l4ty2j	205	11	2325	2325	CD
cord-002542-f7l4ty2j	205	12	^	^	SYM
cord-002542-f7l4ty2j	205	13	1241	1241	CD
cord-002542-f7l4ty2j	205	14	,	,	,
cord-002542-f7l4ty2j	205	15	1484	1484	CD
cord-002542-f7l4ty2j	205	16	^	^	SYM
cord-002542-f7l4ty2j	205	17	1944	1944	CD
cord-002542-f7l4ty2j	205	18	,	,	,
cord-002542-f7l4ty2j	205	19	and	and	CC
cord-002542-f7l4ty2j	205	20	2199	2199	CD
cord-002542-f7l4ty2j	205	21	^	^	SYM
cord-002542-f7l4ty2j	205	22	393	393	CD
cord-002542-f7l4ty2j	205	23	with	with	IN
cord-002542-f7l4ty2j	205	24	514	514	CD
cord-002542-f7l4ty2j	205	25	,	,	,
cord-002542-f7l4ty2j	205	26	229	229	CD
cord-002542-f7l4ty2j	205	27	,	,	,
cord-002542-f7l4ty2j	205	28	and	and	CC
cord-002542-f7l4ty2j	205	29	177	177	CD
cord-002542-f7l4ty2j	205	30	mapped	map	VBD
cord-002542-f7l4ty2j	205	31	reads	read	VBZ
cord-002542-f7l4ty2j	205	32	respectively	respectively	RB
cord-002542-f7l4ty2j	205	33	(	(	-LRB-
cord-002542-f7l4ty2j	205	34	S1	S1	NNP
cord-002542-f7l4ty2j	205	35	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	205	36	)	)	-RRB-
cord-002542-f7l4ty2j	205	37	.	.	.
cord-002542-f7l4ty2j	206	1	Read	read	VB
cord-002542-f7l4ty2j	206	2	depth	depth	NN
cord-002542-f7l4ty2j	206	3	for	for	IN
cord-002542-f7l4ty2j	206	4	the	the	DT
cord-002542-f7l4ty2j	206	5	wild	wild	JJ
cord-002542-f7l4ty2j	206	6	-	-	HYPH
cord-002542-f7l4ty2j	206	7	type	type	NN
cord-002542-f7l4ty2j	206	8	genome	genome	NN
cord-002542-f7l4ty2j	206	9	at	at	IN
cord-002542-f7l4ty2j	206	10	these	these	DT
cord-002542-f7l4ty2j	206	11	loci	locus	NNS
cord-002542-f7l4ty2j	206	12	ranges	range	VBZ
cord-002542-f7l4ty2j	206	13	from	from	IN
cord-002542-f7l4ty2j	206	14	400	400	CD
cord-002542-f7l4ty2j	206	15	K	K	NNP
cord-002542-f7l4ty2j	206	16	to	to	IN
cord-002542-f7l4ty2j	206	17	1.9	1.9	CD
cord-002542-f7l4ty2j	206	18	M	M	NNP
cord-002542-f7l4ty2j	206	19	reads	read	NNS
cord-002542-f7l4ty2j	206	20	,	,	,
cord-002542-f7l4ty2j	206	21	therefore	therefore	RB
cord-002542-f7l4ty2j	206	22	these	these	DT
cord-002542-f7l4ty2j	206	23	recombination	recombination	NN
cord-002542-f7l4ty2j	206	24	events	event	NNS
cord-002542-f7l4ty2j	206	25	make	make	VBP
cord-002542-f7l4ty2j	206	26	-	-	HYPH
cord-002542-f7l4ty2j	206	27	up	up	NN
cord-002542-f7l4ty2j	206	28	at	at	IN
cord-002542-f7l4ty2j	206	29	less	less	JJR
cord-002542-f7l4ty2j	206	30	than	than	IN
cord-002542-f7l4ty2j	206	31	0.1	0.1	CD
cord-002542-f7l4ty2j	206	32	%	%	NN
cord-002542-f7l4ty2j	206	33	of	of	IN
cord-002542-f7l4ty2j	206	34	the	the	DT
cord-002542-f7l4ty2j	206	35	total	total	JJ
cord-002542-f7l4ty2j	206	36	viral	viral	JJ
cord-002542-f7l4ty2j	206	37	population	population	NN
cord-002542-f7l4ty2j	206	38	.	.	.
cord-002542-f7l4ty2j	207	1	These	these	DT
cord-002542-f7l4ty2j	207	2	are	be	VBP
cord-002542-f7l4ty2j	207	3	not	not	RB
cord-002542-f7l4ty2j	207	4	the	the	DT
cord-002542-f7l4ty2j	207	5	events	event	NNS
cord-002542-f7l4ty2j	207	6	that	that	WDT
cord-002542-f7l4ty2j	207	7	have	have	VBP
cord-002542-f7l4ty2j	207	8	been	be	VBN
cord-002542-f7l4ty2j	207	9	previously	previously	RB
cord-002542-f7l4ty2j	207	10	reported	report	VBN
cord-002542-f7l4ty2j	207	11	as	as	IN
cord-002542-f7l4ty2j	207	12	forming	form	VBG
cord-002542-f7l4ty2j	207	13	FHV	FHV	NNP
cord-002542-f7l4ty2j	207	14	DI	DI	NNP
cord-002542-f7l4ty2j	207	15	-	-	HYPH
cord-002542-f7l4ty2j	207	16	RNAs	rna	NNS
cord-002542-f7l4ty2j	207	17	,	,	,
cord-002542-f7l4ty2j	207	18	moreover	moreover	RB
cord-002542-f7l4ty2j	207	19	none	none	NN
cord-002542-f7l4ty2j	207	20	of	of	IN
cord-002542-f7l4ty2j	207	21	these	these	DT
cord-002542-f7l4ty2j	207	22	events	event	NNS
cord-002542-f7l4ty2j	207	23	are	be	VBP
cord-002542-f7l4ty2j	207	24	observed	observe	VBN
cord-002542-f7l4ty2j	207	25	again	again	RB
cord-002542-f7l4ty2j	207	26	in	in	IN
cord-002542-f7l4ty2j	207	27	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	207	28	passages	passage	NNS
cord-002542-f7l4ty2j	207	29	,	,	,
cord-002542-f7l4ty2j	207	30	perhaps	perhaps	RB
cord-002542-f7l4ty2j	207	31	due	due	IN
cord-002542-f7l4ty2j	207	32	to	to	IN
cord-002542-f7l4ty2j	207	33	approaching	approach	VBG
cord-002542-f7l4ty2j	207	34	the	the	DT
cord-002542-f7l4ty2j	207	35	sensitivity	sensitivity	NN
cord-002542-f7l4ty2j	207	36	of	of	IN
cord-002542-f7l4ty2j	207	37	discovery	discovery	NN
cord-002542-f7l4ty2j	207	38	limit	limit	NN
cord-002542-f7l4ty2j	207	39	as	as	IN
cord-002542-f7l4ty2j	207	40	described	describe	VBN
cord-002542-f7l4ty2j	207	41	above	above	RB
cord-002542-f7l4ty2j	207	42	.	.	.
cord-002542-f7l4ty2j	208	1	However	however	RB
cord-002542-f7l4ty2j	208	2	,	,	,
cord-002542-f7l4ty2j	208	3	due	due	IN
cord-002542-f7l4ty2j	208	4	to	to	IN
cord-002542-f7l4ty2j	208	5	the	the	DT
cord-002542-f7l4ty2j	208	6	low	low	JJ
cord-002542-f7l4ty2j	208	7	-	-	HYPH
cord-002542-f7l4ty2j	208	8	rate	rate	NN
cord-002542-f7l4ty2j	208	9	of	of	IN
cord-002542-f7l4ty2j	208	10	artifactual	artifactual	JJ
cord-002542-f7l4ty2j	208	11	recombination	recombination	NN
cord-002542-f7l4ty2j	208	12	of	of	IN
cord-002542-f7l4ty2j	208	13	the	the	DT
cord-002542-f7l4ty2j	208	14	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	208	15	approach	approach	NN
cord-002542-f7l4ty2j	208	16	(	(	-LRB-
cord-002542-f7l4ty2j	208	17	>	>	NFP
cord-002542-f7l4ty2j	208	18	3	3	CD
cord-002542-f7l4ty2j	208	19	events	event	NNS
cord-002542-f7l4ty2j	208	20	per	per	IN
cord-002542-f7l4ty2j	208	21	millions	million	NNS
cord-002542-f7l4ty2j	208	22	reads	read	VBZ
cord-002542-f7l4ty2j	208	23	[	[	-LRB-
cord-002542-f7l4ty2j	208	24	35	35	CD
cord-002542-f7l4ty2j	208	25	]	]	-RRB-
cord-002542-f7l4ty2j	208	26	)	)	-RRB-
cord-002542-f7l4ty2j	208	27	,	,	,
cord-002542-f7l4ty2j	208	28	we	-PRON-	PRP
cord-002542-f7l4ty2j	208	29	can	can	MD
cord-002542-f7l4ty2j	208	30	be	be	VB
cord-002542-f7l4ty2j	208	31	confident	confident	JJ
cord-002542-f7l4ty2j	208	32	that	that	IN
cord-002542-f7l4ty2j	208	33	these	these	DT
cord-002542-f7l4ty2j	208	34	are	be	VBP
cord-002542-f7l4ty2j	208	35	not	not	RB
cord-002542-f7l4ty2j	208	36	sequencing	sequence	VBG
cord-002542-f7l4ty2j	208	37	artifacts	artifact	NNS
cord-002542-f7l4ty2j	208	38	[	[	-LRB-
cord-002542-f7l4ty2j	208	39	35	35	CD
cord-002542-f7l4ty2j	208	40	]	]	-RRB-
cord-002542-f7l4ty2j	208	41	.	.	.
cord-002542-f7l4ty2j	209	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	209	2	,	,	,
cord-002542-f7l4ty2j	209	3	these	these	DT
cord-002542-f7l4ty2j	209	4	events	event	NNS
cord-002542-f7l4ty2j	209	5	likely	likely	RB
cord-002542-f7l4ty2j	209	6	represent	represent	VBP
cord-002542-f7l4ty2j	209	7	non	non	JJ
cord-002542-f7l4ty2j	209	8	-	-	JJ
cord-002542-f7l4ty2j	209	9	viable	viable	JJ
cord-002542-f7l4ty2j	209	10	or	or	CC
cord-002542-f7l4ty2j	209	11	transient	transient	JJ
cord-002542-f7l4ty2j	209	12	recombination	recombination	NN
cord-002542-f7l4ty2j	209	13	events	event	NNS
cord-002542-f7l4ty2j	209	14	that	that	WDT
cord-002542-f7l4ty2j	209	15	arose	arise	VBD
cord-002542-f7l4ty2j	209	16	due	due	JJ
cord-002542-f7l4ty2j	209	17	to	to	IN
cord-002542-f7l4ty2j	209	18	stochastic	stochastic	JJ
cord-002542-f7l4ty2j	209	19	non	non	JJ
cord-002542-f7l4ty2j	209	20	-	-	JJ
cord-002542-f7l4ty2j	209	21	homologous	homologous	JJ
cord-002542-f7l4ty2j	209	22	recombination	recombination	NN
cord-002542-f7l4ty2j	209	23	.	.	.
cord-002542-f7l4ty2j	210	1	For	for	IN
cord-002542-f7l4ty2j	210	2	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	210	3	in	in	IN
cord-002542-f7l4ty2j	210	4	the	the	DT
cord-002542-f7l4ty2j	210	5	inoculum	inoculum	NN
cord-002542-f7l4ty2j	210	6	,	,	,
cord-002542-f7l4ty2j	210	7	the	the	DT
cord-002542-f7l4ty2j	210	8	three	three	CD
cord-002542-f7l4ty2j	210	9	most	most	RBS
cord-002542-f7l4ty2j	210	10	frequently	frequently	RB
cord-002542-f7l4ty2j	210	11	observed	observe	VBD
cord-002542-f7l4ty2j	210	12	events	event	NNS
cord-002542-f7l4ty2j	210	13	were	be	VBD
cord-002542-f7l4ty2j	210	14	738	738	CD
cord-002542-f7l4ty2j	210	15	^	^	SYM
cord-002542-f7l4ty2j	210	16	1219	1219	CD
cord-002542-f7l4ty2j	210	17	,	,	,
cord-002542-f7l4ty2j	210	18	738	738	CD
cord-002542-f7l4ty2j	210	19	^	^	SYM
cord-002542-f7l4ty2j	210	20	1222	1222	CD
cord-002542-f7l4ty2j	210	21	and	and	CC
cord-002542-f7l4ty2j	210	22	1024	1024	CD
cord-002542-f7l4ty2j	210	23	^	^	SYM
cord-002542-f7l4ty2j	210	24	1190	1190	CD
cord-002542-f7l4ty2j	210	25	,	,	,
cord-002542-f7l4ty2j	210	26	with	with	IN
cord-002542-f7l4ty2j	210	27	9849	9849	CD
cord-002542-f7l4ty2j	210	28	,	,	,
cord-002542-f7l4ty2j	210	29	5237	5237	CD
cord-002542-f7l4ty2j	210	30	,	,	,
cord-002542-f7l4ty2j	210	31	and	and	CC
cord-002542-f7l4ty2j	210	32	3673	3673	CD
cord-002542-f7l4ty2j	210	33	mapped	map	VBN
cord-002542-f7l4ty2j	210	34	reads	read	VBZ
cord-002542-f7l4ty2j	210	35	respectively	respectively	RB
cord-002542-f7l4ty2j	210	36	(	(	-LRB-
cord-002542-f7l4ty2j	210	37	S1	S1	NNP
cord-002542-f7l4ty2j	210	38	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	210	39	)	)	-RRB-
cord-002542-f7l4ty2j	210	40	.	.	.
cord-002542-f7l4ty2j	211	1	Fig	Fig	NNP
cord-002542-f7l4ty2j	211	2	2A	2a	CD
cord-002542-f7l4ty2j	211	3	)	)	-RRB-
cord-002542-f7l4ty2j	211	4	.	.	.
cord-002542-f7l4ty2j	212	1	Again	again	RB
cord-002542-f7l4ty2j	212	2	,	,	,
cord-002542-f7l4ty2j	212	3	these	these	DT
cord-002542-f7l4ty2j	212	4	occur	occur	VBP
cord-002542-f7l4ty2j	212	5	throughout	throughout	IN
cord-002542-f7l4ty2j	212	6	each	each	DT
cord-002542-f7l4ty2j	212	7	of	of	IN
cord-002542-f7l4ty2j	212	8	the	the	DT
cord-002542-f7l4ty2j	212	9	genomic	genomic	JJ
cord-002542-f7l4ty2j	212	10	RNAs	rna	NNS
cord-002542-f7l4ty2j	212	11	.	.	.
cord-002542-f7l4ty2j	213	1	However	however	RB
cord-002542-f7l4ty2j	213	2	,	,	,
cord-002542-f7l4ty2j	213	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	213	4	do	do	VBP
cord-002542-f7l4ty2j	213	5	begin	begin	VB
cord-002542-f7l4ty2j	213	6	to	to	TO
cord-002542-f7l4ty2j	213	7	see	see	VB
cord-002542-f7l4ty2j	213	8	events	event	NNS
cord-002542-f7l4ty2j	213	9	that	that	WDT
cord-002542-f7l4ty2j	213	10	have	have	VBP
cord-002542-f7l4ty2j	213	11	previously	previously	RB
cord-002542-f7l4ty2j	213	12	been	be	VBN
cord-002542-f7l4ty2j	213	13	characterized	characterize	VBN
cord-002542-f7l4ty2j	213	14	as	as	IN
cord-002542-f7l4ty2j	213	15	forming	form	VBG
cord-002542-f7l4ty2j	213	16	DI	DI	NNP
cord-002542-f7l4ty2j	213	17	-	-	HYPH
cord-002542-f7l4ty2j	213	18	RNAs	rna	NNS
cord-002542-f7l4ty2j	213	19	,	,	,
cord-002542-f7l4ty2j	213	20	such	such	JJ
cord-002542-f7l4ty2j	213	21	as	as	IN
cord-002542-f7l4ty2j	213	22	311	311	CD
cord-002542-f7l4ty2j	213	23	^	^	SYM
cord-002542-f7l4ty2j	213	24	1104	1104	CD
cord-002542-f7l4ty2j	213	25	and	and	CC
cord-002542-f7l4ty2j	213	26	301	301	CD
cord-002542-f7l4ty2j	213	27	^	^	SYM
cord-002542-f7l4ty2j	213	28	1100	1100	CD
cord-002542-f7l4ty2j	213	29	,	,	,
cord-002542-f7l4ty2j	213	30	although	although	IN
cord-002542-f7l4ty2j	213	31	these	these	DT
cord-002542-f7l4ty2j	213	32	events	event	NNS
cord-002542-f7l4ty2j	213	33	are	be	VBP
cord-002542-f7l4ty2j	213	34	present	present	JJ
cord-002542-f7l4ty2j	213	35	at	at	IN
cord-002542-f7l4ty2j	213	36	low	low	JJ
cord-002542-f7l4ty2j	213	37	levels	level	NNS
cord-002542-f7l4ty2j	213	38	(	(	-LRB-
cord-002542-f7l4ty2j	213	39	70	70	CD
cord-002542-f7l4ty2j	213	40	and	and	CC
cord-002542-f7l4ty2j	213	41	21	21	CD
cord-002542-f7l4ty2j	213	42	reads	read	NNS
cord-002542-f7l4ty2j	213	43	in	in	IN
cord-002542-f7l4ty2j	213	44	Replicate	Replicate	NNP
cord-002542-f7l4ty2j	213	45	1	1	CD
cord-002542-f7l4ty2j	213	46	from	from	IN
cord-002542-f7l4ty2j	213	47	a	a	DT
cord-002542-f7l4ty2j	213	48	total	total	NN
cord-002542-f7l4ty2j	213	49	of	of	IN
cord-002542-f7l4ty2j	213	50	8.2	8.2	CD
cord-002542-f7l4ty2j	213	51	M	M	NNP
cord-002542-f7l4ty2j	213	52	reads	read	VBZ
cord-002542-f7l4ty2j	213	53	mapped	map	VBN
cord-002542-f7l4ty2j	213	54	to	to	IN
cord-002542-f7l4ty2j	213	55	the	the	DT
cord-002542-f7l4ty2j	213	56	FHV	FHV	NNP
cord-002542-f7l4ty2j	213	57	genome	genome	NN
cord-002542-f7l4ty2j	213	58	)	)	-RRB-
cord-002542-f7l4ty2j	214	1	(	(	-LRB-
cord-002542-f7l4ty2j	214	2	S1	S1	NNP
cord-002542-f7l4ty2j	214	3	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	214	4	)	)	-RRB-
cord-002542-f7l4ty2j	214	5	.	.	.
cord-002542-f7l4ty2j	215	1	In	in	IN
cord-002542-f7l4ty2j	215	2	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	215	3	passages	passage	NNS
cord-002542-f7l4ty2j	215	4	there	there	EX
cord-002542-f7l4ty2j	215	5	was	be	VBD
cord-002542-f7l4ty2j	215	6	a	a	DT
cord-002542-f7l4ty2j	215	7	rapid	rapid	JJ
cord-002542-f7l4ty2j	215	8	increase	increase	NN
cord-002542-f7l4ty2j	215	9	in	in	IN
cord-002542-f7l4ty2j	215	10	the	the	DT
cord-002542-f7l4ty2j	215	11	total	total	JJ
cord-002542-f7l4ty2j	215	12	proportion	proportion	NN
cord-002542-f7l4ty2j	215	13	of	of	IN
cord-002542-f7l4ty2j	215	14	mapped	map	VBN
cord-002542-f7l4ty2j	215	15	recombination	recombination	NN
cord-002542-f7l4ty2j	215	16	events	event	NNS
cord-002542-f7l4ty2j	215	17	(	(	-LRB-
cord-002542-f7l4ty2j	215	18	peaking	peak	VBG
cord-002542-f7l4ty2j	215	19	at	at	IN
cord-002542-f7l4ty2j	215	20	11.9	11.9	CD
cord-002542-f7l4ty2j	215	21	%	%	NN
cord-002542-f7l4ty2j	215	22	in	in	IN
cord-002542-f7l4ty2j	215	23	P8R1	P8R1	NNP
cord-002542-f7l4ty2j	215	24	)	)	-RRB-
cord-002542-f7l4ty2j	216	1	(	(	-LRB-
cord-002542-f7l4ty2j	216	2	Table	table	NN
cord-002542-f7l4ty2j	216	3	1	1	CD
cord-002542-f7l4ty2j	216	4	,	,	,
cord-002542-f7l4ty2j	216	5	Fig	Fig	NNP
cord-002542-f7l4ty2j	216	6	2A	2a	CD
cord-002542-f7l4ty2j	216	7	)	)	-RRB-
cord-002542-f7l4ty2j	216	8	.	.	.
cord-002542-f7l4ty2j	217	1	In	in	IN
cord-002542-f7l4ty2j	217	2	these	these	DT
cord-002542-f7l4ty2j	217	3	later	later	JJ
cord-002542-f7l4ty2j	217	4	passages	passage	NNS
cord-002542-f7l4ty2j	217	5	for	for	IN
cord-002542-f7l4ty2j	217	6	each	each	DT
cord-002542-f7l4ty2j	217	7	replicate	replicate	NN
cord-002542-f7l4ty2j	217	8	,	,	,
cord-002542-f7l4ty2j	217	9	it	-PRON-	PRP
cord-002542-f7l4ty2j	217	10	can	can	MD
cord-002542-f7l4ty2j	217	11	be	be	VB
cord-002542-f7l4ty2j	217	12	seen	see	VBN
cord-002542-f7l4ty2j	217	13	that	that	IN
cord-002542-f7l4ty2j	217	14	the	the	DT
cord-002542-f7l4ty2j	217	15	most	most	RBS
cord-002542-f7l4ty2j	217	16	common	common	JJ
cord-002542-f7l4ty2j	217	17	recombination	recombination	NN
cord-002542-f7l4ty2j	217	18	events	event	NNS
cord-002542-f7l4ty2j	217	19	are	be	VBP
cord-002542-f7l4ty2j	217	20	deletions	deletion	NNS
cord-002542-f7l4ty2j	217	21	that	that	WDT
cord-002542-f7l4ty2j	217	22	span	span	VBP
cord-002542-f7l4ty2j	217	23	two	two	CD
cord-002542-f7l4ty2j	217	24	regions	region	NNS
cord-002542-f7l4ty2j	217	25	in	in	IN
cord-002542-f7l4ty2j	217	26	each	each	DT
cord-002542-f7l4ty2j	217	27	genomic	genomic	JJ
cord-002542-f7l4ty2j	217	28	RNA	RNA	NNP
cord-002542-f7l4ty2j	217	29	including	include	VBG
cord-002542-f7l4ty2j	217	30	:	:	:
cord-002542-f7l4ty2j	217	31	nts	nts	NNP
cord-002542-f7l4ty2j	217	32	300	300	CD
cord-002542-f7l4ty2j	217	33	-	-	SYM
cord-002542-f7l4ty2j	217	34	940	940	CD
cord-002542-f7l4ty2j	217	35	and	and	CC
cord-002542-f7l4ty2j	217	36	nts	nts	NNPS
cord-002542-f7l4ty2j	217	37	1240	1240	CD
cord-002542-f7l4ty2j	217	38	-	-	HYPH
cord-002542-f7l4ty2j	217	39	2300	2300	CD
cord-002542-f7l4ty2j	217	40	of	of	IN
cord-002542-f7l4ty2j	217	41	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	217	42	;	;	:
cord-002542-f7l4ty2j	217	43	and	and	CC
cord-002542-f7l4ty2j	217	44	nts	nts	NNPS
cord-002542-f7l4ty2j	217	45	250	250	CD
cord-002542-f7l4ty2j	217	46	-	-	HYPH
cord-002542-f7l4ty2j	217	47	510	510	CD
cord-002542-f7l4ty2j	217	48	and	and	CC
cord-002542-f7l4ty2j	217	49	nts	nts	NNPS
cord-002542-f7l4ty2j	217	50	740	740	CD
cord-002542-f7l4ty2j	217	51	-	-	HYPH
cord-002542-f7l4ty2j	217	52	1220	1220	CD
cord-002542-f7l4ty2j	217	53	of	of	IN
cord-002542-f7l4ty2j	217	54	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	217	55	,	,	,
cord-002542-f7l4ty2j	217	56	consistent	consistent	JJ
cord-002542-f7l4ty2j	217	57	with	with	IN
cord-002542-f7l4ty2j	217	58	previous	previous	JJ
cord-002542-f7l4ty2j	217	59	observations	observation	NNS
cord-002542-f7l4ty2j	217	60	of	of	IN
cord-002542-f7l4ty2j	217	61	FHV	FHV	NNP
cord-002542-f7l4ty2j	217	62	DI	DI	NNP
cord-002542-f7l4ty2j	217	63	-	-	HYPH
cord-002542-f7l4ty2j	217	64	RNAs	rna	NNS
cord-002542-f7l4ty2j	217	65	[	[	-LRB-
cord-002542-f7l4ty2j	217	66	31	31	CD
cord-002542-f7l4ty2j	217	67	]	]	-RRB-
cord-002542-f7l4ty2j	217	68	(	(	-LRB-
cord-002542-f7l4ty2j	217	69	S1	S1	NNP
cord-002542-f7l4ty2j	217	70	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	217	71	)	)	-RRB-
cord-002542-f7l4ty2j	217	72	.	.	.
cord-002542-f7l4ty2j	218	1	However	however	RB
cord-002542-f7l4ty2j	218	2	,	,	,
cord-002542-f7l4ty2j	218	3	the	the	DT
cord-002542-f7l4ty2j	218	4	exact	exact	JJ
cord-002542-f7l4ty2j	218	5	sites	site	NNS
cord-002542-f7l4ty2j	218	6	of	of	IN
cord-002542-f7l4ty2j	218	7	the	the	DT
cord-002542-f7l4ty2j	218	8	recombination	recombination	NN
cord-002542-f7l4ty2j	218	9	events	event	NNS
cord-002542-f7l4ty2j	218	10	,	,	,
cord-002542-f7l4ty2j	218	11	while	while	IN
cord-002542-f7l4ty2j	218	12	repeatedly	repeatedly	RB
cord-002542-f7l4ty2j	218	13	observed	observe	VBD
cord-002542-f7l4ty2j	218	14	over	over	IN
cord-002542-f7l4ty2j	218	15	time	time	NN
cord-002542-f7l4ty2j	218	16	in	in	IN
cord-002542-f7l4ty2j	218	17	each	each	DT
cord-002542-f7l4ty2j	218	18	replicate	replicate	NN
cord-002542-f7l4ty2j	218	19	,	,	,
cord-002542-f7l4ty2j	218	20	varied	varied	JJ
cord-002542-f7l4ty2j	218	21	between	between	IN
cord-002542-f7l4ty2j	218	22	replicates	replicate	NNS
cord-002542-f7l4ty2j	218	23	and	and	CC
cord-002542-f7l4ty2j	218	24	each	each	DT
cord-002542-f7l4ty2j	218	25	had	have	VBD
cord-002542-f7l4ty2j	218	26	distinct	distinct	JJ
cord-002542-f7l4ty2j	218	27	'	'	``
cord-002542-f7l4ty2j	218	28	most	most	RBS
cord-002542-f7l4ty2j	218	29	popular	popular	JJ
cord-002542-f7l4ty2j	218	30	'	'	``
cord-002542-f7l4ty2j	218	31	species	specie	NNS
cord-002542-f7l4ty2j	218	32	in	in	IN
cord-002542-f7l4ty2j	218	33	the	the	DT
cord-002542-f7l4ty2j	218	34	final	final	JJ
cord-002542-f7l4ty2j	218	35	passages	passage	NNS
cord-002542-f7l4ty2j	218	36	(	(	-LRB-
cord-002542-f7l4ty2j	218	37	Table	table	NN
cord-002542-f7l4ty2j	218	38	2	2	CD
cord-002542-f7l4ty2j	218	39	)	)	-RRB-
cord-002542-f7l4ty2j	218	40	.	.	.
cord-002542-f7l4ty2j	219	1	In	in	IN
cord-002542-f7l4ty2j	219	2	some	some	DT
cord-002542-f7l4ty2j	219	3	instances	instance	NNS
cord-002542-f7l4ty2j	219	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	219	5	are	be	VBP
cord-002542-f7l4ty2j	219	6	able	able	JJ
cord-002542-f7l4ty2j	219	7	to	to	TO
cord-002542-f7l4ty2j	219	8	find	find	VB
cord-002542-f7l4ty2j	219	9	that	that	IN
cord-002542-f7l4ty2j	219	10	a	a	DT
cord-002542-f7l4ty2j	219	11	specific	specific	JJ
cord-002542-f7l4ty2j	219	12	event	event	NN
cord-002542-f7l4ty2j	219	13	is	be	VBZ
cord-002542-f7l4ty2j	219	14	predominant	predominant	JJ
cord-002542-f7l4ty2j	219	15	in	in	IN
cord-002542-f7l4ty2j	219	16	one	one	CD
cord-002542-f7l4ty2j	219	17	replicate	replicate	VB
cord-002542-f7l4ty2j	219	18	while	while	IN
cord-002542-f7l4ty2j	219	19	at	at	IN
cord-002542-f7l4ty2j	219	20	low	low	JJ
cord-002542-f7l4ty2j	219	21	levels	level	NNS
cord-002542-f7l4ty2j	219	22	in	in	IN
cord-002542-f7l4ty2j	219	23	another	another	DT
cord-002542-f7l4ty2j	219	24	.	.	.
cord-002542-f7l4ty2j	220	1	Overall	overall	RB
cord-002542-f7l4ty2j	220	2	,	,	,
cord-002542-f7l4ty2j	220	3	these	these	DT
cord-002542-f7l4ty2j	220	4	trends	trend	NNS
cord-002542-f7l4ty2j	220	5	in	in	IN
cord-002542-f7l4ty2j	220	6	the	the	DT
cord-002542-f7l4ty2j	220	7	frequency	frequency	NN
cord-002542-f7l4ty2j	220	8	of	of	IN
cord-002542-f7l4ty2j	220	9	recombination	recombination	NN
cord-002542-f7l4ty2j	220	10	events	event	NNS
cord-002542-f7l4ty2j	220	11	throughout	throughout	IN
cord-002542-f7l4ty2j	220	12	passaging	passaging	NN
cord-002542-f7l4ty2j	220	13	reveal	reveal	VBP
cord-002542-f7l4ty2j	220	14	that	that	IN
cord-002542-f7l4ty2j	220	15	once	once	RB
cord-002542-f7l4ty2j	220	16	defective	defective	JJ
cord-002542-f7l4ty2j	220	17	RNA	RNA	NNP
cord-002542-f7l4ty2j	220	18	species	specie	NNS
cord-002542-f7l4ty2j	220	19	emerge	emerge	VBP
cord-002542-f7l4ty2j	220	20	during	during	IN
cord-002542-f7l4ty2j	220	21	viral	viral	JJ
cord-002542-f7l4ty2j	220	22	passaging	passaging	NN
cord-002542-f7l4ty2j	220	23	they	-PRON-	PRP
cord-002542-f7l4ty2j	220	24	rapidly	rapidly	RB
cord-002542-f7l4ty2j	220	25	accumulate	accumulate	VBP
cord-002542-f7l4ty2j	220	26	.	.	.
cord-002542-f7l4ty2j	221	1	Despite	despite	IN
cord-002542-f7l4ty2j	221	2	the	the	DT
cord-002542-f7l4ty2j	221	3	predominance	predominance	NN
cord-002542-f7l4ty2j	221	4	of	of	IN
cord-002542-f7l4ty2j	221	5	certain	certain	JJ
cord-002542-f7l4ty2j	221	6	recombination	recombination	NN
cord-002542-f7l4ty2j	221	7	events	event	NNS
cord-002542-f7l4ty2j	221	8	in	in	IN
cord-002542-f7l4ty2j	221	9	the	the	DT
cord-002542-f7l4ty2j	221	10	later	later	JJ
cord-002542-f7l4ty2j	221	11	passages	passage	NNS
cord-002542-f7l4ty2j	221	12	,	,	,
cord-002542-f7l4ty2j	221	13	there	there	EX
cord-002542-f7l4ty2j	221	14	still	still	RB
cord-002542-f7l4ty2j	221	15	remained	remain	VBD
cord-002542-f7l4ty2j	221	16	a	a	DT
cord-002542-f7l4ty2j	221	17	large	large	JJ
cord-002542-f7l4ty2j	221	18	number	number	NN
cord-002542-f7l4ty2j	221	19	of	of	IN
cord-002542-f7l4ty2j	221	20	infrequent	infrequent	JJ
cord-002542-f7l4ty2j	221	21	events	event	NNS
cord-002542-f7l4ty2j	221	22	scattered	scatter	VBN
cord-002542-f7l4ty2j	221	23	throughout	throughout	IN
cord-002542-f7l4ty2j	221	24	the	the	DT
cord-002542-f7l4ty2j	221	25	viral	viral	JJ
cord-002542-f7l4ty2j	221	26	genome	genome	NN
cord-002542-f7l4ty2j	221	27	.	.	.
cord-002542-f7l4ty2j	222	1	Many	many	JJ
cord-002542-f7l4ty2j	222	2	of	of	IN
cord-002542-f7l4ty2j	222	3	these	these	DT
cord-002542-f7l4ty2j	222	4	are	be	VBP
cord-002542-f7l4ty2j	222	5	observed	observe	VBN
cord-002542-f7l4ty2j	222	6	only	only	RB
cord-002542-f7l4ty2j	222	7	in	in	IN
cord-002542-f7l4ty2j	222	8	one	one	CD
cord-002542-f7l4ty2j	222	9	passage	passage	NN
cord-002542-f7l4ty2j	222	10	and	and	CC
cord-002542-f7l4ty2j	222	11	not	not	RB
cord-002542-f7l4ty2j	222	12	in	in	IN
cord-002542-f7l4ty2j	222	13	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	222	14	passages	passage	NNS
cord-002542-f7l4ty2j	222	15	.	.	.
cord-002542-f7l4ty2j	223	1	Again	again	RB
cord-002542-f7l4ty2j	223	2	,	,	,
cord-002542-f7l4ty2j	223	3	these	these	DT
cord-002542-f7l4ty2j	223	4	events	event	NNS
cord-002542-f7l4ty2j	223	5	likely	likely	RB
cord-002542-f7l4ty2j	223	6	correspond	correspond	VBP
cord-002542-f7l4ty2j	223	7	to	to	IN
cord-002542-f7l4ty2j	223	8	stochastically	stochastically	RB
cord-002542-f7l4ty2j	223	9	generated	generate	VBN
cord-002542-f7l4ty2j	223	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	223	11	recombination	recombination	NN
cord-002542-f7l4ty2j	223	12	events	event	NNS
cord-002542-f7l4ty2j	223	13	that	that	WDT
cord-002542-f7l4ty2j	223	14	form	form	VBP
cord-002542-f7l4ty2j	223	15	non	non	JJ
cord-002542-f7l4ty2j	223	16	-	-	JJ
cord-002542-f7l4ty2j	223	17	viable	viable	JJ
cord-002542-f7l4ty2j	223	18	defective	defective	JJ
cord-002542-f7l4ty2j	223	19	RNAs	rna	NNS
cord-002542-f7l4ty2j	223	20	.	.	.
cord-002542-f7l4ty2j	224	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	224	2	reasoned	reason	VBD
cord-002542-f7l4ty2j	224	3	that	that	IN
cord-002542-f7l4ty2j	224	4	analyzing	analyze	VBG
cord-002542-f7l4ty2j	224	5	these	these	DT
cord-002542-f7l4ty2j	224	6	events	event	NNS
cord-002542-f7l4ty2j	224	7	would	would	MD
cord-002542-f7l4ty2j	224	8	more	more	RBR
cord-002542-f7l4ty2j	224	9	accurately	accurately	RB
cord-002542-f7l4ty2j	224	10	reveal	reveal	VB
cord-002542-f7l4ty2j	224	11	the	the	DT
cord-002542-f7l4ty2j	224	12	nucleotide	nucleotide	JJ
cord-002542-f7l4ty2j	224	13	preference	preference	NN
cord-002542-f7l4ty2j	224	14	of	of	IN
cord-002542-f7l4ty2j	224	15	the	the	DT
cord-002542-f7l4ty2j	224	16	FHV	FHV	NNP
cord-002542-f7l4ty2j	224	17	RdRp	RdRp	NNP
cord-002542-f7l4ty2j	224	18	for	for	IN
cord-002542-f7l4ty2j	224	19	RNA	RNA	NNP
cord-002542-f7l4ty2j	224	20	recombination	recombination	NN
cord-002542-f7l4ty2j	224	21	as	as	IN
cord-002542-f7l4ty2j	224	22	they	-PRON-	PRP
cord-002542-f7l4ty2j	224	23	were	be	VBD
cord-002542-f7l4ty2j	224	24	not	not	RB
cord-002542-f7l4ty2j	224	25	subject	subject	JJ
cord-002542-f7l4ty2j	224	26	to	to	IN
cord-002542-f7l4ty2j	224	27	replicative	replicative	JJ
cord-002542-f7l4ty2j	224	28	selection	selection	NN
cord-002542-f7l4ty2j	224	29	(	(	-LRB-
cord-002542-f7l4ty2j	224	30	although	although	IN
cord-002542-f7l4ty2j	224	31	they	-PRON-	PRP
cord-002542-f7l4ty2j	224	32	must	must	MD
cord-002542-f7l4ty2j	224	33	be	be	VB
cord-002542-f7l4ty2j	224	34	packaged	package	VBN
cord-002542-f7l4ty2j	224	35	by	by	IN
cord-002542-f7l4ty2j	224	36	FHV	FHV	NNP
cord-002542-f7l4ty2j	224	37	particles	particle	NNS
cord-002542-f7l4ty2j	224	38	)	)	-RRB-
cord-002542-f7l4ty2j	224	39	,	,	,
cord-002542-f7l4ty2j	224	40	unlike	unlike	IN
cord-002542-f7l4ty2j	224	41	the	the	DT
cord-002542-f7l4ty2j	224	42	DI	DI	NNP
cord-002542-f7l4ty2j	224	43	-	-	HYPH
cord-002542-f7l4ty2j	224	44	RNAs	rna	NNS
cord-002542-f7l4ty2j	224	45	.	.	.
cord-002542-f7l4ty2j	225	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	225	2	we	-PRON-	PRP
cord-002542-f7l4ty2j	225	3	extracted	extract	VBD
cord-002542-f7l4ty2j	225	4	all	all	DT
cord-002542-f7l4ty2j	225	5	recombination	recombination	NN
cord-002542-f7l4ty2j	225	6	events	event	NNS
cord-002542-f7l4ty2j	225	7	occurring	occur	VBG
cord-002542-f7l4ty2j	225	8	with	with	IN
cord-002542-f7l4ty2j	225	9	fewer	few	JJR
cord-002542-f7l4ty2j	225	10	than	than	IN
cord-002542-f7l4ty2j	225	11	10	10	CD
cord-002542-f7l4ty2j	225	12	mapped	map	VBN
cord-002542-f7l4ty2j	225	13	reads	read	NNS
cord-002542-f7l4ty2j	225	14	throughout	throughout	IN
cord-002542-f7l4ty2j	225	15	all	all	DT
cord-002542-f7l4ty2j	225	16	FHV	FHV	NNP
cord-002542-f7l4ty2j	225	17	passages	passage	NNS
cord-002542-f7l4ty2j	225	18	and	and	CC
cord-002542-f7l4ty2j	225	19	replicates	replicate	NNS
cord-002542-f7l4ty2j	225	20	(	(	-LRB-
cord-002542-f7l4ty2j	225	21	20'723	20'723	CD
cord-002542-f7l4ty2j	225	22	unique	unique	JJ
cord-002542-f7l4ty2j	225	23	events	event	NNS
cord-002542-f7l4ty2j	225	24	from	from	IN
cord-002542-f7l4ty2j	225	25	a	a	DT
cord-002542-f7l4ty2j	225	26	total	total	NN
cord-002542-f7l4ty2j	225	27	of	of	IN
cord-002542-f7l4ty2j	225	28	11.6	11.6	CD
cord-002542-f7l4ty2j	225	29	M	m	NN
cord-002542-f7l4ty2j	225	30	possible	possible	JJ
cord-002542-f7l4ty2j	225	31	permutations	permutation	NNS
cord-002542-f7l4ty2j	225	32	[	[	-LRB-
cord-002542-f7l4ty2j	225	33	8	8	CD
cord-002542-f7l4ty2j	225	34	]	]	-RRB-
cord-002542-f7l4ty2j	225	35	)	)	-RRB-
cord-002542-f7l4ty2j	225	36	and	and	CC
cord-002542-f7l4ty2j	225	37	counted	count	VBD
cord-002542-f7l4ty2j	225	38	the	the	DT
cord-002542-f7l4ty2j	225	39	frequency	frequency	NN
cord-002542-f7l4ty2j	225	40	of	of	IN
cord-002542-f7l4ty2j	225	41	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	225	42	found	find	VBN
cord-002542-f7l4ty2j	225	43	both	both	CC
cord-002542-f7l4ty2j	225	44	up	up	IN
cord-002542-f7l4ty2j	225	45	and	and	CC
cord-002542-f7l4ty2j	225	46	down	down	IN
cord-002542-f7l4ty2j	225	47	-	-	HYPH
cord-002542-f7l4ty2j	225	48	stream	stream	NN
cord-002542-f7l4ty2j	225	49	of	of	IN
cord-002542-f7l4ty2j	225	50	5	5	CD
cord-002542-f7l4ty2j	225	51	'	'	''
cord-002542-f7l4ty2j	225	52	and	and	CC
cord-002542-f7l4ty2j	225	53	3	3	CD
cord-002542-f7l4ty2j	225	54	'	'	POS
cord-002542-f7l4ty2j	225	55	recombination	recombination	NN
cord-002542-f7l4ty2j	225	56	sites	site	NNS
cord-002542-f7l4ty2j	225	57	in	in	IN
cord-002542-f7l4ty2j	225	58	the	the	DT
cord-002542-f7l4ty2j	225	59	reference	reference	NN
cord-002542-f7l4ty2j	225	60	genome	genome	NN
cord-002542-f7l4ty2j	225	61	.	.	.
cord-002542-f7l4ty2j	226	1	As	as	IN
cord-002542-f7l4ty2j	226	2	shown	show	VBN
cord-002542-f7l4ty2j	226	3	in	in	IN
cord-002542-f7l4ty2j	226	4	Fig	Fig	NNP
cord-002542-f7l4ty2j	226	5	2C	2c	NN
cord-002542-f7l4ty2j	226	6	,	,	,
cord-002542-f7l4ty2j	226	7	this	this	DT
cord-002542-f7l4ty2j	226	8	revealed	reveal	VBD
cord-002542-f7l4ty2j	226	9	a	a	DT
cord-002542-f7l4ty2j	226	10	preference	preference	NN
cord-002542-f7l4ty2j	226	11	for	for	IN
cord-002542-f7l4ty2j	226	12	A	A	NNP
cord-002542-f7l4ty2j	226	13	's	's	POS
cord-002542-f7l4ty2j	226	14	1	1	CD
cord-002542-f7l4ty2j	226	15	-	-	SYM
cord-002542-f7l4ty2j	226	16	3nts	3nts	CD
cord-002542-f7l4ty2j	226	17	downstream	downstream	NN
cord-002542-f7l4ty2j	226	18	of	of	IN
cord-002542-f7l4ty2j	226	19	5	5	CD
cord-002542-f7l4ty2j	226	20	'	'	''
cord-002542-f7l4ty2j	226	21	sites	site	NNS
cord-002542-f7l4ty2j	226	22	,	,	,
cord-002542-f7l4ty2j	226	23	a	a	DT
cord-002542-f7l4ty2j	226	24	preference	preference	NN
cord-002542-f7l4ty2j	226	25	for	for	IN
cord-002542-f7l4ty2j	226	26	U	U	NNP
cord-002542-f7l4ty2j	226	27	's	's	POS
cord-002542-f7l4ty2j	226	28	1	1	CD
cord-002542-f7l4ty2j	226	29	-	-	SYM
cord-002542-f7l4ty2j	226	30	3nts	3nt	NNS
cord-002542-f7l4ty2j	226	31	upstream	upstream	RB
cord-002542-f7l4ty2j	226	32	of	of	IN
cord-002542-f7l4ty2j	226	33	5	5	CD
cord-002542-f7l4ty2j	226	34	'	'	''
cord-002542-f7l4ty2j	226	35	sites	site	NNS
cord-002542-f7l4ty2j	226	36	,	,	,
cord-002542-f7l4ty2j	226	37	a	a	DT
cord-002542-f7l4ty2j	226	38	weaker	weak	JJR
cord-002542-f7l4ty2j	226	39	preference	preference	NN
cord-002542-f7l4ty2j	226	40	for	for	IN
cord-002542-f7l4ty2j	226	41	a	a	DT
cord-002542-f7l4ty2j	226	42	C	c	NN
cord-002542-f7l4ty2j	226	43	1nt	1nt	NN
cord-002542-f7l4ty2j	226	44	up	up	IN
cord-002542-f7l4ty2j	226	45	stream	stream	NN
cord-002542-f7l4ty2j	226	46	of	of	IN
cord-002542-f7l4ty2j	226	47	5	5	CD
cord-002542-f7l4ty2j	226	48	'	'	''
cord-002542-f7l4ty2j	226	49	sites	site	NNS
cord-002542-f7l4ty2j	226	50	,	,	,
cord-002542-f7l4ty2j	226	51	and	and	CC
cord-002542-f7l4ty2j	226	52	an	an	DT
cord-002542-f7l4ty2j	226	53	aversion	aversion	NN
cord-002542-f7l4ty2j	226	54	to	to	IN
cord-002542-f7l4ty2j	226	55	G	G	NNP
cord-002542-f7l4ty2j	226	56	's	's	POS
cord-002542-f7l4ty2j	226	57	2nts	2nts	CD
cord-002542-f7l4ty2j	226	58	both	both	CC
cord-002542-f7l4ty2j	226	59	upstream	upstream	JJ
cord-002542-f7l4ty2j	226	60	and	and	CC
cord-002542-f7l4ty2j	226	61	downstream	downstream	RB
cord-002542-f7l4ty2j	226	62	of	of	IN
cord-002542-f7l4ty2j	226	63	5	5	CD
cord-002542-f7l4ty2j	226	64	'	'	POS
cord-002542-f7l4ty2j	226	65	sites	site	NNS
cord-002542-f7l4ty2j	226	66	.	.	.
cord-002542-f7l4ty2j	227	1	Interestingly	interestingly	RB
cord-002542-f7l4ty2j	227	2	,	,	,
cord-002542-f7l4ty2j	227	3	an	an	DT
cord-002542-f7l4ty2j	227	4	almost	almost	RB
cord-002542-f7l4ty2j	227	5	identical	identical	JJ
cord-002542-f7l4ty2j	227	6	trend	trend	NN
cord-002542-f7l4ty2j	227	7	was	be	VBD
cord-002542-f7l4ty2j	227	8	observed	observe	VBN
cord-002542-f7l4ty2j	227	9	for	for	IN
cord-002542-f7l4ty2j	227	10	the	the	DT
cord-002542-f7l4ty2j	227	11	3	3	CD
cord-002542-f7l4ty2j	227	12	'	'	''
cord-002542-f7l4ty2j	227	13	sites	site	NNS
cord-002542-f7l4ty2j	227	14	.	.	.
cord-002542-f7l4ty2j	228	1	This	this	DT
cord-002542-f7l4ty2j	228	2	trend	trend	NN
cord-002542-f7l4ty2j	228	3	was	be	VBD
cord-002542-f7l4ty2j	228	4	maintained	maintain	VBN
cord-002542-f7l4ty2j	228	5	also	also	RB
cord-002542-f7l4ty2j	228	6	when	when	WRB
cord-002542-f7l4ty2j	228	7	analyzing	analyze	VBG
cord-002542-f7l4ty2j	228	8	only	only	RB
cord-002542-f7l4ty2j	228	9	recombination	recombination	NN
cord-002542-f7l4ty2j	228	10	events	event	NNS
cord-002542-f7l4ty2j	228	11	without	without	IN
cord-002542-f7l4ty2j	228	12	ambiguity	ambiguity	NN
cord-002542-f7l4ty2j	228	13	Pathways	pathway	NNS
cord-002542-f7l4ty2j	228	14	of	of	IN
cord-002542-f7l4ty2j	228	15	FHV	FHV	NNP
cord-002542-f7l4ty2j	228	16	defective	defective	JJ
cord-002542-f7l4ty2j	228	17	RNA	RNA	NNP
cord-002542-f7l4ty2j	228	18	evolution	evolution	NN
cord-002542-f7l4ty2j	228	19	by	by	IN
cord-002542-f7l4ty2j	228	20	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	228	21	and	and	CC
cord-002542-f7l4ty2j	228	22	the	the	DT
cord-002542-f7l4ty2j	228	23	MinION	MinION	NNS
cord-002542-f7l4ty2j	228	24	in	in	IN
cord-002542-f7l4ty2j	228	25	the	the	DT
cord-002542-f7l4ty2j	228	26	site	site	NN
cord-002542-f7l4ty2j	228	27	of	of	IN
cord-002542-f7l4ty2j	228	28	recombination	recombination	NN
cord-002542-f7l4ty2j	228	29	(	(	-LRB-
cord-002542-f7l4ty2j	228	30	i.e.	i.e.	FW
cord-002542-f7l4ty2j	228	31	sites	site	NNS
cord-002542-f7l4ty2j	228	32	that	that	WDT
cord-002542-f7l4ty2j	228	33	lacked	lack	VBD
cord-002542-f7l4ty2j	228	34	'	'	``
cord-002542-f7l4ty2j	228	35	fuzziness	fuzziness	NN
cord-002542-f7l4ty2j	228	36	'	'	''
cord-002542-f7l4ty2j	228	37	as	as	IN
cord-002542-f7l4ty2j	228	38	reported	report	VBN
cord-002542-f7l4ty2j	228	39	by	by	IN
cord-002542-f7l4ty2j	228	40	the	the	DT
cord-002542-f7l4ty2j	228	41	ViReMa	ViReMa	NNP
cord-002542-f7l4ty2j	228	42	pipeline	pipeline	NN
cord-002542-f7l4ty2j	228	43	[	[	-LRB-
cord-002542-f7l4ty2j	228	44	32	32	CD
cord-002542-f7l4ty2j	228	45	]	]	-RRB-
cord-002542-f7l4ty2j	228	46	)	)	-RRB-
cord-002542-f7l4ty2j	228	47	.	.	.
cord-002542-f7l4ty2j	229	1	This	this	DT
cord-002542-f7l4ty2j	229	2	result	result	NN
cord-002542-f7l4ty2j	229	3	is	be	VBZ
cord-002542-f7l4ty2j	229	4	similar	similar	JJ
cord-002542-f7l4ty2j	229	5	to	to	IN
cord-002542-f7l4ty2j	229	6	what	what	WP
cord-002542-f7l4ty2j	229	7	we	-PRON-	PRP
cord-002542-f7l4ty2j	229	8	have	have	VBP
cord-002542-f7l4ty2j	229	9	previously	previously	RB
cord-002542-f7l4ty2j	229	10	reported	report	VBN
cord-002542-f7l4ty2j	229	11	[	[	-LRB-
cord-002542-f7l4ty2j	229	12	8	8	CD
cord-002542-f7l4ty2j	229	13	]	]	-RRB-
cord-002542-f7l4ty2j	229	14	.	.	.
cord-002542-f7l4ty2j	230	1	However	however	RB
cord-002542-f7l4ty2j	230	2	,	,	,
cord-002542-f7l4ty2j	230	3	here	here	RB
cord-002542-f7l4ty2j	230	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	230	5	provide	provide	VBP
cord-002542-f7l4ty2j	230	6	a	a	DT
cord-002542-f7l4ty2j	230	7	much	much	RB
cord-002542-f7l4ty2j	230	8	larger	large	JJR
cord-002542-f7l4ty2j	230	9	dataset	dataset	NN
cord-002542-f7l4ty2j	230	10	and	and	CC
cord-002542-f7l4ty2j	230	11	analyze	analyze	VB
cord-002542-f7l4ty2j	230	12	events	event	NNS
cord-002542-f7l4ty2j	230	13	that	that	WDT
cord-002542-f7l4ty2j	230	14	we	-PRON-	PRP
cord-002542-f7l4ty2j	230	15	can	can	MD
cord-002542-f7l4ty2j	230	16	determine	determine	VB
cord-002542-f7l4ty2j	230	17	are	be	VBP
cord-002542-f7l4ty2j	230	18	not	not	RB
cord-002542-f7l4ty2j	230	19	amplified	amplify	VBN
cord-002542-f7l4ty2j	230	20	in	in	IN
cord-002542-f7l4ty2j	230	21	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	230	22	passages	passage	NNS
cord-002542-f7l4ty2j	230	23	,	,	,
cord-002542-f7l4ty2j	230	24	providing	provide	VBG
cord-002542-f7l4ty2j	230	25	greater	great	JJR
cord-002542-f7l4ty2j	230	26	confidence	confidence	NN
cord-002542-f7l4ty2j	230	27	that	that	IN
cord-002542-f7l4ty2j	230	28	these	these	DT
cord-002542-f7l4ty2j	230	29	sites	site	NNS
cord-002542-f7l4ty2j	230	30	reflect	reflect	VBP
cord-002542-f7l4ty2j	230	31	the	the	DT
cord-002542-f7l4ty2j	230	32	preference	preference	NN
cord-002542-f7l4ty2j	230	33	for	for	IN
cord-002542-f7l4ty2j	230	34	RNA	RNA	NNP
cord-002542-f7l4ty2j	230	35	recombination	recombination	NN
cord-002542-f7l4ty2j	230	36	at	at	IN
cord-002542-f7l4ty2j	230	37	these	these	DT
cord-002542-f7l4ty2j	230	38	sites	site	NNS
cord-002542-f7l4ty2j	230	39	rather	rather	RB
cord-002542-f7l4ty2j	230	40	than	than	IN
cord-002542-f7l4ty2j	230	41	the	the	DT
cord-002542-f7l4ty2j	230	42	selection	selection	NN
cord-002542-f7l4ty2j	230	43	of	of	IN
cord-002542-f7l4ty2j	230	44	replicatively	replicatively	RB
cord-002542-f7l4ty2j	230	45	viable	viable	JJ
cord-002542-f7l4ty2j	230	46	defective	defective	JJ
cord-002542-f7l4ty2j	230	47	RNA	RNA	NNP
cord-002542-f7l4ty2j	230	48	species	specie	NNS
cord-002542-f7l4ty2j	230	49	.	.	.
cord-002542-f7l4ty2j	231	1	Open	open	JJ
cord-002542-f7l4ty2j	231	2	reading	reading	NN
cord-002542-f7l4ty2j	231	3	frames	frame	NNS
cord-002542-f7l4ty2j	231	4	are	be	VBP
cord-002542-f7l4ty2j	231	5	maintained	maintain	VBN
cord-002542-f7l4ty2j	231	6	in	in	IN
cord-002542-f7l4ty2j	231	7	most	most	JJS
cord-002542-f7l4ty2j	231	8	DI	DI	NNP
cord-002542-f7l4ty2j	231	9	-	-	HYPH
cord-002542-f7l4ty2j	231	10	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	232	1	Since	since	IN
cord-002542-f7l4ty2j	232	2	many	many	JJ
cord-002542-f7l4ty2j	232	3	recombination	recombination	NN
cord-002542-f7l4ty2j	232	4	events	event	NNS
cord-002542-f7l4ty2j	232	5	resulted	result	VBD
cord-002542-f7l4ty2j	232	6	in	in	IN
cord-002542-f7l4ty2j	232	7	deletions	deletion	NNS
cord-002542-f7l4ty2j	232	8	of	of	IN
cord-002542-f7l4ty2j	232	9	the	the	DT
cord-002542-f7l4ty2j	232	10	viral	viral	JJ
cord-002542-f7l4ty2j	232	11	genome	genome	NN
cord-002542-f7l4ty2j	232	12	,	,	,
cord-002542-f7l4ty2j	232	13	we	-PRON-	PRP
cord-002542-f7l4ty2j	232	14	were	be	VBD
cord-002542-f7l4ty2j	232	15	curious	curious	JJ
cord-002542-f7l4ty2j	232	16	to	to	TO
cord-002542-f7l4ty2j	232	17	see	see	VB
cord-002542-f7l4ty2j	232	18	if	if	IN
cord-002542-f7l4ty2j	232	19	the	the	DT
cord-002542-f7l4ty2j	232	20	open	open	JJ
cord-002542-f7l4ty2j	232	21	reading	reading	NN
cord-002542-f7l4ty2j	232	22	frame	frame	NN
cord-002542-f7l4ty2j	232	23	(	(	-LRB-
cord-002542-f7l4ty2j	232	24	ORF	ORF	NNP
cord-002542-f7l4ty2j	232	25	)	)	-RRB-
cord-002542-f7l4ty2j	232	26	was	be	VBD
cord-002542-f7l4ty2j	232	27	conserved	conserve	VBN
cord-002542-f7l4ty2j	232	28	,	,	,
cord-002542-f7l4ty2j	232	29	as	as	IN
cord-002542-f7l4ty2j	232	30	conservation	conservation	NN
cord-002542-f7l4ty2j	232	31	of	of	IN
cord-002542-f7l4ty2j	232	32	an	an	DT
cord-002542-f7l4ty2j	232	33	ORF	ORF	NNP
cord-002542-f7l4ty2j	232	34	has	have	VBZ
cord-002542-f7l4ty2j	232	35	frequently	frequently	RB
cord-002542-f7l4ty2j	232	36	been	be	VBN
cord-002542-f7l4ty2j	232	37	observed	observe	VBN
cord-002542-f7l4ty2j	232	38	to	to	TO
cord-002542-f7l4ty2j	232	39	be	be	VB
cord-002542-f7l4ty2j	232	40	a	a	DT
cord-002542-f7l4ty2j	232	41	property	property	NN
cord-002542-f7l4ty2j	232	42	of	of	IN
cord-002542-f7l4ty2j	232	43	defective	defective	JJ
cord-002542-f7l4ty2j	232	44	and	and	CC
cord-002542-f7l4ty2j	232	45	defective	defective	JJ
cord-002542-f7l4ty2j	232	46	-	-	HYPH
cord-002542-f7l4ty2j	232	47	interfering	interfere	VBG
cord-002542-f7l4ty2j	232	48	RNAs	rna	NNS
cord-002542-f7l4ty2j	232	49	[	[	-LRB-
cord-002542-f7l4ty2j	232	50	58	58	CD
cord-002542-f7l4ty2j	232	51	]	]	-RRB-
cord-002542-f7l4ty2j	232	52	.	.	.
cord-002542-f7l4ty2j	233	1	Moreover	moreover	RB
cord-002542-f7l4ty2j	233	2	,	,	,
cord-002542-f7l4ty2j	233	3	it	-PRON-	PRP
cord-002542-f7l4ty2j	233	4	has	have	VBZ
cord-002542-f7l4ty2j	233	5	previously	previously	RB
cord-002542-f7l4ty2j	233	6	been	be	VBN
cord-002542-f7l4ty2j	233	7	shown	show	VBN
cord-002542-f7l4ty2j	233	8	that	that	IN
cord-002542-f7l4ty2j	233	9	cloned	clone	VBN
cord-002542-f7l4ty2j	233	10	DI	DI	NNP
cord-002542-f7l4ty2j	233	11	-	-	HYPH
cord-002542-f7l4ty2j	233	12	RNAs	rna	NNS
cord-002542-f7l4ty2j	233	13	vectors	vector	NNS
cord-002542-f7l4ty2j	233	14	containing	contain	VBG
cord-002542-f7l4ty2j	233	15	eGPF	egpf	NN
cord-002542-f7l4ty2j	233	16	in	in	IN
cord-002542-f7l4ty2j	233	17	their	-PRON-	PRP$
cord-002542-f7l4ty2j	233	18	putative	putative	JJ
cord-002542-f7l4ty2j	233	19	ORFs	orf	NNS
cord-002542-f7l4ty2j	233	20	do	do	VBP
cord-002542-f7l4ty2j	233	21	indeed	indeed	RB
cord-002542-f7l4ty2j	233	22	express	express	VB
cord-002542-f7l4ty2j	233	23	fluorescent	fluorescent	JJ
cord-002542-f7l4ty2j	233	24	protein	protein	NN
cord-002542-f7l4ty2j	233	25	[	[	-LRB-
cord-002542-f7l4ty2j	233	26	59	59	CD
cord-002542-f7l4ty2j	233	27	]	]	-RRB-
cord-002542-f7l4ty2j	233	28	although	although	IN
cord-002542-f7l4ty2j	233	29	it	-PRON-	PRP
cord-002542-f7l4ty2j	233	30	is	be	VBZ
cord-002542-f7l4ty2j	233	31	not	not	RB
cord-002542-f7l4ty2j	233	32	clear	clear	JJ
cord-002542-f7l4ty2j	233	33	whether	whether	IN
cord-002542-f7l4ty2j	233	34	a	a	DT
cord-002542-f7l4ty2j	233	35	functional	functional	JJ
cord-002542-f7l4ty2j	233	36	ORF	ORF	NNP
cord-002542-f7l4ty2j	233	37	is	be	VBZ
cord-002542-f7l4ty2j	233	38	essential	essential	JJ
cord-002542-f7l4ty2j	233	39	for	for	IN
cord-002542-f7l4ty2j	233	40	DI	DI	NNP
cord-002542-f7l4ty2j	233	41	-	-	HYPH
cord-002542-f7l4ty2j	233	42	RNA	RNA	NNP
cord-002542-f7l4ty2j	233	43	formation	formation	NN
cord-002542-f7l4ty2j	233	44	or	or	CC
cord-002542-f7l4ty2j	233	45	propagation	propagation	NN
cord-002542-f7l4ty2j	233	46	.	.	.
cord-002542-f7l4ty2j	234	1	In	in	IN
cord-002542-f7l4ty2j	234	2	the	the	DT
cord-002542-f7l4ty2j	234	3	earliest	early	JJS
cord-002542-f7l4ty2j	234	4	passages	passage	NNS
cord-002542-f7l4ty2j	234	5	,	,	,
cord-002542-f7l4ty2j	234	6	only~33	only~33	JJ
cord-002542-f7l4ty2j	234	7	%	%	NN
cord-002542-f7l4ty2j	234	8	of	of	IN
cord-002542-f7l4ty2j	234	9	deletions	deletion	NNS
cord-002542-f7l4ty2j	234	10	removed	remove	VBD
cord-002542-f7l4ty2j	234	11	a	a	DT
cord-002542-f7l4ty2j	234	12	multiple	multiple	NN
cord-002542-f7l4ty2j	234	13	of	of	IN
cord-002542-f7l4ty2j	234	14	3	3	CD
cord-002542-f7l4ty2j	234	15	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	234	16	(	(	-LRB-
cord-002542-f7l4ty2j	234	17	i.e.	i.e.	FW
cord-002542-f7l4ty2j	234	18	they	-PRON-	PRP
cord-002542-f7l4ty2j	234	19	thus	thus	RB
cord-002542-f7l4ty2j	234	20	conserved	conserve	VBD
cord-002542-f7l4ty2j	234	21	the	the	DT
cord-002542-f7l4ty2j	234	22	ORF	ORF	NNP
cord-002542-f7l4ty2j	234	23	)	)	-RRB-
cord-002542-f7l4ty2j	234	24	,	,	,
cord-002542-f7l4ty2j	234	25	as	as	IN
cord-002542-f7l4ty2j	234	26	would	would	MD
cord-002542-f7l4ty2j	234	27	be	be	VB
cord-002542-f7l4ty2j	234	28	expected	expect	VBN
cord-002542-f7l4ty2j	234	29	if	if	IN
cord-002542-f7l4ty2j	234	30	deletion	deletion	NN
cord-002542-f7l4ty2j	234	31	events	event	NNS
cord-002542-f7l4ty2j	234	32	occurred	occur	VBD
cord-002542-f7l4ty2j	234	33	randomly	randomly	RB
cord-002542-f7l4ty2j	234	34	throughout	throughout	IN
cord-002542-f7l4ty2j	234	35	the	the	DT
cord-002542-f7l4ty2j	234	36	genome	genome	NN
cord-002542-f7l4ty2j	234	37	.	.	.
cord-002542-f7l4ty2j	235	1	However	however	RB
cord-002542-f7l4ty2j	235	2	,	,	,
cord-002542-f7l4ty2j	235	3	with	with	IN
cord-002542-f7l4ty2j	235	4	continued	continue	VBN
cord-002542-f7l4ty2j	235	5	passaging	passaging	NN
cord-002542-f7l4ty2j	235	6	,	,	,
cord-002542-f7l4ty2j	235	7	there	there	EX
cord-002542-f7l4ty2j	235	8	was	be	VBD
cord-002542-f7l4ty2j	235	9	a	a	DT
cord-002542-f7l4ty2j	235	10	general	general	JJ
cord-002542-f7l4ty2j	235	11	trend	trend	NN
cord-002542-f7l4ty2j	235	12	toward	toward	IN
cord-002542-f7l4ty2j	235	13	conservation	conservation	NN
cord-002542-f7l4ty2j	235	14	of	of	IN
cord-002542-f7l4ty2j	235	15	the	the	DT
cord-002542-f7l4ty2j	235	16	ORF	ORF	NNP
cord-002542-f7l4ty2j	235	17	for	for	IN
cord-002542-f7l4ty2j	235	18	both	both	DT
cord-002542-f7l4ty2j	235	19	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	235	20	and	and	CC
cord-002542-f7l4ty2j	235	21	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	236	1	(	(	-LRB-
cord-002542-f7l4ty2j	236	2	Fig	Fig	NNP
cord-002542-f7l4ty2j	236	3	2D	2d	NN
cord-002542-f7l4ty2j	236	4	)	)	-RRB-
cord-002542-f7l4ty2j	236	5	,	,	,
cord-002542-f7l4ty2j	236	6	although	although	IN
cord-002542-f7l4ty2j	236	7	this	this	DT
cord-002542-f7l4ty2j	236	8	was	be	VBD
cord-002542-f7l4ty2j	236	9	not	not	RB
cord-002542-f7l4ty2j	236	10	the	the	DT
cord-002542-f7l4ty2j	236	11	case	case	NN
cord-002542-f7l4ty2j	236	12	for	for	IN
cord-002542-f7l4ty2j	236	13	all	all	DT
cord-002542-f7l4ty2j	236	14	replicates	replicate	NNS
cord-002542-f7l4ty2j	236	15	.	.	.
cord-002542-f7l4ty2j	237	1	Specifically	specifically	RB
cord-002542-f7l4ty2j	237	2	,	,	,
cord-002542-f7l4ty2j	237	3	while	while	IN
cord-002542-f7l4ty2j	237	4	initially	initially	RB
cord-002542-f7l4ty2j	237	5	showing	show	VBG
cord-002542-f7l4ty2j	237	6	an	an	DT
cord-002542-f7l4ty2j	237	7	increase	increase	NN
cord-002542-f7l4ty2j	237	8	in	in	IN
cord-002542-f7l4ty2j	237	9	ORF	ORF	NNP
cord-002542-f7l4ty2j	237	10	conservation	conservation	NN
cord-002542-f7l4ty2j	237	11	,	,	,
cord-002542-f7l4ty2j	237	12	replicate	replicate	VB
cord-002542-f7l4ty2j	237	13	2	2	CD
cord-002542-f7l4ty2j	237	14	of	of	IN
cord-002542-f7l4ty2j	237	15	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	237	16	showed	show	VBD
cord-002542-f7l4ty2j	237	17	a	a	DT
cord-002542-f7l4ty2j	237	18	decrease	decrease	NN
cord-002542-f7l4ty2j	237	19	in	in	IN
cord-002542-f7l4ty2j	237	20	the	the	DT
cord-002542-f7l4ty2j	237	21	conservation	conservation	NN
cord-002542-f7l4ty2j	237	22	of	of	IN
cord-002542-f7l4ty2j	237	23	the	the	DT
cord-002542-f7l4ty2j	237	24	ORF	ORF	NNP
cord-002542-f7l4ty2j	237	25	after	after	IN
cord-002542-f7l4ty2j	237	26	passage	passage	NN
cord-002542-f7l4ty2j	237	27	4	4	CD
cord-002542-f7l4ty2j	237	28	,	,	,
cord-002542-f7l4ty2j	237	29	in	in	IN
cord-002542-f7l4ty2j	237	30	contrast	contrast	NN
cord-002542-f7l4ty2j	237	31	to	to	IN
cord-002542-f7l4ty2j	237	32	the	the	DT
cord-002542-f7l4ty2j	237	33	other	other	JJ
cord-002542-f7l4ty2j	237	34	two	two	CD
cord-002542-f7l4ty2j	237	35	replicates	replicate	NNS
cord-002542-f7l4ty2j	237	36	,	,	,
cord-002542-f7l4ty2j	237	37	and	and	CC
cord-002542-f7l4ty2j	237	38	in	in	IN
cord-002542-f7l4ty2j	237	39	fact	fact	NN
cord-002542-f7l4ty2j	237	40	dips	dip	VBZ
cord-002542-f7l4ty2j	237	41	below	below	IN
cord-002542-f7l4ty2j	237	42	33	33	CD
cord-002542-f7l4ty2j	237	43	%	%	NN
cord-002542-f7l4ty2j	237	44	.	.	.
cord-002542-f7l4ty2j	238	1	Closer	close	JJR
cord-002542-f7l4ty2j	238	2	inspection	inspection	NN
cord-002542-f7l4ty2j	238	3	of	of	IN
cord-002542-f7l4ty2j	238	4	individual	individual	JJ
cord-002542-f7l4ty2j	238	5	recombination	recombination	NN
cord-002542-f7l4ty2j	238	6	events	event	NNS
cord-002542-f7l4ty2j	238	7	shows	show	VBZ
cord-002542-f7l4ty2j	238	8	that	that	IN
cord-002542-f7l4ty2j	238	9	this	this	DT
cord-002542-f7l4ty2j	238	10	trend	trend	NN
cord-002542-f7l4ty2j	238	11	is	be	VBZ
cord-002542-f7l4ty2j	238	12	driven	drive	VBN
cord-002542-f7l4ty2j	238	13	by	by	IN
cord-002542-f7l4ty2j	238	14	three	three	CD
cord-002542-f7l4ty2j	238	15	of	of	IN
cord-002542-f7l4ty2j	238	16	the	the	DT
cord-002542-f7l4ty2j	238	17	four	four	CD
cord-002542-f7l4ty2j	238	18	most	most	RBS
cord-002542-f7l4ty2j	238	19	common	common	JJ
cord-002542-f7l4ty2j	238	20	recombination	recombination	NN
cord-002542-f7l4ty2j	238	21	events	event	NNS
cord-002542-f7l4ty2j	238	22	in	in	IN
cord-002542-f7l4ty2j	238	23	replicate	replicate	VBP
cord-002542-f7l4ty2j	238	24	2	2	CD
cord-002542-f7l4ty2j	238	25	passages	passage	NNS
cord-002542-f7l4ty2j	238	26	4	4	CD
cord-002542-f7l4ty2j	238	27	to	to	TO
cord-002542-f7l4ty2j	238	28	9	9	CD
cord-002542-f7l4ty2j	238	29	:	:	SYM
cord-002542-f7l4ty2j	238	30	249	249	CD
cord-002542-f7l4ty2j	238	31	^	^	SYM
cord-002542-f7l4ty2j	238	32	517	517	CD
cord-002542-f7l4ty2j	238	33	,	,	,
cord-002542-f7l4ty2j	238	34	736	736	CD
cord-002542-f7l4ty2j	238	35	^	^	SYM
cord-002542-f7l4ty2j	238	36	1219	1219	CD
cord-002542-f7l4ty2j	238	37	,	,	,
cord-002542-f7l4ty2j	238	38	250	250	CD
cord-002542-f7l4ty2j	238	39	^	^	SYM
cord-002542-f7l4ty2j	238	40	513	513	CD
cord-002542-f7l4ty2j	238	41	and	and	CC
cord-002542-f7l4ty2j	239	1	249	249	CD
cord-002542-f7l4ty2j	239	2	^	^	NFP
cord-002542-f7l4ty2j	239	3	519	519	CD
cord-002542-f7l4ty2j	239	4	(	(	-LRB-
cord-002542-f7l4ty2j	239	5	the	the	DT
cord-002542-f7l4ty2j	239	6	latter	latter	JJ
cord-002542-f7l4ty2j	239	7	three	three	CD
cord-002542-f7l4ty2j	239	8	events	event	NNS
cord-002542-f7l4ty2j	239	9	in	in	IN
cord-002542-f7l4ty2j	239	10	bold	bold	JJ
cord-002542-f7l4ty2j	239	11	do	do	VBP
cord-002542-f7l4ty2j	239	12	not	not	RB
cord-002542-f7l4ty2j	239	13	maintain	maintain	VB
cord-002542-f7l4ty2j	239	14	the	the	DT
cord-002542-f7l4ty2j	239	15	ORF	ORF	NNP
cord-002542-f7l4ty2j	239	16	)	)	-RRB-
cord-002542-f7l4ty2j	239	17	.	.	.
cord-002542-f7l4ty2j	240	1	These	these	DT
cord-002542-f7l4ty2j	240	2	events	event	NNS
cord-002542-f7l4ty2j	240	3	are	be	VBP
cord-002542-f7l4ty2j	240	4	observed	observe	VBN
cord-002542-f7l4ty2j	240	5	in	in	IN
cord-002542-f7l4ty2j	240	6	the	the	DT
cord-002542-f7l4ty2j	240	7	other	other	JJ
cord-002542-f7l4ty2j	240	8	replicates	replicate	NNS
cord-002542-f7l4ty2j	240	9	,	,	,
cord-002542-f7l4ty2j	240	10	but	but	CC
cord-002542-f7l4ty2j	240	11	at	at	IN
cord-002542-f7l4ty2j	240	12	a	a	DT
cord-002542-f7l4ty2j	240	13	much	much	RB
cord-002542-f7l4ty2j	240	14	reduced	reduce	VBN
cord-002542-f7l4ty2j	240	15	frequency	frequency	NN
cord-002542-f7l4ty2j	240	16	(	(	-LRB-
cord-002542-f7l4ty2j	240	17	no	no	DT
cord-002542-f7l4ty2j	240	18	more	more	JJR
cord-002542-f7l4ty2j	240	19	than	than	IN
cord-002542-f7l4ty2j	240	20	1	1	CD
cord-002542-f7l4ty2j	240	21	%	%	NN
cord-002542-f7l4ty2j	240	22	of	of	IN
cord-002542-f7l4ty2j	240	23	the	the	DT
cord-002542-f7l4ty2j	240	24	total	total	JJ
cord-002542-f7l4ty2j	240	25	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	240	26	recombination	recombination	NN
cord-002542-f7l4ty2j	240	27	events	event	NNS
cord-002542-f7l4ty2j	240	28	for	for	IN
cord-002542-f7l4ty2j	240	29	reps	rep	NNS
cord-002542-f7l4ty2j	240	30	1	1	CD
cord-002542-f7l4ty2j	240	31	and	and	CC
cord-002542-f7l4ty2j	240	32	3	3	CD
cord-002542-f7l4ty2j	240	33	)	)	-RRB-
cord-002542-f7l4ty2j	240	34	(	(	-LRB-
cord-002542-f7l4ty2j	240	35	S1	S1	NNP
cord-002542-f7l4ty2j	240	36	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	240	37	)	)	-RRB-
cord-002542-f7l4ty2j	240	38	.	.	.
cord-002542-f7l4ty2j	240	39	 	 	_SP
cord-002542-f7l4ty2j	241	1	Using	use	VBG
cord-002542-f7l4ty2j	241	2	ViReMa	virema	NN
cord-002542-f7l4ty2j	241	3	,	,	,
cord-002542-f7l4ty2j	241	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	241	5	were	be	VBD
cord-002542-f7l4ty2j	241	6	able	able	JJ
cord-002542-f7l4ty2j	241	7	to	to	TO
cord-002542-f7l4ty2j	241	8	calculate	calculate	VB
cord-002542-f7l4ty2j	241	9	the	the	DT
cord-002542-f7l4ty2j	241	10	frequency	frequency	NN
cord-002542-f7l4ty2j	241	11	with	with	IN
cord-002542-f7l4ty2j	241	12	which	which	WDT
cord-002542-f7l4ty2j	241	13	each	each	DT
cord-002542-f7l4ty2j	241	14	nucleotide	nucleotide	NN
cord-002542-f7l4ty2j	241	15	was	be	VBD
cord-002542-f7l4ty2j	241	16	deleted	delete	VBN
cord-002542-f7l4ty2j	241	17	,	,	,
cord-002542-f7l4ty2j	241	18	revealing	reveal	VBG
cord-002542-f7l4ty2j	241	19	areas	area	NNS
cord-002542-f7l4ty2j	241	20	of	of	IN
cord-002542-f7l4ty2j	241	21	the	the	DT
cord-002542-f7l4ty2j	241	22	viral	viral	JJ
cord-002542-f7l4ty2j	241	23	genome	genome	NN
cord-002542-f7l4ty2j	241	24	that	that	WDT
cord-002542-f7l4ty2j	241	25	are	be	VBP
cord-002542-f7l4ty2j	241	26	conserved	conserve	VBN
cord-002542-f7l4ty2j	241	27	during	during	IN
cord-002542-f7l4ty2j	241	28	serial	serial	JJ
cord-002542-f7l4ty2j	241	29	passaging	passaging	NN
cord-002542-f7l4ty2j	241	30	and	and	CC
cord-002542-f7l4ty2j	241	31	required	require	VBN
cord-002542-f7l4ty2j	241	32	for	for	IN
cord-002542-f7l4ty2j	241	33	DI	DI	NNP
cord-002542-f7l4ty2j	241	34	-	-	HYPH
cord-002542-f7l4ty2j	241	35	RNA	RNA	NNP
cord-002542-f7l4ty2j	241	36	replication	replication	NN
cord-002542-f7l4ty2j	241	37	.	.	.
cord-002542-f7l4ty2j	242	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	242	2	plotted	plot	VBD
cord-002542-f7l4ty2j	242	3	these	these	DT
cord-002542-f7l4ty2j	242	4	data	datum	NNS
cord-002542-f7l4ty2j	242	5	to	to	TO
cord-002542-f7l4ty2j	242	6	generate	generate	VB
cord-002542-f7l4ty2j	242	7	recombination	recombination	NN
cord-002542-f7l4ty2j	242	8	profiling	profiling	NN
cord-002542-f7l4ty2j	242	9	maps	map	NNS
cord-002542-f7l4ty2j	242	10	for	for	IN
cord-002542-f7l4ty2j	242	11	each	each	DT
cord-002542-f7l4ty2j	242	12	RNA	RNA	NNP
cord-002542-f7l4ty2j	242	13	of	of	IN
cord-002542-f7l4ty2j	242	14	FHV	FHV	NNP
cord-002542-f7l4ty2j	242	15	throughout	throughout	IN
cord-002542-f7l4ty2j	242	16	passaging	passage	VBG
cord-002542-f7l4ty2j	242	17	(	(	-LRB-
cord-002542-f7l4ty2j	242	18	Fig	Fig	NNP
cord-002542-f7l4ty2j	242	19	3	3	CD
cord-002542-f7l4ty2j	242	20	and	and	CC
cord-002542-f7l4ty2j	242	21	S2	S2	NNP
cord-002542-f7l4ty2j	242	22	Fig	Fig	NNP
cord-002542-f7l4ty2j	242	23	)	)	-RRB-
cord-002542-f7l4ty2j	242	24	.	.	.
cord-002542-f7l4ty2j	243	1	In	in	IN
cord-002542-f7l4ty2j	243	2	the	the	DT
cord-002542-f7l4ty2j	243	3	first	first	JJ
cord-002542-f7l4ty2j	243	4	passage	passage	NN
cord-002542-f7l4ty2j	243	5	,	,	,
cord-002542-f7l4ty2j	243	6	there	there	EX
cord-002542-f7l4ty2j	243	7	is	be	VBZ
cord-002542-f7l4ty2j	243	8	a	a	DT
cord-002542-f7l4ty2j	243	9	relatively	relatively	RB
cord-002542-f7l4ty2j	243	10	even	even	JJ
cord-002542-f7l4ty2j	243	11	distribution	distribution	NN
cord-002542-f7l4ty2j	243	12	of	of	IN
cord-002542-f7l4ty2j	243	13	nucleotide	nucleotide	JJ
cord-002542-f7l4ty2j	243	14	deletions	deletion	NNS
cord-002542-f7l4ty2j	243	15	along	along	IN
cord-002542-f7l4ty2j	243	16	the	the	DT
cord-002542-f7l4ty2j	243	17	whole	whole	JJ
cord-002542-f7l4ty2j	243	18	length	length	NN
cord-002542-f7l4ty2j	243	19	of	of	IN
cord-002542-f7l4ty2j	243	20	the	the	DT
cord-002542-f7l4ty2j	243	21	genome	genome	NN
cord-002542-f7l4ty2j	243	22	with	with	IN
cord-002542-f7l4ty2j	243	23	the	the	DT
cord-002542-f7l4ty2j	243	24	exception	exception	NN
cord-002542-f7l4ty2j	243	25	of	of	IN
cord-002542-f7l4ty2j	243	26	two	two	CD
cord-002542-f7l4ty2j	243	27	frequently	frequently	RB
cord-002542-f7l4ty2j	243	28	excised	excise	VBN
cord-002542-f7l4ty2j	243	29	regions	region	NNS
cord-002542-f7l4ty2j	243	30	in	in	IN
cord-002542-f7l4ty2j	243	31	the	the	DT
cord-002542-f7l4ty2j	243	32	3	3	CD
cord-002542-f7l4ty2j	243	33	'	'	NN
cord-002542-f7l4ty2j	243	34	end	end	NN
cord-002542-f7l4ty2j	243	35	in	in	IN
cord-002542-f7l4ty2j	243	36	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	243	37	due	due	IN
cord-002542-f7l4ty2j	243	38	to	to	IN
cord-002542-f7l4ty2j	243	39	two	two	CD
cord-002542-f7l4ty2j	243	40	common	common	JJ
cord-002542-f7l4ty2j	243	41	recombination	recombination	NN
cord-002542-f7l4ty2j	243	42	events	event	NNS
cord-002542-f7l4ty2j	243	43	in	in	IN
cord-002542-f7l4ty2j	243	44	each	each	DT
cord-002542-f7l4ty2j	243	45	of	of	IN
cord-002542-f7l4ty2j	243	46	the	the	DT
cord-002542-f7l4ty2j	243	47	replicates	replicate	NNS
cord-002542-f7l4ty2j	243	48	:	:	:
cord-002542-f7l4ty2j	243	49	2545	2545	CD
cord-002542-f7l4ty2j	243	50	^	^	NFP
cord-002542-f7l4ty2j	243	51	2685	2685	CD
cord-002542-f7l4ty2j	243	52	and	and	CC
cord-002542-f7l4ty2j	243	53	2277	2277	CD
cord-002542-f7l4ty2j	243	54	^	^	NFP
cord-002542-f7l4ty2j	243	55	2435	2435	CD
cord-002542-f7l4ty2j	243	56	.	.	.
cord-002542-f7l4ty2j	244	1	By	by	IN
cord-002542-f7l4ty2j	244	2	passage	passage	NN
cord-002542-f7l4ty2j	244	3	3	3	CD
cord-002542-f7l4ty2j	244	4	the	the	DT
cord-002542-f7l4ty2j	244	5	deletions	deletion	NNS
cord-002542-f7l4ty2j	244	6	along	along	IN
cord-002542-f7l4ty2j	244	7	the	the	DT
cord-002542-f7l4ty2j	244	8	genomic	genomic	JJ
cord-002542-f7l4ty2j	244	9	landscape	landscape	NN
cord-002542-f7l4ty2j	244	10	begin	begin	VBP
cord-002542-f7l4ty2j	244	11	to	to	TO
cord-002542-f7l4ty2j	244	12	be	be	VB
cord-002542-f7l4ty2j	244	13	'	'	``
cord-002542-f7l4ty2j	244	14	sculpted	sculpt	VBN
cord-002542-f7l4ty2j	244	15	'	'	''
cord-002542-f7l4ty2j	244	16	whereby	whereby	WRB
cord-002542-f7l4ty2j	244	17	certain	certain	JJ
cord-002542-f7l4ty2j	244	18	regions	region	NNS
cord-002542-f7l4ty2j	244	19	are	be	VBP
cord-002542-f7l4ty2j	244	20	deleted	delete	VBN
cord-002542-f7l4ty2j	244	21	with	with	IN
cord-002542-f7l4ty2j	244	22	a	a	DT
cord-002542-f7l4ty2j	244	23	greater	great	JJR
cord-002542-f7l4ty2j	244	24	frequency	frequency	NN
cord-002542-f7l4ty2j	244	25	than	than	IN
cord-002542-f7l4ty2j	244	26	others	other	NNS
cord-002542-f7l4ty2j	244	27	.	.	.
cord-002542-f7l4ty2j	245	1	Passages	passage	NNS
cord-002542-f7l4ty2j	245	2	5	5	CD
cord-002542-f7l4ty2j	245	3	,	,	,
cord-002542-f7l4ty2j	245	4	7	7	CD
cord-002542-f7l4ty2j	245	5	,	,	,
cord-002542-f7l4ty2j	245	6	and	and	CC
cord-002542-f7l4ty2j	245	7	9	9	CD
cord-002542-f7l4ty2j	245	8	were	be	VBD
cord-002542-f7l4ty2j	245	9	sculpted	sculpt	VBN
cord-002542-f7l4ty2j	245	10	further	further	RB
cord-002542-f7l4ty2j	245	11	revealing	reveal	VBG
cord-002542-f7l4ty2j	245	12	three	three	CD
cord-002542-f7l4ty2j	245	13	major	major	JJ
cord-002542-f7l4ty2j	245	14	regions	region	NNS
cord-002542-f7l4ty2j	245	15	that	that	WDT
cord-002542-f7l4ty2j	245	16	were	be	VBD
cord-002542-f7l4ty2j	245	17	deleted	delete	VBN
cord-002542-f7l4ty2j	245	18	in	in	IN
cord-002542-f7l4ty2j	245	19	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	245	20	and	and	CC
cord-002542-f7l4ty2j	245	21	two	two	CD
cord-002542-f7l4ty2j	245	22	in	in	IN
cord-002542-f7l4ty2j	245	23	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	245	24	.	.	.
cord-002542-f7l4ty2j	246	1	Interestingly	interestingly	RB
cord-002542-f7l4ty2j	246	2	,	,	,
cord-002542-f7l4ty2j	246	3	for	for	IN
cord-002542-f7l4ty2j	246	4	both	both	DT
cord-002542-f7l4ty2j	246	5	RNA	RNA	NNP
cord-002542-f7l4ty2j	246	6	segments	segment	NNS
cord-002542-f7l4ty2j	246	7	,	,	,
cord-002542-f7l4ty2j	246	8	while	while	IN
cord-002542-f7l4ty2j	246	9	a	a	DT
cord-002542-f7l4ty2j	246	10	range	range	NN
cord-002542-f7l4ty2j	246	11	of	of	IN
cord-002542-f7l4ty2j	246	12	deletions	deletion	NNS
cord-002542-f7l4ty2j	246	13	and	and	CC
cord-002542-f7l4ty2j	246	14	rearrangements	rearrangement	NNS
cord-002542-f7l4ty2j	246	15	are	be	VBP
cord-002542-f7l4ty2j	246	16	generated	generate	VBN
cord-002542-f7l4ty2j	246	17	during	during	IN
cord-002542-f7l4ty2j	246	18	early	early	JJ
cord-002542-f7l4ty2j	246	19	passages	passage	NNS
cord-002542-f7l4ty2j	246	20	,	,	,
cord-002542-f7l4ty2j	246	21	only	only	RB
cord-002542-f7l4ty2j	246	22	the	the	DT
cord-002542-f7l4ty2j	246	23	deletions	deletion	NNS
cord-002542-f7l4ty2j	246	24	that	that	WDT
cord-002542-f7l4ty2j	246	25	maintain	maintain	VBP
cord-002542-f7l4ty2j	246	26	regulatory	regulatory	JJ
cord-002542-f7l4ty2j	246	27	and	and	CC
cord-002542-f7l4ty2j	246	28	control	control	NN
cord-002542-f7l4ty2j	246	29	elements	element	NNS
cord-002542-f7l4ty2j	246	30	are	be	VBP
cord-002542-f7l4ty2j	246	31	amplified	amplify	VBN
cord-002542-f7l4ty2j	246	32	during	during	IN
cord-002542-f7l4ty2j	246	33	continued	continued	JJ
cord-002542-f7l4ty2j	246	34	passaging	passaging	NN
cord-002542-f7l4ty2j	246	35	,	,	,
cord-002542-f7l4ty2j	246	36	as	as	IN
cord-002542-f7l4ty2j	246	37	previously	previously	RB
cord-002542-f7l4ty2j	246	38	observed	observe	VBN
cord-002542-f7l4ty2j	246	39	in	in	IN
cord-002542-f7l4ty2j	246	40	FHV	FHV	NNP
cord-002542-f7l4ty2j	246	41	[	[	-LRB-
cord-002542-f7l4ty2j	246	42	32	32	CD
cord-002542-f7l4ty2j	246	43	]	]	-RRB-
cord-002542-f7l4ty2j	246	44	.	.	.
cord-002542-f7l4ty2j	247	1	These	these	DT
cord-002542-f7l4ty2j	247	2	include	include	VBP
cord-002542-f7l4ty2j	247	3	the	the	DT
cord-002542-f7l4ty2j	247	4	5'/3	5'/3	CD
cord-002542-f7l4ty2j	247	5	'	'	POS
cord-002542-f7l4ty2j	247	6	UTRs	utr	NNS
cord-002542-f7l4ty2j	247	7	and	and	CC
cord-002542-f7l4ty2j	247	8	internal	internal	JJ
cord-002542-f7l4ty2j	247	9	response	response	NN
cord-002542-f7l4ty2j	247	10	elements	element	NNS
cord-002542-f7l4ty2j	247	11	(	(	-LRB-
cord-002542-f7l4ty2j	247	12	intRE	intRE	NNP
cord-002542-f7l4ty2j	247	13	)	)	-RRB-
cord-002542-f7l4ty2j	247	14	of	of	IN
cord-002542-f7l4ty2j	247	15	both	both	DT
cord-002542-f7l4ty2j	247	16	genomes	genome	NNS
cord-002542-f7l4ty2j	247	17	,	,	,
cord-002542-f7l4ty2j	247	18	as	as	RB
cord-002542-f7l4ty2j	247	19	well	well	RB
cord-002542-f7l4ty2j	247	20	as	as	IN
cord-002542-f7l4ty2j	247	21	the	the	DT
cord-002542-f7l4ty2j	247	22	Proximal	Proximal	NNP
cord-002542-f7l4ty2j	247	23	-	-	:
cord-002542-f7l4ty2j	247	24	and	and	CC
cord-002542-f7l4ty2j	247	25	Distal	Distal	NNP
cord-002542-f7l4ty2j	247	26	-	-	HYPH
cord-002542-f7l4ty2j	247	27	Subgenomic	Subgenomic	NNP
cord-002542-f7l4ty2j	247	28	Control	Control	NNP
cord-002542-f7l4ty2j	247	29	Elements	Elements	NNP
cord-002542-f7l4ty2j	247	30	(	(	-LRB-
cord-002542-f7l4ty2j	247	31	PSCE	PSCE	NNP
cord-002542-f7l4ty2j	247	32	and	and	CC
cord-002542-f7l4ty2j	247	33	DSCE	DSCE	NNP
cord-002542-f7l4ty2j	247	34	)	)	-RRB-
cord-002542-f7l4ty2j	247	35	in	in	IN
cord-002542-f7l4ty2j	247	36	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	247	37	(	(	-LRB-
cord-002542-f7l4ty2j	247	38	Fig	Fig	NNP
cord-002542-f7l4ty2j	247	39	3	3	CD
cord-002542-f7l4ty2j	247	40	)	)	-RRB-
cord-002542-f7l4ty2j	247	41	,	,	,
cord-002542-f7l4ty2j	247	42	which	which	WDT
cord-002542-f7l4ty2j	247	43	correlates	correlate	VBZ
cord-002542-f7l4ty2j	247	44	to	to	IN
cord-002542-f7l4ty2j	247	45	the	the	DT
cord-002542-f7l4ty2j	247	46	findings	finding	NNS
cord-002542-f7l4ty2j	247	47	that	that	IN
cord-002542-f7l4ty2j	247	48	these	these	DT
cord-002542-f7l4ty2j	247	49	regions	region	NNS
cord-002542-f7l4ty2j	247	50	are	be	VBP
cord-002542-f7l4ty2j	247	51	important	important	JJ
cord-002542-f7l4ty2j	247	52	and	and	CC
cord-002542-f7l4ty2j	247	53	required	require	VBN
cord-002542-f7l4ty2j	247	54	for	for	IN
cord-002542-f7l4ty2j	247	55	RNA	RNA	NNP
cord-002542-f7l4ty2j	247	56	replication	replication	NN
cord-002542-f7l4ty2j	247	57	and	and	CC
cord-002542-f7l4ty2j	247	58	encapsidation	encapsidation	NN
cord-002542-f7l4ty2j	247	59	[	[	-LRB-
cord-002542-f7l4ty2j	247	60	29	29	CD
cord-002542-f7l4ty2j	247	61	,	,	,
cord-002542-f7l4ty2j	247	62	30	30	CD
cord-002542-f7l4ty2j	247	63	,	,	,
cord-002542-f7l4ty2j	247	64	32	32	CD
cord-002542-f7l4ty2j	247	65	,	,	,
cord-002542-f7l4ty2j	247	66	[	[	-LRB-
cord-002542-f7l4ty2j	247	67	60	60	CD
cord-002542-f7l4ty2j	247	68	]	]	-RRB-
cord-002542-f7l4ty2j	247	69	[	[	-LRB-
cord-002542-f7l4ty2j	247	70	61	61	CD
cord-002542-f7l4ty2j	247	71	]	]	-RRB-
cord-002542-f7l4ty2j	247	72	[	[	-LRB-
cord-002542-f7l4ty2j	247	73	62	62	CD
cord-002542-f7l4ty2j	247	74	]	]	-RRB-
cord-002542-f7l4ty2j	247	75	[	[	-LRB-
cord-002542-f7l4ty2j	247	76	63	63	CD
cord-002542-f7l4ty2j	247	77	]	]	-RRB-
cord-002542-f7l4ty2j	247	78	[	[	-LRB-
cord-002542-f7l4ty2j	247	79	64	64	CD
cord-002542-f7l4ty2j	247	80	]	]	-RRB-
cord-002542-f7l4ty2j	247	81	.	.	.
cord-002542-f7l4ty2j	248	1	The	the	DT
cord-002542-f7l4ty2j	248	2	short	short	RB
cord-002542-f7l4ty2j	248	3	-	-	HYPH
cord-002542-f7l4ty2j	248	4	read	read	VBN
cord-002542-f7l4ty2j	248	5	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	248	6	data	datum	NNS
cord-002542-f7l4ty2j	248	7	provide	provide	VBP
cord-002542-f7l4ty2j	248	8	in	in	IN
cord-002542-f7l4ty2j	248	9	-	-	HYPH
cord-002542-f7l4ty2j	248	10	depth	depth	NN
cord-002542-f7l4ty2j	248	11	and	and	CC
cord-002542-f7l4ty2j	248	12	high	high	JJ
cord-002542-f7l4ty2j	248	13	resolution	resolution	NN
cord-002542-f7l4ty2j	248	14	details	detail	NNS
cord-002542-f7l4ty2j	248	15	of	of	IN
cord-002542-f7l4ty2j	248	16	individual	individual	JJ
cord-002542-f7l4ty2j	248	17	recombination	recombination	NN
cord-002542-f7l4ty2j	248	18	events	event	NNS
cord-002542-f7l4ty2j	248	19	.	.	.
cord-002542-f7l4ty2j	249	1	However	however	RB
cord-002542-f7l4ty2j	249	2	,	,	,
cord-002542-f7l4ty2j	249	3	in	in	IN
cord-002542-f7l4ty2j	249	4	order	order	NN
cord-002542-f7l4ty2j	249	5	to	to	TO
cord-002542-f7l4ty2j	249	6	determine	determine	VB
cord-002542-f7l4ty2j	249	7	the	the	DT
cord-002542-f7l4ty2j	249	8	correlation	correlation	NN
cord-002542-f7l4ty2j	249	9	of	of	IN
cord-002542-f7l4ty2j	249	10	these	these	DT
cord-002542-f7l4ty2j	249	11	events	event	NNS
cord-002542-f7l4ty2j	249	12	over	over	IN
cord-002542-f7l4ty2j	249	13	time	time	NN
cord-002542-f7l4ty2j	249	14	,	,	,
cord-002542-f7l4ty2j	249	15	we	-PRON-	PRP
cord-002542-f7l4ty2j	249	16	used	use	VBD
cord-002542-f7l4ty2j	249	17	long	long	RB
cord-002542-f7l4ty2j	249	18	-	-	HYPH
cord-002542-f7l4ty2j	249	19	read	read	VBN
cord-002542-f7l4ty2j	249	20	ONT	ONT	NNP
cord-002542-f7l4ty2j	249	21	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	249	22	sequencing	sequencing	NN
cord-002542-f7l4ty2j	249	23	,	,	,
cord-002542-f7l4ty2j	249	24	which	which	WDT
cord-002542-f7l4ty2j	249	25	can	can	MD
cord-002542-f7l4ty2j	249	26	characterize	characterize	VB
cord-002542-f7l4ty2j	249	27	full	full	JJ
cord-002542-f7l4ty2j	249	28	-	-	HYPH
cord-002542-f7l4ty2j	249	29	length	length	NN
cord-002542-f7l4ty2j	249	30	wildtype	wildtype	NN
cord-002542-f7l4ty2j	249	31	and	and	CC
cord-002542-f7l4ty2j	249	32	defective	defective	JJ
cord-002542-f7l4ty2j	249	33	genomes	genome	NNS
cord-002542-f7l4ty2j	249	34	(	(	-LRB-
cord-002542-f7l4ty2j	249	35	Fig	Fig	NNP
cord-002542-f7l4ty2j	249	36	4	4	CD
cord-002542-f7l4ty2j	249	37	and	and	CC
cord-002542-f7l4ty2j	249	38	S4	S4	NNP
cord-002542-f7l4ty2j	249	39	Fig	Fig	NNP
cord-002542-f7l4ty2j	249	40	)	)	-RRB-
cord-002542-f7l4ty2j	249	41	.	.	.
cord-002542-f7l4ty2j	250	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	250	2	reverse	reverse	VBP
cord-002542-f7l4ty2j	250	3	transcribed	transcribe	VBN
cord-002542-f7l4ty2j	250	4	and	and	CC
cord-002542-f7l4ty2j	250	5	amplified	amplify	VBN
cord-002542-f7l4ty2j	250	6	both	both	DT
cord-002542-f7l4ty2j	250	7	RNA	RNA	NNP
cord-002542-f7l4ty2j	250	8	genes	gene	NNS
cord-002542-f7l4ty2j	250	9	using	use	VBG
cord-002542-f7l4ty2j	250	10	primers	primer	NNS
cord-002542-f7l4ty2j	250	11	specific	specific	JJ
cord-002542-f7l4ty2j	250	12	to	to	IN
cord-002542-f7l4ty2j	250	13	the	the	DT
cord-002542-f7l4ty2j	250	14	5	5	CD
cord-002542-f7l4ty2j	250	15	'	'	''
cord-002542-f7l4ty2j	250	16	and	and	CC
cord-002542-f7l4ty2j	250	17	3	3	CD
cord-002542-f7l4ty2j	250	18	'	'	POS
cord-002542-f7l4ty2j	250	19	UTRs	utr	NNS
cord-002542-f7l4ty2j	250	20	of	of	IN
cord-002542-f7l4ty2j	250	21	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	250	22	and	and	CC
cord-002542-f7l4ty2j	250	23	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	250	24	from	from	IN
cord-002542-f7l4ty2j	250	25	all	all	DT
cord-002542-f7l4ty2j	250	26	passages	passage	NNS
cord-002542-f7l4ty2j	250	27	of	of	IN
cord-002542-f7l4ty2j	250	28	replicate	replicate	VB
cord-002542-f7l4ty2j	250	29	2	2	CD
cord-002542-f7l4ty2j	250	30	to	to	TO
cord-002542-f7l4ty2j	250	31	obtain	obtain	VB
cord-002542-f7l4ty2j	250	32	cDNA	cdna	NN
cord-002542-f7l4ty2j	250	33	that	that	WDT
cord-002542-f7l4ty2j	250	34	could	could	MD
cord-002542-f7l4ty2j	250	35	be	be	VB
cord-002542-f7l4ty2j	250	36	barcoded	barcode	VBN
cord-002542-f7l4ty2j	250	37	and	and	CC
cord-002542-f7l4ty2j	250	38	analyzed	analyze	VBN
cord-002542-f7l4ty2j	250	39	using	use	VBG
cord-002542-f7l4ty2j	250	40	protocols	protocol	NNS
cord-002542-f7l4ty2j	250	41	for	for	IN
cord-002542-f7l4ty2j	250	42	2D	2d	NN
cord-002542-f7l4ty2j	250	43	sequencing	sequencing	NN
cord-002542-f7l4ty2j	250	44	on	on	IN
cord-002542-f7l4ty2j	250	45	the	the	DT
cord-002542-f7l4ty2j	250	46	ONT	ONT	NNP
cord-002542-f7l4ty2j	250	47	MinION	minion	NN
cord-002542-f7l4ty2j	250	48	.	.	.
cord-002542-f7l4ty2j	251	1	The	the	DT
cord-002542-f7l4ty2j	251	2	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	251	3	data	datum	NNS
cord-002542-f7l4ty2j	251	4	shows	show	VBZ
cord-002542-f7l4ty2j	251	5	that	that	IN
cord-002542-f7l4ty2j	251	6	these	these	DT
cord-002542-f7l4ty2j	251	7	regions	region	NNS
cord-002542-f7l4ty2j	251	8	were	be	VBD
cord-002542-f7l4ty2j	251	9	highly	highly	RB
cord-002542-f7l4ty2j	251	10	conserved	conserve	VBN
cord-002542-f7l4ty2j	251	11	during	during	IN
cord-002542-f7l4ty2j	251	12	passaging	passage	VBG
cord-002542-f7l4ty2j	251	13	(	(	-LRB-
cord-002542-f7l4ty2j	251	14	Fig	Fig	NNP
cord-002542-f7l4ty2j	251	15	3	3	CD
cord-002542-f7l4ty2j	251	16	)	)	-RRB-
cord-002542-f7l4ty2j	251	17	,	,	,
cord-002542-f7l4ty2j	251	18	therefore	therefore	RB
cord-002542-f7l4ty2j	251	19	we	-PRON-	PRP
cord-002542-f7l4ty2j	251	20	were	be	VBD
cord-002542-f7l4ty2j	251	21	confident	confident	JJ
cord-002542-f7l4ty2j	251	22	using	use	VBG
cord-002542-f7l4ty2j	251	23	template	template	NN
cord-002542-f7l4ty2j	251	24	-	-	HYPH
cord-002542-f7l4ty2j	251	25	specific	specific	JJ
cord-002542-f7l4ty2j	251	26	primers	primer	NNS
cord-002542-f7l4ty2j	251	27	to	to	IN
cord-002542-f7l4ty2j	251	28	these	these	DT
cord-002542-f7l4ty2j	251	29	regions	region	NNS
cord-002542-f7l4ty2j	251	30	would	would	MD
cord-002542-f7l4ty2j	251	31	capture	capture	VB
cord-002542-f7l4ty2j	251	32	both	both	CC
cord-002542-f7l4ty2j	251	33	the	the	DT
cord-002542-f7l4ty2j	251	34	full	full	JJ
cord-002542-f7l4ty2j	251	35	-	-	HYPH
cord-002542-f7l4ty2j	251	36	length	length	NN
cord-002542-f7l4ty2j	251	37	wild	wild	JJ
cord-002542-f7l4ty2j	251	38	-	-	HYPH
cord-002542-f7l4ty2j	251	39	type	type	NN
cord-002542-f7l4ty2j	251	40	virus	virus	NN
cord-002542-f7l4ty2j	251	41	genomes	genome	NNS
cord-002542-f7l4ty2j	251	42	as	as	RB
cord-002542-f7l4ty2j	251	43	well	well	RB
cord-002542-f7l4ty2j	251	44	as	as	IN
cord-002542-f7l4ty2j	251	45	any	any	DT
cord-002542-f7l4ty2j	251	46	defective	defective	JJ
cord-002542-f7l4ty2j	251	47	RNAs	rna	NNS
cord-002542-f7l4ty2j	251	48	.	.	.
cord-002542-f7l4ty2j	252	1	After	after	IN
cord-002542-f7l4ty2j	252	2	PCR	PCR	NNP
cord-002542-f7l4ty2j	252	3	amplification	amplification	NN
cord-002542-f7l4ty2j	252	4	,	,	,
cord-002542-f7l4ty2j	252	5	we	-PRON-	PRP
cord-002542-f7l4ty2j	252	6	analyzed	analyze	VBD
cord-002542-f7l4ty2j	252	7	the	the	DT
cord-002542-f7l4ty2j	252	8	MinION	minion	FW
cord-002542-f7l4ty2j	252	9	cDNA	cdna	NN
cord-002542-f7l4ty2j	252	10	libraries	library	NNS
cord-002542-f7l4ty2j	252	11	using	use	VBG
cord-002542-f7l4ty2j	252	12	agarose	agarose	VBN
cord-002542-f7l4ty2j	252	13	gel	gel	NN
cord-002542-f7l4ty2j	252	14	electrophoresis	electrophoresis	NN
cord-002542-f7l4ty2j	252	15	to	to	TO
cord-002542-f7l4ty2j	252	16	observe	observe	VB
cord-002542-f7l4ty2j	252	17	the	the	DT
cord-002542-f7l4ty2j	252	18	distribution	distribution	NN
cord-002542-f7l4ty2j	252	19	of	of	IN
cord-002542-f7l4ty2j	252	20	cDNA	cdna	NN
cord-002542-f7l4ty2j	252	21	fragments	fragment	NNS
cord-002542-f7l4ty2j	252	22	and	and	CC
cord-002542-f7l4ty2j	252	23	ratios	ratio	NNS
cord-002542-f7l4ty2j	252	24	of	of	IN
cord-002542-f7l4ty2j	252	25	full	full	JJ
cord-002542-f7l4ty2j	252	26	-	-	HYPH
cord-002542-f7l4ty2j	252	27	length	length	NN
cord-002542-f7l4ty2j	252	28	to	to	IN
cord-002542-f7l4ty2j	252	29	defective	defective	JJ
cord-002542-f7l4ty2j	252	30	RNA	RNA	NNP
cord-002542-f7l4ty2j	252	31	genomes	genome	NNS
cord-002542-f7l4ty2j	252	32	(	(	-LRB-
cord-002542-f7l4ty2j	252	33	Fig	Fig	NNP
cord-002542-f7l4ty2j	252	34	5A	5a	NN
cord-002542-f7l4ty2j	252	35	)	)	-RRB-
cord-002542-f7l4ty2j	252	36	.	.	.
cord-002542-f7l4ty2j	253	1	While	while	IN
cord-002542-f7l4ty2j	253	2	the	the	DT
cord-002542-f7l4ty2j	253	3	cDNAs	cdna	NNS
cord-002542-f7l4ty2j	253	4	from	from	IN
cord-002542-f7l4ty2j	253	5	the	the	DT
cord-002542-f7l4ty2j	253	6	early	early	JJ
cord-002542-f7l4ty2j	253	7	passages	passage	NNS
cord-002542-f7l4ty2j	253	8	are	be	VBP
cord-002542-f7l4ty2j	253	9	predominantly	predominantly	RB
cord-002542-f7l4ty2j	253	10	of	of	IN
cord-002542-f7l4ty2j	253	11	the	the	DT
cord-002542-f7l4ty2j	253	12	expected	expect	VBN
cord-002542-f7l4ty2j	253	13	size	size	NN
cord-002542-f7l4ty2j	253	14	for	for	IN
cord-002542-f7l4ty2j	253	15	full	full	JJ
cord-002542-f7l4ty2j	253	16	-	-	HYPH
cord-002542-f7l4ty2j	253	17	length	length	NN
cord-002542-f7l4ty2j	253	18	RNA	RNA	NNP
cord-002542-f7l4ty2j	253	19	genomes	genome	NNS
cord-002542-f7l4ty2j	253	20	,	,	,
cord-002542-f7l4ty2j	253	21	later	later	RB
cord-002542-f7l4ty2j	253	22	passages	passage	NNS
cord-002542-f7l4ty2j	253	23	contain	contain	VBP
cord-002542-f7l4ty2j	253	24	an	an	DT
cord-002542-f7l4ty2j	253	25	array	array	NN
cord-002542-f7l4ty2j	253	26	of	of	IN
cord-002542-f7l4ty2j	253	27	band	band	NN
cord-002542-f7l4ty2j	253	28	sizes	size	NNS
cord-002542-f7l4ty2j	253	29	.	.	.
cord-002542-f7l4ty2j	254	1	This	this	DT
cord-002542-f7l4ty2j	254	2	shows	show	VBZ
cord-002542-f7l4ty2j	254	3	that	that	IN
cord-002542-f7l4ty2j	254	4	in	in	IN
cord-002542-f7l4ty2j	254	5	the	the	DT
cord-002542-f7l4ty2j	254	6	early	early	JJ
cord-002542-f7l4ty2j	254	7	passages	passage	NNS
cord-002542-f7l4ty2j	254	8	the	the	DT
cord-002542-f7l4ty2j	254	9	full	full	JJ
cord-002542-f7l4ty2j	254	10	-	-	HYPH
cord-002542-f7l4ty2j	254	11	length	length	NN
cord-002542-f7l4ty2j	254	12	genome	genome	NN
cord-002542-f7l4ty2j	254	13	is	be	VBZ
cord-002542-f7l4ty2j	254	14	the	the	DT
cord-002542-f7l4ty2j	254	15	predominant	predominant	JJ
cord-002542-f7l4ty2j	254	16	species	specie	NNS
cord-002542-f7l4ty2j	254	17	while	while	IN
cord-002542-f7l4ty2j	254	18	in	in	IN
cord-002542-f7l4ty2j	254	19	later	later	JJ
cord-002542-f7l4ty2j	254	20	passages	passage	VBZ
cord-002542-f7l4ty2j	254	21	the	the	DT
cord-002542-f7l4ty2j	254	22	truncated	truncated	JJ
cord-002542-f7l4ty2j	254	23	version	version	NN
cord-002542-f7l4ty2j	254	24	becomes	become	VBZ
cord-002542-f7l4ty2j	254	25	predominant	predominant	JJ
cord-002542-f7l4ty2j	254	26	.	.	.
cord-002542-f7l4ty2j	255	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	255	2	also	also	RB
cord-002542-f7l4ty2j	255	3	observe	observe	VBP
cord-002542-f7l4ty2j	255	4	species	specie	NNS
cord-002542-f7l4ty2j	255	5	appearing	appear	VBG
cord-002542-f7l4ty2j	255	6	to	to	TO
cord-002542-f7l4ty2j	255	7	be	be	VB
cord-002542-f7l4ty2j	255	8	larger	large	JJR
cord-002542-f7l4ty2j	255	9	than	than	IN
cord-002542-f7l4ty2j	255	10	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	255	11	.	.	.
cord-002542-f7l4ty2j	256	1	It	-PRON-	PRP
cord-002542-f7l4ty2j	256	2	is	be	VBZ
cord-002542-f7l4ty2j	256	3	possible	possible	JJ
cord-002542-f7l4ty2j	256	4	that	that	IN
cord-002542-f7l4ty2j	256	5	some	some	DT
cord-002542-f7l4ty2j	256	6	of	of	IN
cord-002542-f7l4ty2j	256	7	these	these	DT
cord-002542-f7l4ty2j	256	8	species	specie	NNS
cord-002542-f7l4ty2j	256	9	correspond	correspond	VBP
cord-002542-f7l4ty2j	256	10	to	to	IN
cord-002542-f7l4ty2j	256	11	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	256	12	homodimers	homodimer	NNS
cord-002542-f7l4ty2j	256	13	or	or	CC
cord-002542-f7l4ty2j	256	14	other	other	JJ
cord-002542-f7l4ty2j	256	15	complex	complex	JJ
cord-002542-f7l4ty2j	256	16	rearrangements	rearrangement	NNS
cord-002542-f7l4ty2j	256	17	that	that	WDT
cord-002542-f7l4ty2j	256	18	have	have	VBP
cord-002542-f7l4ty2j	256	19	previously	previously	RB
cord-002542-f7l4ty2j	256	20	been	be	VBN
cord-002542-f7l4ty2j	256	21	observed	observe	VBN
cord-002542-f7l4ty2j	256	22	[	[	-LRB-
cord-002542-f7l4ty2j	256	23	65	65	CD
cord-002542-f7l4ty2j	256	24	]	]	-RRB-
cord-002542-f7l4ty2j	256	25	and	and	CC
cord-002542-f7l4ty2j	256	26	would	would	MD
cord-002542-f7l4ty2j	256	27	result	result	VB
cord-002542-f7l4ty2j	256	28	in	in	IN
cord-002542-f7l4ty2j	256	29	an	an	DT
cord-002542-f7l4ty2j	256	30	increased	increase	VBN
cord-002542-f7l4ty2j	256	31	molecular	molecular	JJ
cord-002542-f7l4ty2j	256	32	weight	weight	NN
cord-002542-f7l4ty2j	256	33	.	.	.
cord-002542-f7l4ty2j	257	1	Evidence	evidence	NN
cord-002542-f7l4ty2j	257	2	of	of	IN
cord-002542-f7l4ty2j	257	3	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	257	4	homodimers	homodimer	NNS
cord-002542-f7l4ty2j	257	5	(	(	-LRB-
cord-002542-f7l4ty2j	257	6	3107	3107	CD
cord-002542-f7l4ty2j	257	7	^	^	SYM
cord-002542-f7l4ty2j	257	8	1	1	CD
cord-002542-f7l4ty2j	257	9	)	)	-RRB-
cord-002542-f7l4ty2j	257	10	,	,	,
cord-002542-f7l4ty2j	257	11	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	257	12	homodimers	homodimer	NNS
cord-002542-f7l4ty2j	257	13	(	(	-LRB-
cord-002542-f7l4ty2j	257	14	1400	1400	CD
cord-002542-f7l4ty2j	257	15	^	^	SYM
cord-002542-f7l4ty2j	257	16	1	1	CD
cord-002542-f7l4ty2j	257	17	)	)	-RRB-
cord-002542-f7l4ty2j	257	18	,	,	,
cord-002542-f7l4ty2j	257	19	and	and	CC
cord-002542-f7l4ty2j	257	20	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	257	21	to	to	IN
cord-002542-f7l4ty2j	257	22	RNA3	RNA3	NNP
cord-002542-f7l4ty2j	257	23	heterodimers	heterodimer	NNS
cord-002542-f7l4ty2j	257	24	(	(	-LRB-
cord-002542-f7l4ty2j	257	25	1400	1400	CD
cord-002542-f7l4ty2j	257	26	^	^	SYM
cord-002542-f7l4ty2j	257	27	2720	2720	CD
cord-002542-f7l4ty2j	257	28	)	)	-RRB-
cord-002542-f7l4ty2j	257	29	can	can	MD
cord-002542-f7l4ty2j	257	30	also	also	RB
cord-002542-f7l4ty2j	257	31	be	be	VB
cord-002542-f7l4ty2j	257	32	found	find	VBN
cord-002542-f7l4ty2j	257	33	in	in	IN
cord-002542-f7l4ty2j	257	34	the	the	DT
cord-002542-f7l4ty2j	257	35	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	257	36	data	datum	NNS
cord-002542-f7l4ty2j	257	37	(	(	-LRB-
cord-002542-f7l4ty2j	257	38	S1	S1	NNP
cord-002542-f7l4ty2j	257	39	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	257	40	)	)	-RRB-
cord-002542-f7l4ty2j	257	41	.	.	.
cord-002542-f7l4ty2j	258	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	258	2	pooled	pool	VBD
cord-002542-f7l4ty2j	258	3	the	the	DT
cord-002542-f7l4ty2j	258	4	amplified	amplify	VBN
cord-002542-f7l4ty2j	258	5	cDNAs	cDNAs	NNPS
cord-002542-f7l4ty2j	258	6	from	from	IN
cord-002542-f7l4ty2j	258	7	each	each	DT
cord-002542-f7l4ty2j	258	8	sample	sample	NN
cord-002542-f7l4ty2j	258	9	at	at	IN
cord-002542-f7l4ty2j	258	10	equimolar	equimolar	NNP
cord-002542-f7l4ty2j	258	11	ratios	ratio	NNS
cord-002542-f7l4ty2j	258	12	and	and	CC
cord-002542-f7l4ty2j	258	13	loaded	load	VBD
cord-002542-f7l4ty2j	258	14	the	the	DT
cord-002542-f7l4ty2j	258	15	pooled	pool	VBN
cord-002542-f7l4ty2j	258	16	,	,	,
cord-002542-f7l4ty2j	258	17	barcoded	barcoded	JJ
cord-002542-f7l4ty2j	258	18	library	library	NN
cord-002542-f7l4ty2j	258	19	onto	onto	IN
cord-002542-f7l4ty2j	258	20	a	a	DT
cord-002542-f7l4ty2j	258	21	MinION	MinION	NNP
cord-002542-f7l4ty2j	258	22	MkIB	MkIB	NNP
cord-002542-f7l4ty2j	258	23	device	device	NN
cord-002542-f7l4ty2j	258	24	using	use	VBG
cord-002542-f7l4ty2j	258	25	an	an	DT
cord-002542-f7l4ty2j	258	26	R9	R9	NNP
cord-002542-f7l4ty2j	258	27	flowcell	flowcell	NNP
cord-002542-f7l4ty2j	258	28	as	as	IN
cord-002542-f7l4ty2j	258	29	per	per	IN
cord-002542-f7l4ty2j	258	30	the	the	DT
cord-002542-f7l4ty2j	258	31	manufacture	manufacture	NN
cord-002542-f7l4ty2j	258	32	's	's	POS
cord-002542-f7l4ty2j	258	33	protocol	protocol	NN
cord-002542-f7l4ty2j	258	34	.	.	.
cord-002542-f7l4ty2j	259	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	259	2	ran	run	VBD
cord-002542-f7l4ty2j	259	3	the	the	DT
cord-002542-f7l4ty2j	259	4	standard	standard	JJ
cord-002542-f7l4ty2j	259	5	protocol	protocol	NN
cord-002542-f7l4ty2j	259	6	for	for	IN
cord-002542-f7l4ty2j	259	7	obtaining	obtain	VBG
cord-002542-f7l4ty2j	259	8	2-dimensional	2-dimensional	JJ
cord-002542-f7l4ty2j	259	9	reads	read	NNS
cord-002542-f7l4ty2j	259	10	using	use	VBG
cord-002542-f7l4ty2j	259	11	the	the	DT
cord-002542-f7l4ty2j	259	12	MinKNOW	minknow	JJ
cord-002542-f7l4ty2j	259	13	control	control	NN
cord-002542-f7l4ty2j	259	14	software	software	NN
cord-002542-f7l4ty2j	259	15	and	and	CC
cord-002542-f7l4ty2j	259	16	collected	collect	VBD
cord-002542-f7l4ty2j	259	17	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	259	18	reads	read	VBZ
cord-002542-f7l4ty2j	259	19	for	for	IN
cord-002542-f7l4ty2j	259	20	approximately	approximately	RB
cord-002542-f7l4ty2j	259	21	36	36	CD
cord-002542-f7l4ty2j	259	22	hours	hour	NNS
cord-002542-f7l4ty2j	259	23	,	,	,
cord-002542-f7l4ty2j	259	24	upon	upon	IN
cord-002542-f7l4ty2j	259	25	which	which	WDT
cord-002542-f7l4ty2j	259	26	the	the	DT
cord-002542-f7l4ty2j	259	27	quality	quality	NN
cord-002542-f7l4ty2j	259	28	and	and	CC
cord-002542-f7l4ty2j	259	29	yield	yield	NN
cord-002542-f7l4ty2j	259	30	of	of	IN
cord-002542-f7l4ty2j	259	31	reads	read	NNS
cord-002542-f7l4ty2j	259	32	dropped	drop	VBN
cord-002542-f7l4ty2j	259	33	substantially	substantially	RB
cord-002542-f7l4ty2j	259	34	.	.	.
cord-002542-f7l4ty2j	260	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	260	2	obtained	obtain	VBD
cord-002542-f7l4ty2j	260	3	a	a	DT
cord-002542-f7l4ty2j	260	4	total	total	NN
cord-002542-f7l4ty2j	260	5	of	of	IN
cord-002542-f7l4ty2j	260	6	169'814	169'814	CD
cord-002542-f7l4ty2j	260	7	reads	read	NNS
cord-002542-f7l4ty2j	260	8	,	,	,
cord-002542-f7l4ty2j	260	9	of	of	IN
cord-002542-f7l4ty2j	260	10	which	which	WDT
cord-002542-f7l4ty2j	260	11	46'183	46'183	CD
cord-002542-f7l4ty2j	260	12	passed	pass	VBD
cord-002542-f7l4ty2j	260	13	the	the	DT
cord-002542-f7l4ty2j	260	14	default	default	NN
cord-002542-f7l4ty2j	260	15	ONT	ONT	NNP
cord-002542-f7l4ty2j	260	16	filter	filter	NN
cord-002542-f7l4ty2j	260	17	and	and	CC
cord-002542-f7l4ty2j	260	18	were	be	VBD
cord-002542-f7l4ty2j	260	19	successfully	successfully	RB
cord-002542-f7l4ty2j	260	20	demultiplexed	demultiplexe	VBN
cord-002542-f7l4ty2j	260	21	.	.	.
cord-002542-f7l4ty2j	261	1	This	this	DT
cord-002542-f7l4ty2j	261	2	yielded	yield	VBD
cord-002542-f7l4ty2j	261	3	between	between	IN
cord-002542-f7l4ty2j	261	4	2688	2688	CD
cord-002542-f7l4ty2j	261	5	and	and	CC
cord-002542-f7l4ty2j	261	6	8815	8815	CD
cord-002542-f7l4ty2j	261	7	full	full	JJ
cord-002542-f7l4ty2j	261	8	-	-	HYPH
cord-002542-f7l4ty2j	261	9	length	length	NN
cord-002542-f7l4ty2j	261	10	reads	read	NNS
cord-002542-f7l4ty2j	261	11	per	per	IN
cord-002542-f7l4ty2j	261	12	passage	passage	NN
cord-002542-f7l4ty2j	261	13	and	and	CC
cord-002542-f7l4ty2j	261	14	corresponds	correspond	VBZ
cord-002542-f7l4ty2j	261	15	to	to	IN
cord-002542-f7l4ty2j	261	16	approximately	approximately	RB
cord-002542-f7l4ty2j	261	17	0.1	0.1	CD
cord-002542-f7l4ty2j	261	18	Gigabases	gigabase	NNS
cord-002542-f7l4ty2j	261	19	of	of	IN
cord-002542-f7l4ty2j	261	20	sequence	sequence	NN
cord-002542-f7l4ty2j	261	21	information	information	NN
cord-002542-f7l4ty2j	261	22	.	.	.
cord-002542-f7l4ty2j	262	1	This	this	DT
cord-002542-f7l4ty2j	262	2	would	would	MD
cord-002542-f7l4ty2j	262	3	correspond	correspond	VB
cord-002542-f7l4ty2j	262	4	to~80'000	to~80'000	WP
cord-002542-f7l4ty2j	262	5	1x150bp	1x150bp	CD
cord-002542-f7l4ty2j	262	6	Illumina	Illumina	NNP
cord-002542-f7l4ty2j	262	7	reads	read	VBZ
cord-002542-f7l4ty2j	262	8	per	per	IN
cord-002542-f7l4ty2j	262	9	sample	sample	NN
cord-002542-f7l4ty2j	262	10	,	,	,
cord-002542-f7l4ty2j	262	11	assuming	assume	VBG
cord-002542-f7l4ty2j	262	12	even	even	RB
cord-002542-f7l4ty2j	262	13	coverage	coverage	NN
cord-002542-f7l4ty2j	262	14	.	.	.
cord-002542-f7l4ty2j	263	1	With	with	IN
cord-002542-f7l4ty2j	263	2	this	this	DT
cord-002542-f7l4ty2j	263	3	depth	depth	NN
cord-002542-f7l4ty2j	263	4	,	,	,
cord-002542-f7l4ty2j	263	5	we	-PRON-	PRP
cord-002542-f7l4ty2j	263	6	can	can	MD
cord-002542-f7l4ty2j	263	7	build	build	VB
cord-002542-f7l4ty2j	263	8	up	up	RP
cord-002542-f7l4ty2j	263	9	a	a	DT
cord-002542-f7l4ty2j	263	10	comprehensive	comprehensive	JJ
cord-002542-f7l4ty2j	263	11	picture	picture	NN
cord-002542-f7l4ty2j	263	12	of	of	IN
cord-002542-f7l4ty2j	263	13	the	the	DT
cord-002542-f7l4ty2j	263	14	full	full	JJ
cord-002542-f7l4ty2j	263	15	-	-	HYPH
cord-002542-f7l4ty2j	263	16	length	length	NN
cord-002542-f7l4ty2j	263	17	genomic	genomic	JJ
cord-002542-f7l4ty2j	263	18	landscape	landscape	NN
cord-002542-f7l4ty2j	263	19	of	of	IN
cord-002542-f7l4ty2j	263	20	the	the	DT
cord-002542-f7l4ty2j	263	21	viral	viral	JJ
cord-002542-f7l4ty2j	263	22	samples	sample	NNS
cord-002542-f7l4ty2j	263	23	,	,	,
cord-002542-f7l4ty2j	263	24	allowing	allow	VBG
cord-002542-f7l4ty2j	263	25	us	-PRON-	PRP
cord-002542-f7l4ty2j	263	26	to	to	TO
cord-002542-f7l4ty2j	263	27	resolve	resolve	VB
cord-002542-f7l4ty2j	263	28	DI	DI	NNP
cord-002542-f7l4ty2j	263	29	-	-	HYPH
cord-002542-f7l4ty2j	263	30	RNA	RNA	NNP
cord-002542-f7l4ty2j	263	31	species	specie	NNS
cord-002542-f7l4ty2j	263	32	even	even	RB
cord-002542-f7l4ty2j	263	33	if	if	IN
cord-002542-f7l4ty2j	263	34	they	-PRON-	PRP
cord-002542-f7l4ty2j	263	35	were	be	VBD
cord-002542-f7l4ty2j	263	36	present	present	JJ
cord-002542-f7l4ty2j	263	37	at	at	IN
cord-002542-f7l4ty2j	263	38	less	less	JJR
cord-002542-f7l4ty2j	263	39	than	than	IN
cord-002542-f7l4ty2j	263	40	1	1	CD
cord-002542-f7l4ty2j	263	41	%	%	NN
cord-002542-f7l4ty2j	263	42	of	of	IN
cord-002542-f7l4ty2j	263	43	the	the	DT
cord-002542-f7l4ty2j	263	44	total	total	JJ
cord-002542-f7l4ty2j	263	45	viral	viral	JJ
cord-002542-f7l4ty2j	263	46	genomic	genomic	JJ
cord-002542-f7l4ty2j	263	47	population	population	NN
cord-002542-f7l4ty2j	263	48	.	.	.
cord-002542-f7l4ty2j	264	1	The	the	DT
cord-002542-f7l4ty2j	264	2	long	long	RB
cord-002542-f7l4ty2j	264	3	-	-	HYPH
cord-002542-f7l4ty2j	264	4	read	read	VBN
cord-002542-f7l4ty2j	264	5	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	264	6	sequencing	sequencing	NN
cord-002542-f7l4ty2j	264	7	data	datum	NNS
cord-002542-f7l4ty2j	264	8	were	be	VBD
cord-002542-f7l4ty2j	264	9	aligned	align	VBN
cord-002542-f7l4ty2j	264	10	to	to	IN
cord-002542-f7l4ty2j	264	11	the	the	DT
cord-002542-f7l4ty2j	264	12	full	full	JJ
cord-002542-f7l4ty2j	264	13	-	-	HYPH
cord-002542-f7l4ty2j	264	14	length	length	NN
cord-002542-f7l4ty2j	264	15	FHV	FHV	NNP
cord-002542-f7l4ty2j	264	16	genome	genome	NN
cord-002542-f7l4ty2j	264	17	using	use	VBG
cord-002542-f7l4ty2j	264	18	the	the	DT
cord-002542-f7l4ty2j	264	19	BBMAP	BBMAP	NNP
cord-002542-f7l4ty2j	264	20	suite	suite	NN
cord-002542-f7l4ty2j	264	21	(	(	-LRB-
cord-002542-f7l4ty2j	264	22	https://sourceforge.net/projects/bbmap/	https://sourceforge.net/projects/bbmap/	NNP
cord-002542-f7l4ty2j	264	23	)	)	-RRB-
cord-002542-f7l4ty2j	264	24	.	.	.
cord-002542-f7l4ty2j	265	1	This	this	DT
cord-002542-f7l4ty2j	265	2	pipeline	pipeline	NN
cord-002542-f7l4ty2j	265	3	tolerates	tolerate	VBZ
cord-002542-f7l4ty2j	265	4	large	large	JJ
cord-002542-f7l4ty2j	265	5	insertions	insertion	NNS
cord-002542-f7l4ty2j	265	6	and	and	CC
cord-002542-f7l4ty2j	265	7	deletions	deletion	NNS
cord-002542-f7l4ty2j	265	8	in	in	IN
cord-002542-f7l4ty2j	265	9	the	the	DT
cord-002542-f7l4ty2j	265	10	long	long	RB
cord-002542-f7l4ty2j	265	11	-	-	HYPH
cord-002542-f7l4ty2j	265	12	reads	read	NNS
cord-002542-f7l4ty2j	265	13	,	,	,
cord-002542-f7l4ty2j	265	14	thus	thus	RB
cord-002542-f7l4ty2j	265	15	allowing	allow	VBG
cord-002542-f7l4ty2j	265	16	us	-PRON-	PRP
cord-002542-f7l4ty2j	265	17	to	to	TO
cord-002542-f7l4ty2j	265	18	characterize	characterize	VB
cord-002542-f7l4ty2j	265	19	the	the	DT
cord-002542-f7l4ty2j	265	20	overall	overall	JJ
cord-002542-f7l4ty2j	265	21	topology	topology	NN
cord-002542-f7l4ty2j	265	22	of	of	IN
cord-002542-f7l4ty2j	265	23	the	the	DT
cord-002542-f7l4ty2j	265	24	defective	defective	JJ
cord-002542-f7l4ty2j	265	25	RNAs	rna	NNS
cord-002542-f7l4ty2j	265	26	.	.	.
cord-002542-f7l4ty2j	266	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	266	2	mapped	map	VBD
cord-002542-f7l4ty2j	266	3	between	between	IN
cord-002542-f7l4ty2j	266	4	94	94	CD
cord-002542-f7l4ty2j	266	5	and	and	CC
cord-002542-f7l4ty2j	266	6	97.5	97.5	CD
cord-002542-f7l4ty2j	266	7	%	%	NN
cord-002542-f7l4ty2j	266	8	of	of	IN
cord-002542-f7l4ty2j	266	9	the	the	DT
cord-002542-f7l4ty2j	266	10	MinION	minion	XX
cord-002542-f7l4ty2j	266	11	reads	read	VBZ
cord-002542-f7l4ty2j	266	12	from	from	IN
cord-002542-f7l4ty2j	266	13	each	each	DT
cord-002542-f7l4ty2j	266	14	passage	passage	NN
cord-002542-f7l4ty2j	266	15	to	to	IN
cord-002542-f7l4ty2j	266	16	the	the	DT
cord-002542-f7l4ty2j	266	17	FHV	FHV	NNP
cord-002542-f7l4ty2j	266	18	reference	reference	NN
cord-002542-f7l4ty2j	266	19	genome	genome	NN
cord-002542-f7l4ty2j	266	20	(	(	-LRB-
cord-002542-f7l4ty2j	266	21	Table	Table	NNP
cord-002542-f7l4ty2j	266	22	3	3	CD
cord-002542-f7l4ty2j	266	23	)	)	-RRB-
cord-002542-f7l4ty2j	266	24	.	.	.
cord-002542-f7l4ty2j	267	1	An	an	DT
cord-002542-f7l4ty2j	267	2	example	example	NN
cord-002542-f7l4ty2j	267	3	of	of	IN
cord-002542-f7l4ty2j	267	4	reads	read	NNS
cord-002542-f7l4ty2j	267	5	aligned	align	VBN
cord-002542-f7l4ty2j	267	6	to	to	IN
cord-002542-f7l4ty2j	267	7	FHV	FHV	NNP
cord-002542-f7l4ty2j	267	8	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	267	9	is	be	VBZ
cord-002542-f7l4ty2j	267	10	shown	show	VBN
cord-002542-f7l4ty2j	267	11	in	in	IN
cord-002542-f7l4ty2j	267	12	S4	S4	NNP
cord-002542-f7l4ty2j	267	13	Fig	Fig	NNP
cord-002542-f7l4ty2j	267	14	.	.	.
cord-002542-f7l4ty2j	268	1	The	the	DT
cord-002542-f7l4ty2j	268	2	error	error	NN
cord-002542-f7l4ty2j	268	3	rate	rate	NN
cord-002542-f7l4ty2j	268	4	of	of	IN
cord-002542-f7l4ty2j	268	5	aligned	align	VBN
cord-002542-f7l4ty2j	268	6	reads	read	VBZ
cord-002542-f7l4ty2j	268	7	,	,	,
cord-002542-f7l4ty2j	268	8	including	include	VBG
cord-002542-f7l4ty2j	268	9	single	single	JJ
cord-002542-f7l4ty2j	268	10	nucleotide	nucleotide	JJ
cord-002542-f7l4ty2j	268	11	mismatches	mismatch	NNS
cord-002542-f7l4ty2j	268	12	and	and	CC
cord-002542-f7l4ty2j	268	13	small	small	JJ
cord-002542-f7l4ty2j	268	14	InDels	InDels	NNPS
cord-002542-f7l4ty2j	268	15	,	,	,
cord-002542-f7l4ty2j	268	16	was	be	VBD
cord-002542-f7l4ty2j	268	17	determined	determine	VBN
cord-002542-f7l4ty2j	268	18	from	from	IN
cord-002542-f7l4ty2j	268	19	alignment	alignment	NN
cord-002542-f7l4ty2j	268	20	pileup	pileup	NN
cord-002542-f7l4ty2j	268	21	files	file	NNS
cord-002542-f7l4ty2j	268	22	.	.	.
cord-002542-f7l4ty2j	269	1	Consistent	consistent	JJ
cord-002542-f7l4ty2j	269	2	with	with	IN
cord-002542-f7l4ty2j	269	3	recent	recent	JJ
cord-002542-f7l4ty2j	269	4	reports	report	NNS
cord-002542-f7l4ty2j	269	5	[	[	-LRB-
cord-002542-f7l4ty2j	269	6	66	66	CD
cord-002542-f7l4ty2j	269	7	]	]	-RRB-
cord-002542-f7l4ty2j	269	8	,	,	,
cord-002542-f7l4ty2j	269	9	we	-PRON-	PRP
cord-002542-f7l4ty2j	269	10	found	find	VBD
cord-002542-f7l4ty2j	269	11	the	the	DT
cord-002542-f7l4ty2j	269	12	overall	overall	JJ
cord-002542-f7l4ty2j	269	13	modal	modal	JJ
cord-002542-f7l4ty2j	269	14	and	and	CC
cord-002542-f7l4ty2j	269	15	mean	mean	JJ
cord-002542-f7l4ty2j	269	16	error	error	NN
cord-002542-f7l4ty2j	269	17	rates	rate	NNS
cord-002542-f7l4ty2j	269	18	for	for	IN
cord-002542-f7l4ty2j	269	19	all	all	DT
cord-002542-f7l4ty2j	269	20	mapped	map	VBN
cord-002542-f7l4ty2j	269	21	position	position	NN
cord-002542-f7l4ty2j	269	22	was	be	VBD
cord-002542-f7l4ty2j	269	23	5.0	5.0	CD
cord-002542-f7l4ty2j	269	24	%	%	NN
cord-002542-f7l4ty2j	269	25	and	and	CC
cord-002542-f7l4ty2j	269	26	6.3	6.3	CD
cord-002542-f7l4ty2j	269	27	%	%	NN
cord-002542-f7l4ty2j	269	28	respectively	respectively	RB
cord-002542-f7l4ty2j	269	29	,	,	,
cord-002542-f7l4ty2j	269	30	with	with	IN
cord-002542-f7l4ty2j	269	31	95	95	CD
cord-002542-f7l4ty2j	269	32	%	%	NN
cord-002542-f7l4ty2j	269	33	of	of	IN
cord-002542-f7l4ty2j	269	34	the	the	DT
cord-002542-f7l4ty2j	269	35	sites	site	NNS
cord-002542-f7l4ty2j	269	36	having	have	VBG
cord-002542-f7l4ty2j	269	37	an	an	DT
cord-002542-f7l4ty2j	269	38	error	error	NN
cord-002542-f7l4ty2j	269	39	rate	rate	NN
cord-002542-f7l4ty2j	269	40	better	well	JJR
cord-002542-f7l4ty2j	269	41	than	than	IN
cord-002542-f7l4ty2j	269	42	13.6	13.6	CD
cord-002542-f7l4ty2j	269	43	%	%	NN
cord-002542-f7l4ty2j	270	1	(	(	-LRB-
cord-002542-f7l4ty2j	270	2	N95	N95	NNP
cord-002542-f7l4ty2j	270	3	value	value	NN
cord-002542-f7l4ty2j	270	4	=	=	SYM
cord-002542-f7l4ty2j	270	5	0.864	0.864	CD
cord-002542-f7l4ty2j	270	6	)	)	-RRB-
cord-002542-f7l4ty2j	270	7	.	.	.
cord-002542-f7l4ty2j	271	1	Example	example	NN
cord-002542-f7l4ty2j	271	2	of	of	IN
cord-002542-f7l4ty2j	271	3	how	how	WRB
cord-002542-f7l4ty2j	271	4	reads	read	VBZ
cord-002542-f7l4ty2j	271	5	generated	generate	VBN
cord-002542-f7l4ty2j	271	6	from	from	IN
cord-002542-f7l4ty2j	271	7	the	the	DT
cord-002542-f7l4ty2j	271	8	Illumina	Illumina	NNP
cord-002542-f7l4ty2j	271	9	HiSeq	HiSeq	NNP
cord-002542-f7l4ty2j	271	10	would	would	MD
cord-002542-f7l4ty2j	271	11	map	map	VB
cord-002542-f7l4ty2j	271	12	to	to	IN
cord-002542-f7l4ty2j	271	13	a	a	DT
cord-002542-f7l4ty2j	271	14	reference	reference	NN
cord-002542-f7l4ty2j	271	15	genome	genome	NN
cord-002542-f7l4ty2j	271	16	.	.	.
cord-002542-f7l4ty2j	272	1	The	the	DT
cord-002542-f7l4ty2j	272	2	Bowtie	Bowtie	NNP
cord-002542-f7l4ty2j	272	3	alignment	alignment	NN
cord-002542-f7l4ty2j	272	4	is	be	VBZ
cord-002542-f7l4ty2j	272	5	able	able	JJ
cord-002542-f7l4ty2j	272	6	to	to	TO
cord-002542-f7l4ty2j	272	7	map	map	VB
cord-002542-f7l4ty2j	272	8	150bp	150bp	NNP
cord-002542-f7l4ty2j	272	9	reads	read	VBZ
cord-002542-f7l4ty2j	272	10	along	along	IN
cord-002542-f7l4ty2j	272	11	the	the	DT
cord-002542-f7l4ty2j	272	12	reference	reference	NN
cord-002542-f7l4ty2j	272	13	with	with	IN
cord-002542-f7l4ty2j	272	14	a	a	DT
cord-002542-f7l4ty2j	272	15	relatively	relatively	RB
cord-002542-f7l4ty2j	272	16	even	even	JJ
cord-002542-f7l4ty2j	272	17	coverage	coverage	NN
cord-002542-f7l4ty2j	272	18	distribution	distribution	NN
cord-002542-f7l4ty2j	272	19	.	.	.
cord-002542-f7l4ty2j	273	1	Unmapped	unmapped	JJ
cord-002542-f7l4ty2j	273	2	reads	read	NNS
cord-002542-f7l4ty2j	273	3	are	be	VBP
cord-002542-f7l4ty2j	273	4	then	then	RB
cord-002542-f7l4ty2j	273	5	aligned	align	VBN
cord-002542-f7l4ty2j	273	6	with	with	IN
cord-002542-f7l4ty2j	273	7	ViReMa	virema	NN
cord-002542-f7l4ty2j	273	8	to	to	TO
cord-002542-f7l4ty2j	273	9	accurately	accurately	RB
cord-002542-f7l4ty2j	273	10	identify	identify	VB
cord-002542-f7l4ty2j	273	11	recombination	recombination	NN
cord-002542-f7l4ty2j	273	12	events	event	NNS
cord-002542-f7l4ty2j	273	13	.	.	.
cord-002542-f7l4ty2j	274	1	The	the	DT
cord-002542-f7l4ty2j	274	2	low	low	JJ
cord-002542-f7l4ty2j	274	3	error	error	NN
cord-002542-f7l4ty2j	274	4	rate	rate	NN
cord-002542-f7l4ty2j	274	5	of	of	IN
cord-002542-f7l4ty2j	274	6	highthroughput	highthroughput	NN
cord-002542-f7l4ty2j	274	7	sequencing	sequencing	NN
cord-002542-f7l4ty2j	274	8	allows	allow	VBZ
cord-002542-f7l4ty2j	274	9	us	-PRON-	PRP
cord-002542-f7l4ty2j	274	10	to	to	TO
cord-002542-f7l4ty2j	274	11	precisely	precisely	RB
cord-002542-f7l4ty2j	274	12	define	define	VB
cord-002542-f7l4ty2j	274	13	the	the	DT
cord-002542-f7l4ty2j	274	14	boundaries	boundary	NNS
cord-002542-f7l4ty2j	274	15	of	of	IN
cord-002542-f7l4ty2j	274	16	the	the	DT
cord-002542-f7l4ty2j	274	17	junctions	junction	NNS
cord-002542-f7l4ty2j	274	18	.	.	.
cord-002542-f7l4ty2j	275	1	Below	below	IN
cord-002542-f7l4ty2j	275	2	the	the	DT
cord-002542-f7l4ty2j	275	3	reference	reference	NN
cord-002542-f7l4ty2j	275	4	genome	genome	NN
cord-002542-f7l4ty2j	275	5	is	be	VBZ
cord-002542-f7l4ty2j	275	6	an	an	DT
cord-002542-f7l4ty2j	275	7	example	example	NN
cord-002542-f7l4ty2j	275	8	of	of	IN
cord-002542-f7l4ty2j	275	9	how	how	WRB
cord-002542-f7l4ty2j	275	10	reads	read	VBZ
cord-002542-f7l4ty2j	275	11	generated	generate	VBN
cord-002542-f7l4ty2j	275	12	from	from	IN
cord-002542-f7l4ty2j	275	13	Oxford	Oxford	NNP
cord-002542-f7l4ty2j	275	14	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	275	15	Technologies	Technologies	NNPS
cord-002542-f7l4ty2j	275	16	's	's	POS
cord-002542-f7l4ty2j	275	17	MinION	minion	NN
cord-002542-f7l4ty2j	275	18	sequencing	sequencing	NN
cord-002542-f7l4ty2j	275	19	would	would	MD
cord-002542-f7l4ty2j	275	20	map	map	VB
cord-002542-f7l4ty2j	275	21	to	to	IN
cord-002542-f7l4ty2j	275	22	a	a	DT
cord-002542-f7l4ty2j	275	23	reference	reference	NN
cord-002542-f7l4ty2j	275	24	genome	genome	NN
cord-002542-f7l4ty2j	275	25	.	.	.
cord-002542-f7l4ty2j	276	1	The	the	DT
cord-002542-f7l4ty2j	276	2	MinION	minion	NN
cord-002542-f7l4ty2j	276	3	is	be	VBZ
cord-002542-f7l4ty2j	276	4	able	able	JJ
cord-002542-f7l4ty2j	276	5	to	to	TO
cord-002542-f7l4ty2j	276	6	generate	generate	VB
cord-002542-f7l4ty2j	276	7	full	full	JJ
cord-002542-f7l4ty2j	276	8	length	length	NN
cord-002542-f7l4ty2j	276	9	reads	read	VBZ
cord-002542-f7l4ty2j	276	10	at	at	IN
cord-002542-f7l4ty2j	276	11	the	the	DT
cord-002542-f7l4ty2j	276	12	expense	expense	NN
cord-002542-f7l4ty2j	276	13	of	of	IN
cord-002542-f7l4ty2j	276	14	a	a	DT
cord-002542-f7l4ty2j	276	15	high	high	JJ
cord-002542-f7l4ty2j	276	16	error	error	NN
cord-002542-f7l4ty2j	276	17	rate	rate	NN
cord-002542-f7l4ty2j	276	18	,	,	,
cord-002542-f7l4ty2j	276	19	which	which	WDT
cord-002542-f7l4ty2j	276	20	is~7	is~7	NNP
cord-002542-f7l4ty2j	276	21	%	%	NN
cord-002542-f7l4ty2j	276	22	.	.	.
cord-002542-f7l4ty2j	277	1	Full	full	JJ
cord-002542-f7l4ty2j	277	2	length	length	NN
cord-002542-f7l4ty2j	277	3	analysis	analysis	NN
cord-002542-f7l4ty2j	277	4	allows	allow	VBZ
cord-002542-f7l4ty2j	277	5	us	-PRON-	PRP
cord-002542-f7l4ty2j	277	6	to	to	TO
cord-002542-f7l4ty2j	277	7	determine	determine	VB
cord-002542-f7l4ty2j	277	8	what	what	WP
cord-002542-f7l4ty2j	277	9	recombination	recombination	NN
cord-002542-f7l4ty2j	277	10	events	event	VBZ
cord-002542-f7l4ty2j	277	11	a	a	DT
cord-002542-f7l4ty2j	277	12	genome	genome	NN
cord-002542-f7l4ty2j	277	13	contains	contain	VBZ
cord-002542-f7l4ty2j	277	14	.	.	.
cord-002542-f7l4ty2j	278	1	Due	due	IN
cord-002542-f7l4ty2j	278	2	to	to	IN
cord-002542-f7l4ty2j	278	3	the	the	DT
cord-002542-f7l4ty2j	278	4	error	error	NN
cord-002542-f7l4ty2j	278	5	rate	rate	NN
cord-002542-f7l4ty2j	278	6	the	the	DT
cord-002542-f7l4ty2j	278	7	exact	exact	JJ
cord-002542-f7l4ty2j	278	8	boundaries	boundary	NNS
cord-002542-f7l4ty2j	278	9	of	of	IN
cord-002542-f7l4ty2j	278	10	the	the	DT
cord-002542-f7l4ty2j	278	11	recombination	recombination	NN
cord-002542-f7l4ty2j	278	12	event	event	NN
cord-002542-f7l4ty2j	278	13	are	be	VBP
cord-002542-f7l4ty2j	278	14	imprecise	imprecise	JJ
cord-002542-f7l4ty2j	278	15	.	.	.
cord-002542-f7l4ty2j	279	1	(	(	-LRB-
cord-002542-f7l4ty2j	279	2	S5B	S5B	NNP
cord-002542-f7l4ty2j	279	3	and	and	CC
cord-002542-f7l4ty2j	279	4	S5C	S5C	NNP
cord-002542-f7l4ty2j	279	5	Fig	Fig	NNP
cord-002542-f7l4ty2j	279	6	)	)	-RRB-
cord-002542-f7l4ty2j	279	7	.	.	.
cord-002542-f7l4ty2j	280	1	This	this	DT
cord-002542-f7l4ty2j	280	2	shows	show	VBZ
cord-002542-f7l4ty2j	280	3	that	that	IN
cord-002542-f7l4ty2j	280	4	small	small	JJ
cord-002542-f7l4ty2j	280	5	InDels	InDels	NNPS
cord-002542-f7l4ty2j	280	6	are	be	VBP
cord-002542-f7l4ty2j	280	7	frequent	frequent	JJ
cord-002542-f7l4ty2j	280	8	,	,	,
cord-002542-f7l4ty2j	280	9	but	but	CC
cord-002542-f7l4ty2j	280	10	fall	fall	VB
cord-002542-f7l4ty2j	280	11	quickly	quickly	RB
cord-002542-f7l4ty2j	280	12	in	in	IN
cord-002542-f7l4ty2j	280	13	abundance	abundance	NN
cord-002542-f7l4ty2j	280	14	with	with	IN
cord-002542-f7l4ty2j	280	15	increasing	increase	VBG
cord-002542-f7l4ty2j	280	16	length	length	NN
cord-002542-f7l4ty2j	280	17	.	.	.
cord-002542-f7l4ty2j	281	1	99.8	99.8	CD
cord-002542-f7l4ty2j	281	2	%	%	NN
cord-002542-f7l4ty2j	281	3	and	and	CC
cord-002542-f7l4ty2j	281	4	99.9	99.9	CD
cord-002542-f7l4ty2j	281	5	%	%	NN
cord-002542-f7l4ty2j	281	6	of	of	IN
cord-002542-f7l4ty2j	281	7	all	all	DT
cord-002542-f7l4ty2j	281	8	MinION	minion	NN
cord-002542-f7l4ty2j	281	9	deletions	deletion	NNS
cord-002542-f7l4ty2j	281	10	and	and	CC
cord-002542-f7l4ty2j	281	11	insertions	insertion	NNS
cord-002542-f7l4ty2j	281	12	respectively	respectively	RB
cord-002542-f7l4ty2j	281	13	were	be	VBD
cord-002542-f7l4ty2j	281	14	shorter	short	JJR
cord-002542-f7l4ty2j	281	15	than	than	IN
cord-002542-f7l4ty2j	281	16	25nts	25nt	NNS
cord-002542-f7l4ty2j	281	17	.	.	.
cord-002542-f7l4ty2j	282	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	282	2	,	,	,
cord-002542-f7l4ty2j	282	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	282	4	considered	consider	VBD
cord-002542-f7l4ty2j	282	5	only	only	JJ
cord-002542-f7l4ty2j	282	6	deletions	deletion	NNS
cord-002542-f7l4ty2j	282	7	and	and	CC
cord-002542-f7l4ty2j	282	8	insertions	insertion	NNS
cord-002542-f7l4ty2j	282	9	of	of	IN
cord-002542-f7l4ty2j	282	10	at	at	RB
cord-002542-f7l4ty2j	282	11	least	least	JJS
cord-002542-f7l4ty2j	282	12	25nts	25nts	CD
cord-002542-f7l4ty2j	282	13	to	to	TO
cord-002542-f7l4ty2j	282	14	be	be	VB
cord-002542-f7l4ty2j	282	15	likely	likely	JJ
cord-002542-f7l4ty2j	282	16	to	to	TO
cord-002542-f7l4ty2j	282	17	be	be	VB
cord-002542-f7l4ty2j	282	18	bona	bona	JJ
cord-002542-f7l4ty2j	282	19	fide	fide	JJ
cord-002542-f7l4ty2j	282	20	InDels	InDels	NNPS
cord-002542-f7l4ty2j	282	21	present	present	JJ
cord-002542-f7l4ty2j	282	22	in	in	IN
cord-002542-f7l4ty2j	282	23	the	the	DT
cord-002542-f7l4ty2j	282	24	original	original	JJ
cord-002542-f7l4ty2j	282	25	viral	viral	JJ
cord-002542-f7l4ty2j	282	26	RNA	RNA	NNP
cord-002542-f7l4ty2j	282	27	and	and	CC
cord-002542-f7l4ty2j	282	28	corresponding	correspond	VBG
cord-002542-f7l4ty2j	282	29	to	to	IN
cord-002542-f7l4ty2j	282	30	recombination	recombination	NN
cord-002542-f7l4ty2j	282	31	events	event	NNS
cord-002542-f7l4ty2j	282	32	comprising	comprise	VBG
cord-002542-f7l4ty2j	282	33	defective	defective	JJ
cord-002542-f7l4ty2j	282	34	RNA	RNA	NNP
cord-002542-f7l4ty2j	282	35	species	specie	NNS
cord-002542-f7l4ty2j	282	36	rather	rather	RB
cord-002542-f7l4ty2j	282	37	than	than	IN
cord-002542-f7l4ty2j	282	38	a	a	DT
cord-002542-f7l4ty2j	282	39	sequencing	sequencing	NN
cord-002542-f7l4ty2j	282	40	error	error	NN
cord-002542-f7l4ty2j	282	41	.	.	.
cord-002542-f7l4ty2j	283	1	The	the	DT
cord-002542-f7l4ty2j	283	2	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	283	3	data	data	NN
cord-002542-f7l4ty2j	283	4	reveals	reveal	VBZ
cord-002542-f7l4ty2j	283	5	the	the	DT
cord-002542-f7l4ty2j	283	6	presence	presence	NN
cord-002542-f7l4ty2j	283	7	and	and	CC
cord-002542-f7l4ty2j	283	8	frequency	frequency	NN
cord-002542-f7l4ty2j	283	9	of	of	IN
cord-002542-f7l4ty2j	283	10	large	large	JJ
cord-002542-f7l4ty2j	283	11	deletions	deletion	NNS
cord-002542-f7l4ty2j	283	12	and	and	CC
cord-002542-f7l4ty2j	283	13	insertions	insertion	NNS
cord-002542-f7l4ty2j	283	14	within	within	IN
cord-002542-f7l4ty2j	283	15	defective	defective	JJ
cord-002542-f7l4ty2j	283	16	RNA	RNA	NNP
cord-002542-f7l4ty2j	283	17	genomes	genome	NNS
cord-002542-f7l4ty2j	283	18	.	.	.
cord-002542-f7l4ty2j	284	1	From	from	IN
cord-002542-f7l4ty2j	284	2	these	these	DT
cord-002542-f7l4ty2j	284	3	,	,	,
cord-002542-f7l4ty2j	284	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	284	5	can	can	MD
cord-002542-f7l4ty2j	284	6	reconstruct	reconstruct	VB
cord-002542-f7l4ty2j	284	7	the	the	DT
cord-002542-f7l4ty2j	284	8	population	population	NN
cord-002542-f7l4ty2j	284	9	of	of	IN
cord-002542-f7l4ty2j	284	10	either	either	DT
cord-002542-f7l4ty2j	284	11	full	full	JJ
cord-002542-f7l4ty2j	284	12	-	-	HYPH
cord-002542-f7l4ty2j	284	13	length	length	NN
cord-002542-f7l4ty2j	284	14	or	or	CC
cord-002542-f7l4ty2j	284	15	defective	defective	JJ
cord-002542-f7l4ty2j	284	16	RNA	RNA	NNP
cord-002542-f7l4ty2j	284	17	genomes	genome	NNS
cord-002542-f7l4ty2j	284	18	present	present	JJ
cord-002542-f7l4ty2j	284	19	in	in	IN
cord-002542-f7l4ty2j	284	20	each	each	DT
cord-002542-f7l4ty2j	284	21	of	of	IN
cord-002542-f7l4ty2j	284	22	the	the	DT
cord-002542-f7l4ty2j	284	23	viral	viral	JJ
cord-002542-f7l4ty2j	284	24	passages	passage	NNS
cord-002542-f7l4ty2j	284	25	(	(	-LRB-
cord-002542-f7l4ty2j	284	26	annotated	annotate	VBN
cord-002542-f7l4ty2j	284	27	as	as	IN
cord-002542-f7l4ty2j	284	28	described	describe	VBN
cord-002542-f7l4ty2j	284	29	in	in	IN
cord-002542-f7l4ty2j	284	30	the	the	DT
cord-002542-f7l4ty2j	284	31	Methods	Methods	NNPS
cord-002542-f7l4ty2j	284	32	section	section	NN
cord-002542-f7l4ty2j	284	33	)	)	-RRB-
cord-002542-f7l4ty2j	284	34	.	.	.
cord-002542-f7l4ty2j	285	1	The	the	DT
cord-002542-f7l4ty2j	285	2	full	full	JJ
cord-002542-f7l4ty2j	285	3	table	table	NN
cord-002542-f7l4ty2j	285	4	of	of	IN
cord-002542-f7l4ty2j	285	5	characterized	characterize	VBN
cord-002542-f7l4ty2j	285	6	defective	defective	JJ
cord-002542-f7l4ty2j	285	7	RNAs	rna	NNS
cord-002542-f7l4ty2j	285	8	and	and	CC
cord-002542-f7l4ty2j	285	9	their	-PRON-	PRP$
cord-002542-f7l4ty2j	285	10	frequencies	frequency	NNS
cord-002542-f7l4ty2j	285	11	in	in	IN
cord-002542-f7l4ty2j	285	12	each	each	DT
cord-002542-f7l4ty2j	285	13	passage	passage	NN
cord-002542-f7l4ty2j	285	14	is	be	VBZ
cord-002542-f7l4ty2j	285	15	detailed	detail	VBN
cord-002542-f7l4ty2j	285	16	in	in	IN
cord-002542-f7l4ty2j	285	17	S2	S2	NNP
cord-002542-f7l4ty2j	285	18	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	285	19	.	.	.
cord-002542-f7l4ty2j	286	1	In	in	IN
cord-002542-f7l4ty2j	286	2	total	total	NN
cord-002542-f7l4ty2j	286	3	,	,	,
cord-002542-f7l4ty2j	286	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	286	5	found	find	VBD
cord-002542-f7l4ty2j	286	6	6030	6030	CD
cord-002542-f7l4ty2j	286	7	and	and	CC
cord-002542-f7l4ty2j	286	8	3639	3639	CD
cord-002542-f7l4ty2j	286	9	unique	unique	JJ
cord-002542-f7l4ty2j	286	10	defective	defective	JJ
cord-002542-f7l4ty2j	286	11	RNAs	rna	NNS
cord-002542-f7l4ty2j	286	12	of	of	IN
cord-002542-f7l4ty2j	286	13	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	286	14	and	and	CC
cord-002542-f7l4ty2j	286	15	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	286	16	respectively	respectively	RB
cord-002542-f7l4ty2j	286	17	throughout	throughout	IN
cord-002542-f7l4ty2j	286	18	all	all	DT
cord-002542-f7l4ty2j	286	19	passages	passage	NNS
cord-002542-f7l4ty2j	286	20	.	.	.
cord-002542-f7l4ty2j	287	1	The	the	DT
cord-002542-f7l4ty2j	287	2	frequency	frequency	NN
cord-002542-f7l4ty2j	287	3	of	of	IN
cord-002542-f7l4ty2j	287	4	individual	individual	JJ
cord-002542-f7l4ty2j	287	5	recombination	recombination	NN
cord-002542-f7l4ty2j	287	6	events	event	NNS
cord-002542-f7l4ty2j	287	7	found	find	VBN
cord-002542-f7l4ty2j	287	8	in	in	IN
cord-002542-f7l4ty2j	287	9	both	both	CC
cord-002542-f7l4ty2j	287	10	the	the	DT
cord-002542-f7l4ty2j	287	11	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	287	12	data	datum	NNS
cord-002542-f7l4ty2j	287	13	and	and	CC
cord-002542-f7l4ty2j	287	14	the	the	DT
cord-002542-f7l4ty2j	287	15	MinION	MinION	NNP
cord-002542-f7l4ty2j	287	16	data	datum	NNS
cord-002542-f7l4ty2j	287	17	were	be	VBD
cord-002542-f7l4ty2j	287	18	compared	compare	VBN
cord-002542-f7l4ty2j	287	19	and	and	CC
cord-002542-f7l4ty2j	287	20	correlation	correlation	NN
cord-002542-f7l4ty2j	287	21	coefficients	coefficient	NNS
cord-002542-f7l4ty2j	287	22	calculated	calculate	VBN
cord-002542-f7l4ty2j	287	23	(	(	-LRB-
cord-002542-f7l4ty2j	287	24	Table	Table	NNP
cord-002542-f7l4ty2j	287	25	3	3	CD
cord-002542-f7l4ty2j	287	26	)	)	-RRB-
cord-002542-f7l4ty2j	287	27	.	.	.
cord-002542-f7l4ty2j	288	1	The	the	DT
cord-002542-f7l4ty2j	288	2	correlation	correlation	NN
cord-002542-f7l4ty2j	288	3	in	in	IN
cord-002542-f7l4ty2j	288	4	the	the	DT
cord-002542-f7l4ty2j	288	5	earliest	early	JJS
cord-002542-f7l4ty2j	288	6	passages	passage	NNS
cord-002542-f7l4ty2j	288	7	was	be	VBD
cord-002542-f7l4ty2j	288	8	poor	poor	JJ
cord-002542-f7l4ty2j	288	9	,	,	,
cord-002542-f7l4ty2j	288	10	due	due	IN
cord-002542-f7l4ty2j	288	11	to	to	IN
cord-002542-f7l4ty2j	288	12	the	the	DT
cord-002542-f7l4ty2j	288	13	low	low	JJ
cord-002542-f7l4ty2j	288	14	abundance	abundance	NN
cord-002542-f7l4ty2j	288	15	of	of	IN
cord-002542-f7l4ty2j	288	16	events	event	NNS
cord-002542-f7l4ty2j	288	17	in	in	IN
cord-002542-f7l4ty2j	288	18	both	both	DT
cord-002542-f7l4ty2j	288	19	datasets	dataset	NNS
cord-002542-f7l4ty2j	288	20	.	.	.
cord-002542-f7l4ty2j	289	1	However	however	RB
cord-002542-f7l4ty2j	289	2	,	,	,
cord-002542-f7l4ty2j	289	3	later	later	RB
cord-002542-f7l4ty2j	289	4	passages	passage	NNS
cord-002542-f7l4ty2j	289	5	correlate	correlate	VBP
cord-002542-f7l4ty2j	289	6	well	well	RB
cord-002542-f7l4ty2j	289	7	with	with	IN
cord-002542-f7l4ty2j	289	8	Pearson	Pearson	NNP
cord-002542-f7l4ty2j	289	9	coefficients	coefficient	NNS
cord-002542-f7l4ty2j	289	10	reaching	reach	VBG
cord-002542-f7l4ty2j	289	11	0.85	0.85	CD
cord-002542-f7l4ty2j	289	12	.	.	.
cord-002542-f7l4ty2j	290	1	This	this	DT
cord-002542-f7l4ty2j	290	2	is	be	VBZ
cord-002542-f7l4ty2j	290	3	important	important	JJ
cord-002542-f7l4ty2j	290	4	as	as	IN
cord-002542-f7l4ty2j	290	5	it	-PRON-	PRP
cord-002542-f7l4ty2j	290	6	demonstrates	demonstrate	VBZ
cord-002542-f7l4ty2j	290	7	that	that	IN
cord-002542-f7l4ty2j	290	8	the	the	DT
cord-002542-f7l4ty2j	290	9	frequency	frequency	NN
cord-002542-f7l4ty2j	290	10	of	of	IN
cord-002542-f7l4ty2j	290	11	recombination	recombination	NN
cord-002542-f7l4ty2j	290	12	events	event	NNS
cord-002542-f7l4ty2j	290	13	was	be	VBD
cord-002542-f7l4ty2j	290	14	not	not	RB
cord-002542-f7l4ty2j	290	15	biased	bias	VBN
cord-002542-f7l4ty2j	290	16	during	during	IN
cord-002542-f7l4ty2j	290	17	cDNA	cdna	NN
cord-002542-f7l4ty2j	290	18	amplification	amplification	NN
cord-002542-f7l4ty2j	290	19	of	of	IN
cord-002542-f7l4ty2j	290	20	the	the	DT
cord-002542-f7l4ty2j	290	21	full	full	JJ
cord-002542-f7l4ty2j	290	22	-	-	HYPH
cord-002542-f7l4ty2j	290	23	length	length	NN
cord-002542-f7l4ty2j	290	24	or	or	CC
cord-002542-f7l4ty2j	290	25	defective	defective	JJ
cord-002542-f7l4ty2j	290	26	viral	viral	JJ
cord-002542-f7l4ty2j	290	27	genomes	genome	NNS
cord-002542-f7l4ty2j	290	28	.	.	.
cord-002542-f7l4ty2j	291	1	Similarly	similarly	RB
cord-002542-f7l4ty2j	291	2	,	,	,
cord-002542-f7l4ty2j	291	3	the	the	DT
cord-002542-f7l4ty2j	291	4	Shannon	Shannon	NNP
cord-002542-f7l4ty2j	291	5	Entropy	Entropy	NNP
cord-002542-f7l4ty2j	291	6	indices	index	NNS
cord-002542-f7l4ty2j	291	7	increase	increase	VBP
cord-002542-f7l4ty2j	291	8	during	during	IN
cord-002542-f7l4ty2j	291	9	passaging	passage	VBG
cord-002542-f7l4ty2j	291	10	(	(	-LRB-
cord-002542-f7l4ty2j	291	11	Fig	Fig	NNP
cord-002542-f7l4ty2j	291	12	5C	5c	CD
cord-002542-f7l4ty2j	291	13	)	)	-RRB-
cord-002542-f7l4ty2j	291	14	,	,	,
cord-002542-f7l4ty2j	291	15	consistent	consistent	JJ
cord-002542-f7l4ty2j	291	16	with	with	IN
cord-002542-f7l4ty2j	291	17	those	those	DT
cord-002542-f7l4ty2j	291	18	from	from	IN
cord-002542-f7l4ty2j	291	19	the	the	DT
cord-002542-f7l4ty2j	291	20	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	291	21	data	datum	NNS
cord-002542-f7l4ty2j	291	22	.	.	.
cord-002542-f7l4ty2j	292	1	The	the	DT
cord-002542-f7l4ty2j	292	2	number	number	NN
cord-002542-f7l4ty2j	292	3	of	of	IN
cord-002542-f7l4ty2j	292	4	deletions	deletion	NNS
cord-002542-f7l4ty2j	292	5	in	in	IN
cord-002542-f7l4ty2j	292	6	each	each	DT
cord-002542-f7l4ty2j	292	7	passage	passage	NN
cord-002542-f7l4ty2j	292	8	in	in	IN
cord-002542-f7l4ty2j	292	9	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	292	10	and	and	CC
cord-002542-f7l4ty2j	292	11	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	292	12	are	be	VBP
cord-002542-f7l4ty2j	292	13	given	give	VBN
cord-002542-f7l4ty2j	292	14	in	in	IN
cord-002542-f7l4ty2j	292	15	Table	Table	NNP
cord-002542-f7l4ty2j	292	16	3	3	CD
cord-002542-f7l4ty2j	292	17	and	and	CC
cord-002542-f7l4ty2j	292	18	illustrated	illustrate	VBN
cord-002542-f7l4ty2j	292	19	in	in	IN
cord-002542-f7l4ty2j	292	20	Fig	Fig	NNP
cord-002542-f7l4ty2j	292	21	5B.	5B.	NNP
cord-002542-f7l4ty2j	293	1	The	the	DT
cord-002542-f7l4ty2j	293	2	earliest	early	JJS
cord-002542-f7l4ty2j	293	3	passage	passage	NN
cord-002542-f7l4ty2j	293	4	contains	contain	VBZ
cord-002542-f7l4ty2j	293	5	very	very	RB
cord-002542-f7l4ty2j	293	6	few	few	JJ
cord-002542-f7l4ty2j	293	7	deletions	deletion	NNS
cord-002542-f7l4ty2j	293	8	.	.	.
cord-002542-f7l4ty2j	294	1	In	in	IN
cord-002542-f7l4ty2j	294	2	passage	passage	NN
cord-002542-f7l4ty2j	294	3	1	1	CD
cord-002542-f7l4ty2j	294	4	,	,	,
cord-002542-f7l4ty2j	294	5	95.8	95.8	CD
cord-002542-f7l4ty2j	294	6	%	%	NN
cord-002542-f7l4ty2j	294	7	of	of	IN
cord-002542-f7l4ty2j	294	8	the	the	DT
cord-002542-f7l4ty2j	294	9	reads	read	NNS
cord-002542-f7l4ty2j	294	10	map	map	NN
cord-002542-f7l4ty2j	294	11	to	to	IN
cord-002542-f7l4ty2j	294	12	the	the	DT
cord-002542-f7l4ty2j	294	13	full	full	JJ
cord-002542-f7l4ty2j	294	14	-	-	HYPH
cord-002542-f7l4ty2j	294	15	length	length	NN
cord-002542-f7l4ty2j	294	16	genome	genome	NN
cord-002542-f7l4ty2j	294	17	in	in	IN
cord-002542-f7l4ty2j	294	18	its	-PRON-	PRP$
cord-002542-f7l4ty2j	294	19	entirety	entirety	NN
cord-002542-f7l4ty2j	294	20	.	.	.
cord-002542-f7l4ty2j	295	1	With	with	IN
cord-002542-f7l4ty2j	295	2	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	295	3	passages	passage	NNS
cord-002542-f7l4ty2j	295	4	,	,	,
cord-002542-f7l4ty2j	295	5	the	the	DT
cord-002542-f7l4ty2j	295	6	number	number	NN
cord-002542-f7l4ty2j	295	7	of	of	IN
cord-002542-f7l4ty2j	295	8	reads	read	NNS
cord-002542-f7l4ty2j	295	9	containing	contain	VBG
cord-002542-f7l4ty2j	295	10	deletions	deletion	NNS
cord-002542-f7l4ty2j	295	11	increases	increase	NNS
cord-002542-f7l4ty2j	295	12	,	,	,
cord-002542-f7l4ty2j	295	13	reaching	reach	VBG
cord-002542-f7l4ty2j	295	14	a	a	DT
cord-002542-f7l4ty2j	295	15	plateau	plateau	NN
cord-002542-f7l4ty2j	295	16	at	at	IN
cord-002542-f7l4ty2j	295	17	passage	passage	NN
cord-002542-f7l4ty2j	295	18	8	8	CD
cord-002542-f7l4ty2j	295	19	with	with	IN
cord-002542-f7l4ty2j	295	20	76.0	76.0	CD
cord-002542-f7l4ty2j	295	21	%	%	NN
cord-002542-f7l4ty2j	295	22	of	of	IN
cord-002542-f7l4ty2j	295	23	the	the	DT
cord-002542-f7l4ty2j	295	24	reads	read	NNS
cord-002542-f7l4ty2j	295	25	containing	contain	VBG
cord-002542-f7l4ty2j	295	26	two	two	CD
cord-002542-f7l4ty2j	295	27	deletions	deletion	NNS
cord-002542-f7l4ty2j	295	28	and	and	CC
cord-002542-f7l4ty2j	295	29	8.2	8.2	CD
cord-002542-f7l4ty2j	295	30	%	%	NN
cord-002542-f7l4ty2j	295	31	containing	contain	VBG
cord-002542-f7l4ty2j	295	32	three	three	CD
cord-002542-f7l4ty2j	295	33	deletions	deletion	NNS
cord-002542-f7l4ty2j	295	34	.	.	.
cord-002542-f7l4ty2j	296	1	DI	DI	NNP
cord-002542-f7l4ty2j	296	2	-	-	HYPH
cord-002542-f7l4ty2j	296	3	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	296	4	(	(	-LRB-
cord-002542-f7l4ty2j	296	5	e.g.	e.g.	RB
cord-002542-f7l4ty2j	296	6	1_317	1_317	CD
cord-002542-f7l4ty2j	296	7	^	^	NFP
cord-002542-f7l4ty2j	296	8	1091	1091	CD
cord-002542-f7l4ty2j	296	9	_	_	NN
cord-002542-f7l4ty2j	296	10	1242	1242	CD
cord-002542-f7l4ty2j	296	11	^	^	:
cord-002542-f7l4ty2j	296	12	2301_3107	2301_3107	CD
cord-002542-f7l4ty2j	296	13	)	)	-RRB-
cord-002542-f7l4ty2j	296	14	are	be	VBP
cord-002542-f7l4ty2j	296	15	easily	easily	RB
cord-002542-f7l4ty2j	296	16	identifiable	identifiable	JJ
cord-002542-f7l4ty2j	296	17	as	as	RB
cord-002542-f7l4ty2j	296	18	early	early	RB
cord-002542-f7l4ty2j	296	19	as	as	IN
cord-002542-f7l4ty2j	296	20	passage	passage	NN
cord-002542-f7l4ty2j	296	21	2	2	CD
cord-002542-f7l4ty2j	296	22	(	(	-LRB-
cord-002542-f7l4ty2j	296	23	S2	S2	NNP
cord-002542-f7l4ty2j	296	24	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	296	25	)	)	-RRB-
cord-002542-f7l4ty2j	296	26	and	and	CC
cord-002542-f7l4ty2j	296	27	match	match	VB
cord-002542-f7l4ty2j	296	28	well	well	RB
cord-002542-f7l4ty2j	296	29	with	with	IN
cord-002542-f7l4ty2j	296	30	The	the	DT
cord-002542-f7l4ty2j	296	31	number	number	NN
cord-002542-f7l4ty2j	296	32	of	of	IN
cord-002542-f7l4ty2j	296	33	demultiplexed	demultiplexed	NNP
cord-002542-f7l4ty2j	296	34	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	297	1	reads	read	VBZ
cord-002542-f7l4ty2j	297	2	passing	pass	VBG
cord-002542-f7l4ty2j	297	3	quality	quality	NN
cord-002542-f7l4ty2j	297	4	filters	filter	NNS
cord-002542-f7l4ty2j	297	5	are	be	VBP
cord-002542-f7l4ty2j	297	6	shown	show	VBN
cord-002542-f7l4ty2j	297	7	for	for	IN
cord-002542-f7l4ty2j	297	8	each	each	DT
cord-002542-f7l4ty2j	297	9	sample	sample	NN
cord-002542-f7l4ty2j	297	10	.	.	.
cord-002542-f7l4ty2j	298	1	These	these	DT
cord-002542-f7l4ty2j	298	2	were	be	VBD
cord-002542-f7l4ty2j	298	3	mapped	map	VBN
cord-002542-f7l4ty2j	298	4	end	end	NN
cord-002542-f7l4ty2j	298	5	-	-	HYPH
cord-002542-f7l4ty2j	298	6	to	to	IN
cord-002542-f7l4ty2j	298	7	-	-	HYPH
cord-002542-f7l4ty2j	298	8	end	end	NN
cord-002542-f7l4ty2j	298	9	to	to	IN
cord-002542-f7l4ty2j	298	10	the	the	DT
cord-002542-f7l4ty2j	298	11	FHV	FHV	NNP
cord-002542-f7l4ty2j	298	12	genome	genome	NN
cord-002542-f7l4ty2j	298	13	using	use	VBG
cord-002542-f7l4ty2j	298	14	the	the	DT
cord-002542-f7l4ty2j	298	15	BBMap	BBMap	NNP
cord-002542-f7l4ty2j	298	16	suite	suite	NN
cord-002542-f7l4ty2j	298	17	,	,	,
cord-002542-f7l4ty2j	298	18	allowing	allow	VBG
cord-002542-f7l4ty2j	298	19	for	for	IN
cord-002542-f7l4ty2j	298	20	large	large	JJ
cord-002542-f7l4ty2j	298	21	deletions	deletion	NNS
cord-002542-f7l4ty2j	298	22	and	and	CC
cord-002542-f7l4ty2j	298	23	insertions	insertion	NNS
cord-002542-f7l4ty2j	298	24	,	,	,
cord-002542-f7l4ty2j	298	25	which	which	WDT
cord-002542-f7l4ty2j	298	26	were	be	VBD
cord-002542-f7l4ty2j	298	27	counted	count	VBN
cord-002542-f7l4ty2j	298	28	using	use	VBG
cord-002542-f7l4ty2j	298	29	the	the	DT
cord-002542-f7l4ty2j	298	30	CIGAR	cigar	NN
cord-002542-f7l4ty2j	298	31	string	stre	VBG
cord-002542-f7l4ty2j	298	32	from	from	IN
cord-002542-f7l4ty2j	298	33	the	the	DT
cord-002542-f7l4ty2j	298	34	output	output	NN
cord-002542-f7l4ty2j	298	35	alignment	alignment	NN
cord-002542-f7l4ty2j	298	36	SAM	SAM	NNP
cord-002542-f7l4ty2j	298	37	file	file	NN
cord-002542-f7l4ty2j	298	38	.	.	.
cord-002542-f7l4ty2j	299	1	The	the	DT
cord-002542-f7l4ty2j	299	2	Pearson	Pearson	NNP
cord-002542-f7l4ty2j	299	3	correlation	correlation	NN
cord-002542-f7l4ty2j	299	4	coefficients	coefficient	NNS
cord-002542-f7l4ty2j	299	5	of	of	IN
cord-002542-f7l4ty2j	299	6	these	these	DT
cord-002542-f7l4ty2j	299	7	events	event	NNS
cord-002542-f7l4ty2j	299	8	to	to	IN
cord-002542-f7l4ty2j	299	9	those	those	DT
cord-002542-f7l4ty2j	299	10	found	find	VBN
cord-002542-f7l4ty2j	299	11	using	use	VBG
cord-002542-f7l4ty2j	299	12	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	299	13	were	be	VBD
cord-002542-f7l4ty2j	299	14	also	also	RB
cord-002542-f7l4ty2j	299	15	calculated	calculate	VBN
cord-002542-f7l4ty2j	299	16	.	.	.
cord-002542-f7l4ty2j	300	1	The	the	DT
cord-002542-f7l4ty2j	300	2	number	number	NN
cord-002542-f7l4ty2j	300	3	of	of	IN
cord-002542-f7l4ty2j	300	4	reads	read	NNS
cord-002542-f7l4ty2j	300	5	mapping	mapping	NN
cord-002542-f7l4ty2j	300	6	to	to	IN
cord-002542-f7l4ty2j	300	7	FHV	FHV	NNP
cord-002542-f7l4ty2j	300	8	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	300	9	and	and	CC
cord-002542-f7l4ty2j	300	10	FHV	FHV	NNP
cord-002542-f7l4ty2j	300	11	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	300	12	are	be	VBP
cord-002542-f7l4ty2j	300	13	indicated	indicate	VBN
cord-002542-f7l4ty2j	300	14	along	along	IN
cord-002542-f7l4ty2j	300	15	with	with	IN
cord-002542-f7l4ty2j	300	16	the	the	DT
cord-002542-f7l4ty2j	300	17	number	number	NN
cord-002542-f7l4ty2j	300	18	that	that	WDT
cord-002542-f7l4ty2j	300	19	contain	contain	VBP
cord-002542-f7l4ty2j	300	20	0	0	CD
cord-002542-f7l4ty2j	300	21	-	-	SYM
cord-002542-f7l4ty2j	300	22	5	5	CD
cord-002542-f7l4ty2j	300	23	or	or	CC
cord-002542-f7l4ty2j	300	24	more	more	JJR
cord-002542-f7l4ty2j	300	25	deletions	deletion	NNS
cord-002542-f7l4ty2j	300	26	of	of	IN
cord-002542-f7l4ty2j	300	27	at	at	RB
cord-002542-f7l4ty2j	300	28	least	least	JJS
cord-002542-f7l4ty2j	300	29	25	25	CD
cord-002542-f7l4ty2j	300	30	nts	nt	NNS
cord-002542-f7l4ty2j	300	31	.	.	.
cord-002542-f7l4ty2j	301	1	Only	only	RB
cord-002542-f7l4ty2j	301	2	a	a	DT
cord-002542-f7l4ty2j	301	3	small	small	JJ
cord-002542-f7l4ty2j	301	4	number	number	NN
cord-002542-f7l4ty2j	301	5	(	(	-LRB-
cord-002542-f7l4ty2j	301	6	<	<	NNP
cord-002542-f7l4ty2j	301	7	5	5	CD
cord-002542-f7l4ty2j	301	8	%	%	NN
cord-002542-f7l4ty2j	301	9	)	)	-RRB-
cord-002542-f7l4ty2j	301	10	remained	remain	VBD
cord-002542-f7l4ty2j	301	11	unmapped	unmapped	JJ
cord-002542-f7l4ty2j	301	12	.	.	.
cord-002542-f7l4ty2j	302	1	https://doi.org/10.1371/journal.ppat.1006365.t003	https://doi.org/10.1371/journal.ppat.1006365.t003	``
cord-002542-f7l4ty2j	302	2	Pathways	pathway	NNS
cord-002542-f7l4ty2j	302	3	of	of	IN
cord-002542-f7l4ty2j	302	4	FHV	FHV	NNP
cord-002542-f7l4ty2j	302	5	defective	defective	JJ
cord-002542-f7l4ty2j	302	6	RNA	RNA	NNP
cord-002542-f7l4ty2j	302	7	evolution	evolution	NN
cord-002542-f7l4ty2j	302	8	by	by	IN
cord-002542-f7l4ty2j	302	9	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	302	10	and	and	CC
cord-002542-f7l4ty2j	302	11	the	the	DT
cord-002542-f7l4ty2j	302	12	MinION	minion	XX
cord-002542-f7l4ty2j	303	1	the	the	DT
cord-002542-f7l4ty2j	303	2	expected	expect	VBN
cord-002542-f7l4ty2j	303	3	identities	identity	NNS
cord-002542-f7l4ty2j	303	4	based	base	VBN
cord-002542-f7l4ty2j	303	5	on	on	IN
cord-002542-f7l4ty2j	303	6	our	-PRON-	PRP$
cord-002542-f7l4ty2j	303	7	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	303	8	results	result	NNS
cord-002542-f7l4ty2j	303	9	and	and	CC
cord-002542-f7l4ty2j	303	10	previous	previous	JJ
cord-002542-f7l4ty2j	303	11	studies	study	NNS
cord-002542-f7l4ty2j	303	12	[	[	-LRB-
cord-002542-f7l4ty2j	303	13	8	8	CD
cord-002542-f7l4ty2j	303	14	,	,	,
cord-002542-f7l4ty2j	303	15	31	31	CD
cord-002542-f7l4ty2j	303	16	]	]	-RRB-
cord-002542-f7l4ty2j	303	17	.	.	.
cord-002542-f7l4ty2j	304	1	By	by	IN
cord-002542-f7l4ty2j	304	2	the	the	DT
cord-002542-f7l4ty2j	304	3	final	final	JJ
cord-002542-f7l4ty2j	304	4	passages	passage	NNS
cord-002542-f7l4ty2j	304	5	these	these	DT
cord-002542-f7l4ty2j	304	6	species	specie	NNS
cord-002542-f7l4ty2j	304	7	predominate	predominate	VBP
cord-002542-f7l4ty2j	304	8	,	,	,
cord-002542-f7l4ty2j	304	9	leaving	leave	VBG
cord-002542-f7l4ty2j	304	10	only	only	RB
cord-002542-f7l4ty2j	304	11	a	a	DT
cord-002542-f7l4ty2j	304	12	small	small	JJ
cord-002542-f7l4ty2j	304	13	percentage	percentage	NN
cord-002542-f7l4ty2j	304	14	of	of	IN
cord-002542-f7l4ty2j	304	15	full	full	JJ
cord-002542-f7l4ty2j	304	16	-	-	HYPH
cord-002542-f7l4ty2j	304	17	length	length	NN
cord-002542-f7l4ty2j	304	18	wild	wild	JJ
cord-002542-f7l4ty2j	304	19	-	-	HYPH
cord-002542-f7l4ty2j	304	20	type	type	NN
cord-002542-f7l4ty2j	304	21	viral	viral	JJ
cord-002542-f7l4ty2j	304	22	RNAs	rna	NNS
cord-002542-f7l4ty2j	304	23	.	.	.
cord-002542-f7l4ty2j	305	1	While	while	IN
cord-002542-f7l4ty2j	305	2	we	-PRON-	PRP
cord-002542-f7l4ty2j	305	3	can	can	MD
cord-002542-f7l4ty2j	305	4	readily	readily	RB
cord-002542-f7l4ty2j	305	5	identify	identify	VB
cord-002542-f7l4ty2j	305	6	mature	mature	JJ
cord-002542-f7l4ty2j	305	7	DI	DI	NNP
cord-002542-f7l4ty2j	305	8	-	-	HYPH
cord-002542-f7l4ty2j	305	9	RNAs	rna	NNS
cord-002542-f7l4ty2j	305	10	containing	contain	VBG
cord-002542-f7l4ty2j	305	11	two	two	CD
cord-002542-f7l4ty2j	305	12	or	or	CC
cord-002542-f7l4ty2j	305	13	more	more	JJR
cord-002542-f7l4ty2j	305	14	deletions	deletion	NNS
cord-002542-f7l4ty2j	305	15	,	,	,
cord-002542-f7l4ty2j	305	16	few	few	JJ
cord-002542-f7l4ty2j	305	17	single	single	JJ
cord-002542-f7l4ty2j	305	18	-	-	HYPH
cord-002542-f7l4ty2j	305	19	reads	read	NNS
cord-002542-f7l4ty2j	305	20	contain	contain	VBP
cord-002542-f7l4ty2j	305	21	just	just	RB
cord-002542-f7l4ty2j	305	22	one	one	CD
cord-002542-f7l4ty2j	305	23	deletion	deletion	NN
cord-002542-f7l4ty2j	305	24	(	(	-LRB-
cord-002542-f7l4ty2j	305	25	<	<	NNP
cord-002542-f7l4ty2j	305	26	6	6	CD
cord-002542-f7l4ty2j	305	27	%	%	NN
cord-002542-f7l4ty2j	305	28	)	)	-RRB-
cord-002542-f7l4ty2j	305	29	in	in	IN
cord-002542-f7l4ty2j	305	30	all	all	DT
cord-002542-f7l4ty2j	305	31	of	of	IN
cord-002542-f7l4ty2j	305	32	the	the	DT
cord-002542-f7l4ty2j	305	33	passages	passage	NNS
cord-002542-f7l4ty2j	305	34	.	.	.
cord-002542-f7l4ty2j	306	1	Moreover	moreover	RB
cord-002542-f7l4ty2j	306	2	,	,	,
cord-002542-f7l4ty2j	306	3	individual	individual	JJ
cord-002542-f7l4ty2j	306	4	species	specie	NNS
cord-002542-f7l4ty2j	306	5	are	be	VBP
cord-002542-f7l4ty2j	306	6	rarely	rarely	RB
cord-002542-f7l4ty2j	306	7	observed	observe	VBN
cord-002542-f7l4ty2j	306	8	again	again	RB
cord-002542-f7l4ty2j	306	9	in	in	IN
cord-002542-f7l4ty2j	306	10	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	306	11	passages	passage	NNS
cord-002542-f7l4ty2j	306	12	(	(	-LRB-
cord-002542-f7l4ty2j	306	13	S6	S6	NNP
cord-002542-f7l4ty2j	306	14	Fig	Fig	NNP
cord-002542-f7l4ty2j	306	15	and	and	CC
cord-002542-f7l4ty2j	306	16	S2	S2	NNP
cord-002542-f7l4ty2j	306	17	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	306	18	)	)	-RRB-
cord-002542-f7l4ty2j	306	19	.	.	.
cord-002542-f7l4ty2j	307	1	Importantly	importantly	RB
cord-002542-f7l4ty2j	307	2	,	,	,
cord-002542-f7l4ty2j	307	3	most	most	JJS
cord-002542-f7l4ty2j	307	4	of	of	IN
cord-002542-f7l4ty2j	307	5	these	these	DT
cord-002542-f7l4ty2j	307	6	single	single	JJ
cord-002542-f7l4ty2j	307	7	events	event	NNS
cord-002542-f7l4ty2j	307	8	do	do	VBP
cord-002542-f7l4ty2j	307	9	not	not	RB
cord-002542-f7l4ty2j	307	10	delete	delete	VB
cord-002542-f7l4ty2j	307	11	the	the	DT
cord-002542-f7l4ty2j	307	12	expected	expect	VBN
cord-002542-f7l4ty2j	307	13	regions	region	NNS
cord-002542-f7l4ty2j	307	14	common	common	JJ
cord-002542-f7l4ty2j	307	15	to	to	IN
cord-002542-f7l4ty2j	307	16	FHV	FHV	NNP
cord-002542-f7l4ty2j	307	17	DI	DI	NNP
cord-002542-f7l4ty2j	307	18	-	-	HYPH
cord-002542-f7l4ty2j	307	19	RNAs	rna	NNS
cord-002542-f7l4ty2j	307	20	.	.	.
cord-002542-f7l4ty2j	308	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	308	2	,	,	,
cord-002542-f7l4ty2j	308	3	they	-PRON-	PRP
cord-002542-f7l4ty2j	308	4	may	may	MD
cord-002542-f7l4ty2j	308	5	either	either	RB
cord-002542-f7l4ty2j	308	6	correspond	correspond	VB
cord-002542-f7l4ty2j	308	7	to	to	IN
cord-002542-f7l4ty2j	308	8	sequencing	sequencing	NN
cord-002542-f7l4ty2j	308	9	artifacts	artifact	NNS
cord-002542-f7l4ty2j	308	10	,	,	,
cord-002542-f7l4ty2j	308	11	or	or	CC
cord-002542-f7l4ty2j	308	12	transient	transient	JJ
cord-002542-f7l4ty2j	308	13	defective	defective	JJ
cord-002542-f7l4ty2j	308	14	RNA	RNA	NNP
cord-002542-f7l4ty2j	308	15	species	specie	NNS
cord-002542-f7l4ty2j	308	16	generated	generate	VBN
cord-002542-f7l4ty2j	308	17	due	due	IN
cord-002542-f7l4ty2j	308	18	to	to	IN
cord-002542-f7l4ty2j	308	19	stochastic	stochastic	JJ
cord-002542-f7l4ty2j	308	20	RNA	RNA	NNP
cord-002542-f7l4ty2j	308	21	recombination	recombination	NN
cord-002542-f7l4ty2j	308	22	,	,	,
cord-002542-f7l4ty2j	308	23	similar	similar	JJ
cord-002542-f7l4ty2j	308	24	to	to	IN
cord-002542-f7l4ty2j	308	25	the	the	DT
cord-002542-f7l4ty2j	308	26	low	low	JJ
cord-002542-f7l4ty2j	308	27	-	-	HYPH
cord-002542-f7l4ty2j	308	28	frequency	frequency	NN
cord-002542-f7l4ty2j	308	29	events	event	NNS
cord-002542-f7l4ty2j	308	30	observed	observe	VBN
cord-002542-f7l4ty2j	308	31	in	in	IN
cord-002542-f7l4ty2j	308	32	the	the	DT
cord-002542-f7l4ty2j	308	33	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	308	34	datasets	dataset	NNS
cord-002542-f7l4ty2j	308	35	.	.	.
cord-002542-f7l4ty2j	309	1	In	in	IN
cord-002542-f7l4ty2j	309	2	later	later	JJ
cord-002542-f7l4ty2j	309	3	passages	passage	NNS
cord-002542-f7l4ty2j	309	4	(	(	-LRB-
cord-002542-f7l4ty2j	309	5	beginning	begin	VBG
cord-002542-f7l4ty2j	309	6	at	at	IN
cord-002542-f7l4ty2j	309	7	passage	passage	NN
cord-002542-f7l4ty2j	309	8	3	3	CD
cord-002542-f7l4ty2j	309	9	)	)	-RRB-
cord-002542-f7l4ty2j	309	10	,	,	,
cord-002542-f7l4ty2j	309	11	we	-PRON-	PRP
cord-002542-f7l4ty2j	309	12	do	do	VBP
cord-002542-f7l4ty2j	309	13	begin	begin	VB
cord-002542-f7l4ty2j	309	14	to	to	TO
cord-002542-f7l4ty2j	309	15	see	see	VB
cord-002542-f7l4ty2j	309	16	the	the	DT
cord-002542-f7l4ty2j	309	17	presumptive	presumptive	JJ
cord-002542-f7l4ty2j	309	18	intermediates	intermediate	NNS
cord-002542-f7l4ty2j	309	19	(	(	-LRB-
cord-002542-f7l4ty2j	310	1	e.g.	e.g.	RB
cord-002542-f7l4ty2j	310	2	1_317	1_317	CD
cord-002542-f7l4ty2j	310	3	^	^	:
cord-002542-f7l4ty2j	310	4	1091_3107	1091_3107	CD
cord-002542-f7l4ty2j	310	5	or	or	CC
cord-002542-f7l4ty2j	310	6	1_1242	1_1242	CD
cord-002542-f7l4ty2j	310	7	^	^	NFP
cord-002542-f7l4ty2j	310	8	2301_3107	2301_3107	CD
cord-002542-f7l4ty2j	310	9	)	)	-RRB-
cord-002542-f7l4ty2j	310	10	of	of	IN
cord-002542-f7l4ty2j	310	11	mature	mature	JJ
cord-002542-f7l4ty2j	310	12	DI	DI	NNP
cord-002542-f7l4ty2j	310	13	-	-	HYPH
cord-002542-f7l4ty2j	310	14	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	310	15	(	(	-LRB-
cord-002542-f7l4ty2j	310	16	e.g.	e.g.	RB
cord-002542-f7l4ty2j	310	17	1_317	1_317	CD
cord-002542-f7l4ty2j	310	18	^	^	:
cord-002542-f7l4ty2j	310	19	1091_1242	1091_1242	CD
cord-002542-f7l4ty2j	310	20	^	^	:
cord-002542-f7l4ty2j	310	21	2301_3107	2301_3107	CD
cord-002542-f7l4ty2j	310	22	)	)	-RRB-
cord-002542-f7l4ty2j	310	23	.	.	.
cord-002542-f7l4ty2j	311	1	However	however	RB
cord-002542-f7l4ty2j	311	2	,	,	,
cord-002542-f7l4ty2j	311	3	this	this	DT
cord-002542-f7l4ty2j	311	4	is	be	VBZ
cord-002542-f7l4ty2j	311	5	after	after	IN
cord-002542-f7l4ty2j	311	6	the	the	DT
cord-002542-f7l4ty2j	311	7	mature	mature	JJ
cord-002542-f7l4ty2j	311	8	DI	DI	NNP
cord-002542-f7l4ty2j	311	9	-	-	HYPH
cord-002542-f7l4ty2j	311	10	RNAs	rna	NNS
cord-002542-f7l4ty2j	311	11	were	be	VBD
cord-002542-f7l4ty2j	311	12	first	first	RB
cord-002542-f7l4ty2j	311	13	observed	observe	VBN
cord-002542-f7l4ty2j	311	14	,	,	,
cord-002542-f7l4ty2j	311	15	and	and	CC
cord-002542-f7l4ty2j	311	16	after	after	IN
cord-002542-f7l4ty2j	311	17	the	the	DT
cord-002542-f7l4ty2j	311	18	point	point	NN
cord-002542-f7l4ty2j	311	19	at	at	IN
cord-002542-f7l4ty2j	311	20	which	which	WDT
cord-002542-f7l4ty2j	311	21	DI	DI	NNP
cord-002542-f7l4ty2j	311	22	-	-	HYPH
cord-002542-f7l4ty2j	311	23	RNAs	rna	NNS
cord-002542-f7l4ty2j	311	24	have	have	VBP
cord-002542-f7l4ty2j	311	25	begun	begin	VBN
cord-002542-f7l4ty2j	311	26	to	to	TO
cord-002542-f7l4ty2j	311	27	accumulate	accumulate	VB
cord-002542-f7l4ty2j	311	28	.	.	.
cord-002542-f7l4ty2j	312	1	Indeed	indeed	RB
cord-002542-f7l4ty2j	312	2	,	,	,
cord-002542-f7l4ty2j	312	3	in	in	IN
cord-002542-f7l4ty2j	312	4	passages	passage	NNS
cord-002542-f7l4ty2j	312	5	2	2	CD
cord-002542-f7l4ty2j	312	6	and	and	CC
cord-002542-f7l4ty2j	312	7	3	3	CD
cord-002542-f7l4ty2j	312	8	respectively	respectively	RB
cord-002542-f7l4ty2j	312	9	,	,	,
cord-002542-f7l4ty2j	312	10	mature	mature	JJ
cord-002542-f7l4ty2j	312	11	DI	DI	NNP
cord-002542-f7l4ty2j	312	12	-	-	HYPH
cord-002542-f7l4ty2j	312	13	RNAs	rna	NNS
cord-002542-f7l4ty2j	312	14	make	make	VBP
cord-002542-f7l4ty2j	312	15	up	up	RP
cord-002542-f7l4ty2j	312	16	1	1	CD
cord-002542-f7l4ty2j	312	17	%	%	NN
cord-002542-f7l4ty2j	312	18	and	and	CC
cord-002542-f7l4ty2j	312	19	30	30	CD
cord-002542-f7l4ty2j	312	20	%	%	NN
cord-002542-f7l4ty2j	312	21	of	of	IN
cord-002542-f7l4ty2j	312	22	the	the	DT
cord-002542-f7l4ty2j	312	23	viral	viral	JJ
cord-002542-f7l4ty2j	312	24	population	population	NN
cord-002542-f7l4ty2j	312	25	while	while	IN
cord-002542-f7l4ty2j	312	26	the	the	DT
cord-002542-f7l4ty2j	312	27	singly	singly	RB
cord-002542-f7l4ty2j	312	28	-	-	HYPH
cord-002542-f7l4ty2j	312	29	deleted	delete	VBN
cord-002542-f7l4ty2j	312	30	intermediates	intermediate	NNS
cord-002542-f7l4ty2j	312	31	make	make	VBP
cord-002542-f7l4ty2j	312	32	up	up	RP
cord-002542-f7l4ty2j	312	33	0	0	CD
cord-002542-f7l4ty2j	312	34	%	%	NN
cord-002542-f7l4ty2j	312	35	(	(	-LRB-
cord-002542-f7l4ty2j	312	36	unobserved	unobserved	JJ
cord-002542-f7l4ty2j	312	37	)	)	-RRB-
cord-002542-f7l4ty2j	312	38	and	and	CC
cord-002542-f7l4ty2j	312	39	3	3	CD
cord-002542-f7l4ty2j	312	40	%	%	NN
cord-002542-f7l4ty2j	312	41	.	.	.
cord-002542-f7l4ty2j	313	1	Together	together	RB
cord-002542-f7l4ty2j	313	2	with	with	IN
cord-002542-f7l4ty2j	313	3	the	the	DT
cord-002542-f7l4ty2j	313	4	observation	observation	NN
cord-002542-f7l4ty2j	313	5	of	of	IN
cord-002542-f7l4ty2j	313	6	rare	rare	JJ
cord-002542-f7l4ty2j	313	7	DI	DI	NNP
cord-002542-f7l4ty2j	313	8	-	-	HYPH
cord-002542-f7l4ty2j	313	9	RNAs	rna	NNS
cord-002542-f7l4ty2j	313	10	in	in	IN
cord-002542-f7l4ty2j	313	11	the	the	DT
cord-002542-f7l4ty2j	313	12	inoculum	inoculum	NN
cord-002542-f7l4ty2j	313	13	with	with	IN
cord-002542-f7l4ty2j	313	14	the	the	DT
cord-002542-f7l4ty2j	313	15	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	313	16	recombination	recombination	NN
cord-002542-f7l4ty2j	313	17	analysis	analysis	NN
cord-002542-f7l4ty2j	313	18	,	,	,
cord-002542-f7l4ty2j	313	19	these	these	DT
cord-002542-f7l4ty2j	313	20	data	datum	NNS
cord-002542-f7l4ty2j	313	21	indicate	indicate	VBP
cord-002542-f7l4ty2j	313	22	that	that	IN
cord-002542-f7l4ty2j	313	23	single	single	JJ
cord-002542-f7l4ty2j	313	24	-	-	HYPH
cord-002542-f7l4ty2j	313	25	deletion	deletion	NN
cord-002542-f7l4ty2j	313	26	species	specie	NNS
cord-002542-f7l4ty2j	313	27	do	do	VBP
cord-002542-f7l4ty2j	313	28	occur	occur	VB
cord-002542-f7l4ty2j	313	29	early	early	RB
cord-002542-f7l4ty2j	313	30	during	during	IN
cord-002542-f7l4ty2j	313	31	passaging	passaging	NN
cord-002542-f7l4ty2j	313	32	,	,	,
cord-002542-f7l4ty2j	313	33	but	but	CC
cord-002542-f7l4ty2j	313	34	remain	remain	VBP
cord-002542-f7l4ty2j	313	35	poorly	poorly	RB
cord-002542-f7l4ty2j	313	36	abundant	abundant	JJ
cord-002542-f7l4ty2j	313	37	and	and	CC
cord-002542-f7l4ty2j	313	38	do	do	VBP
cord-002542-f7l4ty2j	313	39	not	not	RB
cord-002542-f7l4ty2j	313	40	accumulate	accumulate	VB
cord-002542-f7l4ty2j	313	41	.	.	.
cord-002542-f7l4ty2j	314	1	In	in	IN
cord-002542-f7l4ty2j	314	2	contrast	contrast	NN
cord-002542-f7l4ty2j	314	3	,	,	,
cord-002542-f7l4ty2j	314	4	mature	mature	JJ
cord-002542-f7l4ty2j	314	5	DI	DI	NNP
cord-002542-f7l4ty2j	314	6	-	-	HYPH
cord-002542-f7l4ty2j	314	7	RNAs	rna	NNS
cord-002542-f7l4ty2j	314	8	are	be	VBP
cord-002542-f7l4ty2j	314	9	observed	observe	VBN
cord-002542-f7l4ty2j	314	10	to	to	TO
cord-002542-f7l4ty2j	314	11	rapidly	rapidly	RB
cord-002542-f7l4ty2j	314	12	accumulate	accumulate	VB
cord-002542-f7l4ty2j	314	13	between	between	IN
cord-002542-f7l4ty2j	314	14	passages	passage	NNS
cord-002542-f7l4ty2j	314	15	,	,	,
cord-002542-f7l4ty2j	314	16	indicating	indicate	VBG
cord-002542-f7l4ty2j	314	17	that	that	IN
cord-002542-f7l4ty2j	314	18	they	-PRON-	PRP
cord-002542-f7l4ty2j	314	19	possess	possess	VBP
cord-002542-f7l4ty2j	314	20	a	a	DT
cord-002542-f7l4ty2j	314	21	replicative	replicative	JJ
cord-002542-f7l4ty2j	314	22	advantage	advantage	NN
cord-002542-f7l4ty2j	314	23	above	above	IN
cord-002542-f7l4ty2j	314	24	both	both	DT
cord-002542-f7l4ty2j	314	25	wild	wild	JJ
cord-002542-f7l4ty2j	314	26	-	-	HYPH
cord-002542-f7l4ty2j	314	27	type	type	NN
cord-002542-f7l4ty2j	314	28	viral	viral	JJ
cord-002542-f7l4ty2j	314	29	genomes	genome	NNS
cord-002542-f7l4ty2j	314	30	and	and	CC
cord-002542-f7l4ty2j	314	31	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	314	32	defective	defective	JJ
cord-002542-f7l4ty2j	314	33	RNA	RNA	NNP
cord-002542-f7l4ty2j	314	34	species	specie	NNS
cord-002542-f7l4ty2j	314	35	.	.	.
cord-002542-f7l4ty2j	315	1	In	in	IN
cord-002542-f7l4ty2j	315	2	addition	addition	NN
cord-002542-f7l4ty2j	315	3	to	to	IN
cord-002542-f7l4ty2j	315	4	deletions	deletion	NNS
cord-002542-f7l4ty2j	315	5	,	,	,
cord-002542-f7l4ty2j	315	6	a	a	DT
cord-002542-f7l4ty2j	315	7	small	small	JJ
cord-002542-f7l4ty2j	315	8	number	number	NN
cord-002542-f7l4ty2j	315	9	of	of	IN
cord-002542-f7l4ty2j	315	10	defective	defective	JJ
cord-002542-f7l4ty2j	315	11	RNAs	rna	NNS
cord-002542-f7l4ty2j	315	12	first	first	RB
cord-002542-f7l4ty2j	315	13	appearing	appear	VBG
cord-002542-f7l4ty2j	315	14	at	at	IN
cord-002542-f7l4ty2j	315	15	passage	passage	NN
cord-002542-f7l4ty2j	315	16	5	5	CD
cord-002542-f7l4ty2j	315	17	contained	contain	VBN
cord-002542-f7l4ty2j	315	18	insertions	insertion	NNS
cord-002542-f7l4ty2j	315	19	.	.	.
cord-002542-f7l4ty2j	316	1	Interestingly	interestingly	RB
cord-002542-f7l4ty2j	316	2	,	,	,
cord-002542-f7l4ty2j	316	3	the	the	DT
cord-002542-f7l4ty2j	316	4	majority	majority	NN
cord-002542-f7l4ty2j	316	5	of	of	IN
cord-002542-f7l4ty2j	316	6	these	these	DT
cord-002542-f7l4ty2j	316	7	comprised	comprise	VBN
cord-002542-f7l4ty2j	316	8	short	short	JJ
cord-002542-f7l4ty2j	316	9	insertions	insertion	NNS
cord-002542-f7l4ty2j	316	10	of~200	of~200	DT
cord-002542-f7l4ty2j	316	11	nucleotides	nucleotide	NNS
cord-002542-f7l4ty2j	316	12	that	that	WDT
cord-002542-f7l4ty2j	316	13	were	be	VBD
cord-002542-f7l4ty2j	316	14	found	find	VBN
cord-002542-f7l4ty2j	316	15	in	in	IN
cord-002542-f7l4ty2j	316	16	first	first	JJ
cord-002542-f7l4ty2j	316	17	300nts	300nts	CD
cord-002542-f7l4ty2j	316	18	of	of	IN
cord-002542-f7l4ty2j	316	19	the	the	DT
cord-002542-f7l4ty2j	316	20	MinION	minion	XX
cord-002542-f7l4ty2j	316	21	reads	read	NNS
cord-002542-f7l4ty2j	316	22	and	and	CC
cord-002542-f7l4ty2j	316	23	were	be	VBD
cord-002542-f7l4ty2j	316	24	mapped	map	VBN
cord-002542-f7l4ty2j	316	25	between	between	IN
cord-002542-f7l4ty2j	316	26	nts	nts	NNPS
cord-002542-f7l4ty2j	316	27	19	19	CD
cord-002542-f7l4ty2j	316	28	and	and	CC
cord-002542-f7l4ty2j	316	29	20	20	CD
cord-002542-f7l4ty2j	316	30	of	of	IN
cord-002542-f7l4ty2j	316	31	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	316	32	.	.	.
cord-002542-f7l4ty2j	317	1	In	in	IN
cord-002542-f7l4ty2j	317	2	each	each	DT
cord-002542-f7l4ty2j	317	3	case	case	NN
cord-002542-f7l4ty2j	317	4	,	,	,
cord-002542-f7l4ty2j	317	5	these	these	DT
cord-002542-f7l4ty2j	317	6	inserts	insert	NNS
cord-002542-f7l4ty2j	317	7	corresponded	correspond	VBD
cord-002542-f7l4ty2j	317	8	to	to	IN
cord-002542-f7l4ty2j	317	9	nts	nt	NNS
cord-002542-f7l4ty2j	317	10	2300	2300	CD
cord-002542-f7l4ty2j	317	11	-	-	HYPH
cord-002542-f7l4ty2j	317	12	2513	2513	CD
cord-002542-f7l4ty2j	317	13	of	of	IN
cord-002542-f7l4ty2j	317	14	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	317	15	.	.	.
cord-002542-f7l4ty2j	318	1	This	this	DT
cord-002542-f7l4ty2j	318	2	region	region	NN
cord-002542-f7l4ty2j	318	3	corresponds	correspond	VBZ
cord-002542-f7l4ty2j	318	4	to	to	IN
cord-002542-f7l4ty2j	318	5	an	an	DT
cord-002542-f7l4ty2j	318	6	internal	internal	JJ
cord-002542-f7l4ty2j	318	7	response	response	NN
cord-002542-f7l4ty2j	318	8	element	element	NN
cord-002542-f7l4ty2j	318	9	(	(	-LRB-
cord-002542-f7l4ty2j	318	10	intRE	intRE	NNP
cord-002542-f7l4ty2j	318	11	)	)	-RRB-
cord-002542-f7l4ty2j	318	12	of	of	IN
cord-002542-f7l4ty2j	318	13	the	the	DT
cord-002542-f7l4ty2j	318	14	Proximal	Proximal	NNP
cord-002542-f7l4ty2j	318	15	Sub	Sub	NNP
cord-002542-f7l4ty2j	318	16	-	-	HYPH
cord-002542-f7l4ty2j	318	17	genomic	genomic	JJ
cord-002542-f7l4ty2j	318	18	RNA	RNA	NNP
cord-002542-f7l4ty2j	318	19	Control	Control	NNP
cord-002542-f7l4ty2j	318	20	Element	Element	NNP
cord-002542-f7l4ty2j	318	21	(	(	-LRB-
cord-002542-f7l4ty2j	318	22	PSCE	PSCE	NNP
cord-002542-f7l4ty2j	318	23	)	)	-RRB-
cord-002542-f7l4ty2j	318	24	previously	previously	RB
cord-002542-f7l4ty2j	318	25	identified	identify	VBN
cord-002542-f7l4ty2j	318	26	as	as	IN
cord-002542-f7l4ty2j	318	27	being	be	VBG
cord-002542-f7l4ty2j	318	28	essential	essential	JJ
cord-002542-f7l4ty2j	318	29	for	for	IN
cord-002542-f7l4ty2j	318	30	FHV	FHV	NNP
cord-002542-f7l4ty2j	318	31	RNA	RNA	NNP
cord-002542-f7l4ty2j	318	32	replication	replication	NN
cord-002542-f7l4ty2j	318	33	and	and	CC
cord-002542-f7l4ty2j	318	34	conserved	conserve	VBN
cord-002542-f7l4ty2j	318	35	in	in	IN
cord-002542-f7l4ty2j	318	36	DI	DI	NNP
cord-002542-f7l4ty2j	318	37	-	-	HYPH
cord-002542-f7l4ty2j	318	38	RNAs	rna	NNS
cord-002542-f7l4ty2j	318	39	species	specie	NNS
cord-002542-f7l4ty2j	318	40	[	[	-LRB-
cord-002542-f7l4ty2j	318	41	60	60	CD
cord-002542-f7l4ty2j	318	42	]	]	-RRB-
cord-002542-f7l4ty2j	318	43	.	.	.
cord-002542-f7l4ty2j	319	1	The	the	DT
cord-002542-f7l4ty2j	319	2	most	most	RBS
cord-002542-f7l4ty2j	319	3	common	common	JJ
cord-002542-f7l4ty2j	319	4	deletion	deletion	NN
cord-002542-f7l4ty2j	319	5	in	in	IN
cord-002542-f7l4ty2j	319	6	the	the	DT
cord-002542-f7l4ty2j	319	7	DI	DI	NNP
cord-002542-f7l4ty2j	319	8	-	-	HYPH
cord-002542-f7l4ty2j	319	9	RNAs	rna	NNS
cord-002542-f7l4ty2j	319	10	in	in	IN
cord-002542-f7l4ty2j	319	11	this	this	DT
cord-002542-f7l4ty2j	319	12	region	region	NN
cord-002542-f7l4ty2j	319	13	of	of	IN
cord-002542-f7l4ty2j	319	14	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	319	15	for	for	IN
cord-002542-f7l4ty2j	319	16	the	the	DT
cord-002542-f7l4ty2j	319	17	final	final	JJ
cord-002542-f7l4ty2j	319	18	passages	passage	NNS
cord-002542-f7l4ty2j	319	19	are	be	VBP
cord-002542-f7l4ty2j	319	20	from	from	IN
cord-002542-f7l4ty2j	319	21	1242	1242	CD
cord-002542-f7l4ty2j	319	22	to	to	IN
cord-002542-f7l4ty2j	319	23	2301	2301	CD
cord-002542-f7l4ty2j	319	24	,	,	,
cord-002542-f7l4ty2j	319	25	which	which	WDT
cord-002542-f7l4ty2j	319	26	retains	retain	VBZ
cord-002542-f7l4ty2j	319	27	the	the	DT
cord-002542-f7l4ty2j	319	28	intRE	intRE	NNP
cord-002542-f7l4ty2j	319	29	.	.	.
cord-002542-f7l4ty2j	320	1	However	however	RB
cord-002542-f7l4ty2j	320	2	,	,	,
cord-002542-f7l4ty2j	320	3	there	there	EX
cord-002542-f7l4ty2j	320	4	are	be	VBP
cord-002542-f7l4ty2j	320	5	also	also	RB
cord-002542-f7l4ty2j	320	6	a	a	DT
cord-002542-f7l4ty2j	320	7	large	large	JJ
cord-002542-f7l4ty2j	320	8	number	number	NN
cord-002542-f7l4ty2j	320	9	of	of	IN
cord-002542-f7l4ty2j	320	10	deletions	deletion	NNS
cord-002542-f7l4ty2j	320	11	ranging	range	VBG
cord-002542-f7l4ty2j	320	12	from	from	IN
cord-002542-f7l4ty2j	320	13	1245	1245	CD
cord-002542-f7l4ty2j	320	14	to	to	IN
cord-002542-f7l4ty2j	320	15	2514	2514	CD
cord-002542-f7l4ty2j	320	16	,	,	,
cord-002542-f7l4ty2j	320	17	which	which	WDT
cord-002542-f7l4ty2j	320	18	would	would	MD
cord-002542-f7l4ty2j	320	19	delete	delete	VB
cord-002542-f7l4ty2j	320	20	the	the	DT
cord-002542-f7l4ty2j	320	21	essential	essential	JJ
cord-002542-f7l4ty2j	320	22	intRE	intRE	NNP
cord-002542-f7l4ty2j	320	23	.	.	.
cord-002542-f7l4ty2j	321	1	Closer	close	JJR
cord-002542-f7l4ty2j	321	2	inspection	inspection	NN
cord-002542-f7l4ty2j	321	3	of	of	IN
cord-002542-f7l4ty2j	321	4	the	the	DT
cord-002542-f7l4ty2j	321	5	MinION	MinION	NNP
cord-002542-f7l4ty2j	321	6	data	datum	NNS
cord-002542-f7l4ty2j	321	7	reveals	reveal	VBZ
cord-002542-f7l4ty2j	321	8	that	that	IN
cord-002542-f7l4ty2j	321	9	the	the	DT
cord-002542-f7l4ty2j	321	10	majority	majority	NN
cord-002542-f7l4ty2j	321	11	of	of	IN
cord-002542-f7l4ty2j	321	12	these	these	DT
cord-002542-f7l4ty2j	321	13	reads	read	NNS
cord-002542-f7l4ty2j	321	14	(	(	-LRB-
cord-002542-f7l4ty2j	321	15	>	>	NFP
cord-002542-f7l4ty2j	321	16	90	90	CD
cord-002542-f7l4ty2j	321	17	%	%	NN
cord-002542-f7l4ty2j	321	18	)	)	-RRB-
cord-002542-f7l4ty2j	321	19	that	that	WDT
cord-002542-f7l4ty2j	321	20	contain	contain	VBP
cord-002542-f7l4ty2j	321	21	the	the	DT
cord-002542-f7l4ty2j	321	22	200nt	200nt	NNP
cord-002542-f7l4ty2j	321	23	intRE	intre	JJ
cord-002542-f7l4ty2j	321	24	insertion	insertion	NN
cord-002542-f7l4ty2j	321	25	concomitantly	concomitantly	RB
cord-002542-f7l4ty2j	321	26	contained	contain	VBD
cord-002542-f7l4ty2j	321	27	deletions	deletion	NNS
cord-002542-f7l4ty2j	321	28	from	from	IN
cord-002542-f7l4ty2j	321	29	1245	1245	CD
cord-002542-f7l4ty2j	321	30	-	-	SYM
cord-002542-f7l4ty2j	321	31	2514	2514	CD
cord-002542-f7l4ty2j	321	32	,	,	,
cord-002542-f7l4ty2j	321	33	indicating	indicate	VBG
cord-002542-f7l4ty2j	321	34	that	that	IN
cord-002542-f7l4ty2j	321	35	these	these	DT
cord-002542-f7l4ty2j	321	36	two	two	CD
cord-002542-f7l4ty2j	321	37	events	event	NNS
cord-002542-f7l4ty2j	321	38	are	be	VBP
cord-002542-f7l4ty2j	321	39	correlated	correlate	VBN
cord-002542-f7l4ty2j	321	40	.	.	.
cord-002542-f7l4ty2j	322	1	The	the	DT
cord-002542-f7l4ty2j	322	2	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	322	3	data	datum	NNS
cord-002542-f7l4ty2j	322	4	also	also	RB
cord-002542-f7l4ty2j	322	5	shows	show	VBZ
cord-002542-f7l4ty2j	322	6	a	a	DT
cord-002542-f7l4ty2j	322	7	frequent	frequent	JJ
cord-002542-f7l4ty2j	322	8	recombination	recombination	NN
cord-002542-f7l4ty2j	322	9	event	event	NN
cord-002542-f7l4ty2j	322	10	,	,	,
cord-002542-f7l4ty2j	322	11	2513	2513	CD
cord-002542-f7l4ty2j	322	12	^	^	SYM
cord-002542-f7l4ty2j	322	13	21	21	CD
cord-002542-f7l4ty2j	322	14	,	,	,
cord-002542-f7l4ty2j	322	15	which	which	WDT
cord-002542-f7l4ty2j	322	16	appears	appear	VBZ
cord-002542-f7l4ty2j	322	17	first	first	RB
cord-002542-f7l4ty2j	322	18	in	in	IN
cord-002542-f7l4ty2j	322	19	passage	passage	NN
cord-002542-f7l4ty2j	322	20	4	4	CD
cord-002542-f7l4ty2j	322	21	and	and	CC
cord-002542-f7l4ty2j	322	22	is	be	VBZ
cord-002542-f7l4ty2j	322	23	among	among	IN
cord-002542-f7l4ty2j	322	24	the	the	DT
cord-002542-f7l4ty2j	322	25	10	10	CD
cord-002542-f7l4ty2j	322	26	most	most	RBS
cord-002542-f7l4ty2j	322	27	common	common	JJ
cord-002542-f7l4ty2j	322	28	events	event	NNS
cord-002542-f7l4ty2j	322	29	in	in	IN
cord-002542-f7l4ty2j	322	30	the	the	DT
cord-002542-f7l4ty2j	322	31	final	final	JJ
cord-002542-f7l4ty2j	322	32	5	5	CD
cord-002542-f7l4ty2j	322	33	passages	passage	NNS
cord-002542-f7l4ty2j	322	34	(	(	-LRB-
cord-002542-f7l4ty2j	322	35	S1	S1	NNP
cord-002542-f7l4ty2j	322	36	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	322	37	)	)	-RRB-
cord-002542-f7l4ty2j	322	38	.	.	.
cord-002542-f7l4ty2j	323	1	This	this	DT
cord-002542-f7l4ty2j	323	2	matches	match	VBZ
cord-002542-f7l4ty2j	323	3	precisely	precisely	RB
cord-002542-f7l4ty2j	323	4	the	the	DT
cord-002542-f7l4ty2j	323	5	3	3	CD
cord-002542-f7l4ty2j	323	6	'	'	POS
cord-002542-f7l4ty2j	323	7	junction	junction	NN
cord-002542-f7l4ty2j	323	8	site	site	NN
cord-002542-f7l4ty2j	323	9	of	of	IN
cord-002542-f7l4ty2j	323	10	the	the	DT
cord-002542-f7l4ty2j	323	11	insertion	insertion	NN
cord-002542-f7l4ty2j	323	12	event	event	NN
cord-002542-f7l4ty2j	323	13	detected	detect	VBN
cord-002542-f7l4ty2j	323	14	in	in	IN
cord-002542-f7l4ty2j	323	15	the	the	DT
cord-002542-f7l4ty2j	323	16	Min	Min	NNP
cord-002542-f7l4ty2j	323	17	-	-	HYPH
cord-002542-f7l4ty2j	323	18	ION	ION	NNP
cord-002542-f7l4ty2j	323	19	data	datum	NNS
cord-002542-f7l4ty2j	323	20	.	.	.
cord-002542-f7l4ty2j	324	1	However	however	RB
cord-002542-f7l4ty2j	324	2	,	,	,
cord-002542-f7l4ty2j	324	3	the	the	DT
cord-002542-f7l4ty2j	324	4	event	event	NN
cord-002542-f7l4ty2j	324	5	20	20	CD
cord-002542-f7l4ty2j	324	6	^	^	SYM
cord-002542-f7l4ty2j	324	7	2300	2300	CD
cord-002542-f7l4ty2j	324	8	corresponding	correspond	VBG
cord-002542-f7l4ty2j	324	9	to	to	IN
cord-002542-f7l4ty2j	324	10	the	the	DT
cord-002542-f7l4ty2j	324	11	5	5	CD
cord-002542-f7l4ty2j	324	12	'	'	POS
cord-002542-f7l4ty2j	324	13	junction	junction	NN
cord-002542-f7l4ty2j	324	14	site	site	NN
cord-002542-f7l4ty2j	324	15	was	be	VBD
cord-002542-f7l4ty2j	324	16	not	not	RB
cord-002542-f7l4ty2j	324	17	detected	detect	VBN
cord-002542-f7l4ty2j	324	18	in	in	IN
cord-002542-f7l4ty2j	324	19	our	-PRON-	PRP$
cord-002542-f7l4ty2j	324	20	initial	initial	JJ
cord-002542-f7l4ty2j	324	21	ViReMa	virema	NN
cord-002542-f7l4ty2j	324	22	analysis	analysis	NN
cord-002542-f7l4ty2j	324	23	of	of	IN
cord-002542-f7l4ty2j	324	24	the	the	DT
cord-002542-f7l4ty2j	324	25	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	324	26	data	datum	NNS
cord-002542-f7l4ty2j	324	27	as	as	IN
cord-002542-f7l4ty2j	324	28	this	this	DT
cord-002542-f7l4ty2j	324	29	would	would	MD
cord-002542-f7l4ty2j	324	30	have	have	VB
cord-002542-f7l4ty2j	324	31	required	require	VBN
cord-002542-f7l4ty2j	324	32	a	a	DT
cord-002542-f7l4ty2j	324	33	search	search	NN
cord-002542-f7l4ty2j	324	34	seed	seed	NN
cord-002542-f7l4ty2j	324	35	length	length	NN
cord-002542-f7l4ty2j	324	36	of	of	IN
cord-002542-f7l4ty2j	324	37	less	less	JJR
cord-002542-f7l4ty2j	324	38	than	than	IN
cord-002542-f7l4ty2j	324	39	20	20	CD
cord-002542-f7l4ty2j	324	40	nts	nt	NNS
cord-002542-f7l4ty2j	324	41	.	.	.
cord-002542-f7l4ty2j	325	1	Repeating	repeat	VBG
cord-002542-f7l4ty2j	325	2	the	the	DT
cord-002542-f7l4ty2j	325	3	ViReMa	virema	NN
cord-002542-f7l4ty2j	325	4	analysis	analysis	NN
cord-002542-f7l4ty2j	325	5	using	use	VBG
cord-002542-f7l4ty2j	325	6	a	a	DT
cord-002542-f7l4ty2j	325	7	seed	seed	NN
cord-002542-f7l4ty2j	325	8	length	length	NN
cord-002542-f7l4ty2j	325	9	of	of	IN
cord-002542-f7l4ty2j	325	10	17	17	CD
cord-002542-f7l4ty2j	325	11	does	do	VBZ
cord-002542-f7l4ty2j	325	12	indeed	indeed	RB
cord-002542-f7l4ty2j	325	13	reveal	reveal	VB
cord-002542-f7l4ty2j	325	14	the	the	DT
cord-002542-f7l4ty2j	325	15	presence	presence	NN
cord-002542-f7l4ty2j	325	16	of	of	IN
cord-002542-f7l4ty2j	325	17	the	the	DT
cord-002542-f7l4ty2j	325	18	20	20	CD
cord-002542-f7l4ty2j	325	19	^	^	SYM
cord-002542-f7l4ty2j	325	20	2300	2300	CD
cord-002542-f7l4ty2j	325	21	recombination	recombination	NN
cord-002542-f7l4ty2j	325	22	event	event	NN
cord-002542-f7l4ty2j	325	23	.	.	.
cord-002542-f7l4ty2j	326	1	This	this	DT
cord-002542-f7l4ty2j	326	2	event	event	NN
cord-002542-f7l4ty2j	326	3	is	be	VBZ
cord-002542-f7l4ty2j	326	4	rarely	rarely	RB
cord-002542-f7l4ty2j	326	5	observed	observe	VBN
cord-002542-f7l4ty2j	326	6	in	in	IN
cord-002542-f7l4ty2j	326	7	either	either	DT
cord-002542-f7l4ty2j	326	8	of	of	IN
cord-002542-f7l4ty2j	326	9	the	the	DT
cord-002542-f7l4ty2j	326	10	other	other	JJ
cord-002542-f7l4ty2j	326	11	two	two	CD
cord-002542-f7l4ty2j	326	12	replicate	replicate	VB
cord-002542-f7l4ty2j	326	13	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	326	14	data	datum	NNS
cord-002542-f7l4ty2j	326	15	(	(	-LRB-
cord-002542-f7l4ty2j	326	16	7	7	CD
cord-002542-f7l4ty2j	326	17	and	and	CC
cord-002542-f7l4ty2j	326	18	31	31	CD
cord-002542-f7l4ty2j	326	19	total	total	JJ
cord-002542-f7l4ty2j	326	20	reads	read	NNS
cord-002542-f7l4ty2j	326	21	across	across	IN
cord-002542-f7l4ty2j	326	22	all	all	DT
cord-002542-f7l4ty2j	326	23	passages	passage	NNS
cord-002542-f7l4ty2j	326	24	of	of	IN
cord-002542-f7l4ty2j	326	25	replicates	replicate	NNS
cord-002542-f7l4ty2j	326	26	1	1	CD
cord-002542-f7l4ty2j	326	27	and	and	CC
cord-002542-f7l4ty2j	326	28	3	3	CD
cord-002542-f7l4ty2j	326	29	respectively	respectively	RB
cord-002542-f7l4ty2j	326	30	)	)	-RRB-
cord-002542-f7l4ty2j	326	31	.	.	.
cord-002542-f7l4ty2j	327	1	These	these	DT
cord-002542-f7l4ty2j	327	2	data	datum	NNS
cord-002542-f7l4ty2j	327	3	indicate	indicate	VBP
cord-002542-f7l4ty2j	327	4	that	that	IN
cord-002542-f7l4ty2j	327	5	in	in	IN
cord-002542-f7l4ty2j	327	6	a	a	DT
cord-002542-f7l4ty2j	327	7	number	number	NN
cord-002542-f7l4ty2j	327	8	of	of	IN
cord-002542-f7l4ty2j	327	9	defective	defective	JJ
cord-002542-f7l4ty2j	327	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	327	11	genomes	genome	NNS
cord-002542-f7l4ty2j	327	12	,	,	,
cord-002542-f7l4ty2j	327	13	the	the	DT
cord-002542-f7l4ty2j	327	14	intRE	intre	JJ
cord-002542-f7l4ty2j	327	15	element	element	NN
cord-002542-f7l4ty2j	327	16	has	have	VBZ
cord-002542-f7l4ty2j	327	17	been	be	VBN
cord-002542-f7l4ty2j	327	18	deleted	delete	VBN
cord-002542-f7l4ty2j	327	19	and	and	CC
cord-002542-f7l4ty2j	327	20	subsequently	subsequently	RB
cord-002542-f7l4ty2j	327	21	re	re	VB
cord-002542-f7l4ty2j	327	22	-	-	VBN
cord-002542-f7l4ty2j	327	23	inserted	insert	VBN
cord-002542-f7l4ty2j	327	24	at	at	IN
cord-002542-f7l4ty2j	327	25	the	the	DT
cord-002542-f7l4ty2j	327	26	5	5	CD
cord-002542-f7l4ty2j	327	27	'	'	NN
cord-002542-f7l4ty2j	327	28	end	end	NN
cord-002542-f7l4ty2j	327	29	of	of	IN
cord-002542-f7l4ty2j	327	30	the	the	DT
cord-002542-f7l4ty2j	327	31	defective	defective	JJ
cord-002542-f7l4ty2j	327	32	RNA	RNA	NNP
cord-002542-f7l4ty2j	327	33	genome	genome	NN
cord-002542-f7l4ty2j	327	34	.	.	.
cord-002542-f7l4ty2j	328	1	As	as	IN
cord-002542-f7l4ty2j	328	2	the	the	DT
cord-002542-f7l4ty2j	328	3	intRE	intre	JJ
cord-002542-f7l4ty2j	328	4	element	element	NN
cord-002542-f7l4ty2j	328	5	is	be	VBZ
cord-002542-f7l4ty2j	328	6	required	require	VBN
cord-002542-f7l4ty2j	328	7	for	for	IN
cord-002542-f7l4ty2j	328	8	regulation	regulation	NN
cord-002542-f7l4ty2j	328	9	of	of	IN
cord-002542-f7l4ty2j	328	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	328	11	replication	replication	NN
cord-002542-f7l4ty2j	328	12	,	,	,
cord-002542-f7l4ty2j	328	13	presumably	presumably	RB
cord-002542-f7l4ty2j	328	14	this	this	DT
cord-002542-f7l4ty2j	328	15	maintains	maintain	VBZ
cord-002542-f7l4ty2j	328	16	the	the	DT
cord-002542-f7l4ty2j	328	17	ability	ability	NN
cord-002542-f7l4ty2j	328	18	for	for	IN
cord-002542-f7l4ty2j	328	19	this	this	DT
cord-002542-f7l4ty2j	328	20	highly	highly	RB
cord-002542-f7l4ty2j	328	21	-	-	HYPH
cord-002542-f7l4ty2j	328	22	rearranged	rearrange	VBN
cord-002542-f7l4ty2j	328	23	defective	defective	JJ
cord-002542-f7l4ty2j	328	24	RNA	RNA	NNP
cord-002542-f7l4ty2j	328	25	to	to	TO
cord-002542-f7l4ty2j	328	26	replicate	replicate	VB
cord-002542-f7l4ty2j	328	27	.	.	.
cord-002542-f7l4ty2j	329	1	These	these	DT
cord-002542-f7l4ty2j	329	2	data	datum	NNS
cord-002542-f7l4ty2j	329	3	provide	provide	VBP
cord-002542-f7l4ty2j	329	4	a	a	DT
cord-002542-f7l4ty2j	329	5	comprehensive	comprehensive	JJ
cord-002542-f7l4ty2j	329	6	overview	overview	NN
cord-002542-f7l4ty2j	329	7	of	of	IN
cord-002542-f7l4ty2j	329	8	the	the	DT
cord-002542-f7l4ty2j	329	9	different	different	JJ
cord-002542-f7l4ty2j	329	10	species	specie	NNS
cord-002542-f7l4ty2j	329	11	of	of	IN
cord-002542-f7l4ty2j	329	12	defective	defective	JJ
cord-002542-f7l4ty2j	329	13	RNAs	rna	NNS
cord-002542-f7l4ty2j	329	14	that	that	WDT
cord-002542-f7l4ty2j	329	15	are	be	VBP
cord-002542-f7l4ty2j	329	16	present	present	JJ
cord-002542-f7l4ty2j	329	17	during	during	IN
cord-002542-f7l4ty2j	329	18	viral	viral	JJ
cord-002542-f7l4ty2j	329	19	passaging	passaging	NN
cord-002542-f7l4ty2j	329	20	.	.	.
cord-002542-f7l4ty2j	330	1	Illustrating	illustrate	VBG
cord-002542-f7l4ty2j	330	2	such	such	PDT
cord-002542-f7l4ty2j	330	3	a	a	DT
cord-002542-f7l4ty2j	330	4	complex	complex	JJ
cord-002542-f7l4ty2j	330	5	set	set	NN
cord-002542-f7l4ty2j	330	6	of	of	IN
cord-002542-f7l4ty2j	330	7	data	data	NN
cord-002542-f7l4ty2j	330	8	is	be	VBZ
cord-002542-f7l4ty2j	330	9	a	a	DT
cord-002542-f7l4ty2j	330	10	challenge	challenge	NN
cord-002542-f7l4ty2j	330	11	as	as	IN
cord-002542-f7l4ty2j	330	12	each	each	DT
cord-002542-f7l4ty2j	330	13	sample	sample	NN
cord-002542-f7l4ty2j	330	14	contains	contain	VBZ
cord-002542-f7l4ty2j	330	15	a	a	DT
cord-002542-f7l4ty2j	330	16	large	large	JJ
cord-002542-f7l4ty2j	330	17	number	number	NN
cord-002542-f7l4ty2j	330	18	of	of	IN
cord-002542-f7l4ty2j	330	19	genome	genome	NN
cord-002542-f7l4ty2j	330	20	arrangements	arrangement	NNS
cord-002542-f7l4ty2j	330	21	(	(	-LRB-
cord-002542-f7l4ty2j	330	22	6030	6030	CD
cord-002542-f7l4ty2j	330	23	and	and	CC
cord-002542-f7l4ty2j	330	24	3639	3639	CD
cord-002542-f7l4ty2j	330	25	for	for	IN
cord-002542-f7l4ty2j	330	26	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	330	27	and	and	CC
cord-002542-f7l4ty2j	330	28	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	330	29	respectively	respectively	RB
cord-002542-f7l4ty2j	330	30	)	)	-RRB-
cord-002542-f7l4ty2j	330	31	and	and	CC
cord-002542-f7l4ty2j	330	32	frequencies	frequency	NNS
cord-002542-f7l4ty2j	330	33	of	of	IN
cord-002542-f7l4ty2j	330	34	these	these	DT
cord-002542-f7l4ty2j	330	35	species	specie	NNS
cord-002542-f7l4ty2j	330	36	vary	vary	VBP
cord-002542-f7l4ty2j	330	37	substantially	substantially	RB
cord-002542-f7l4ty2j	330	38	over	over	IN
cord-002542-f7l4ty2j	330	39	time	time	NN
cord-002542-f7l4ty2j	330	40	.	.	.
cord-002542-f7l4ty2j	331	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	331	2	found	find	VBD
cord-002542-f7l4ty2j	331	3	that	that	IN
cord-002542-f7l4ty2j	331	4	illustrating	illustrate	VBG
cord-002542-f7l4ty2j	331	5	these	these	DT
cord-002542-f7l4ty2j	331	6	data	datum	NNS
cord-002542-f7l4ty2j	331	7	as	as	IN
cord-002542-f7l4ty2j	331	8	a	a	DT
cord-002542-f7l4ty2j	331	9	stacked	stack	VBN
cord-002542-f7l4ty2j	331	10	area	area	NN
cord-002542-f7l4ty2j	331	11	plot	plot	NN
cord-002542-f7l4ty2j	331	12	gave	give	VBD
cord-002542-f7l4ty2j	331	13	the	the	DT
cord-002542-f7l4ty2j	331	14	most	most	RBS
cord-002542-f7l4ty2j	331	15	informative	informative	JJ
cord-002542-f7l4ty2j	331	16	summary	summary	NN
cord-002542-f7l4ty2j	331	17	of	of	IN
cord-002542-f7l4ty2j	331	18	the	the	DT
cord-002542-f7l4ty2j	331	19	changes	change	NNS
cord-002542-f7l4ty2j	331	20	of	of	IN
cord-002542-f7l4ty2j	331	21	the	the	DT
cord-002542-f7l4ty2j	331	22	many	many	JJ
cord-002542-f7l4ty2j	331	23	different	different	JJ
cord-002542-f7l4ty2j	331	24	type	type	NN
cord-002542-f7l4ty2j	331	25	of	of	IN
cord-002542-f7l4ty2j	331	26	DI	DI	NNP
cord-002542-f7l4ty2j	331	27	-	-	HYPH
cord-002542-f7l4ty2j	331	28	RNA	RNA	NNP
cord-002542-f7l4ty2j	331	29	species	species	NN
cord-002542-f7l4ty2j	331	30	over	over	IN
cord-002542-f7l4ty2j	331	31	time	time	NN
cord-002542-f7l4ty2j	331	32	.	.	.
cord-002542-f7l4ty2j	332	1	Due	due	IN
cord-002542-f7l4ty2j	332	2	to	to	IN
cord-002542-f7l4ty2j	332	3	the	the	DT
cord-002542-f7l4ty2j	332	4	moderate	moderate	JJ
cord-002542-f7l4ty2j	332	5	errorrate	errorrate	NN
cord-002542-f7l4ty2j	332	6	of	of	IN
cord-002542-f7l4ty2j	332	7	the	the	DT
cord-002542-f7l4ty2j	332	8	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	332	9	read	read	NNP
cord-002542-f7l4ty2j	332	10	data	data	NNP
cord-002542-f7l4ty2j	332	11	,	,	,
cord-002542-f7l4ty2j	332	12	the	the	DT
cord-002542-f7l4ty2j	332	13	exact	exact	JJ
cord-002542-f7l4ty2j	332	14	identification	identification	NN
cord-002542-f7l4ty2j	332	15	of	of	IN
cord-002542-f7l4ty2j	332	16	a	a	DT
cord-002542-f7l4ty2j	332	17	recombination	recombination	NN
cord-002542-f7l4ty2j	332	18	event	event	NN
cord-002542-f7l4ty2j	332	19	and	and	CC
cord-002542-f7l4ty2j	332	20	thus	thus	RB
cord-002542-f7l4ty2j	332	21	annotation	annotation	NN
cord-002542-f7l4ty2j	332	22	of	of	IN
cord-002542-f7l4ty2j	332	23	that	that	DT
cord-002542-f7l4ty2j	332	24	genome	genome	NN
cord-002542-f7l4ty2j	332	25	may	may	MD
cord-002542-f7l4ty2j	332	26	be	be	VB
cord-002542-f7l4ty2j	332	27	incorrect	incorrect	JJ
cord-002542-f7l4ty2j	332	28	.	.	.
cord-002542-f7l4ty2j	333	1	This	this	DT
cord-002542-f7l4ty2j	333	2	would	would	MD
cord-002542-f7l4ty2j	333	3	result	result	VB
cord-002542-f7l4ty2j	333	4	in	in	IN
cord-002542-f7l4ty2j	333	5	an	an	DT
cord-002542-f7l4ty2j	333	6	over	over	IN
cord-002542-f7l4ty2j	333	7	-	-	HYPH
cord-002542-f7l4ty2j	333	8	estimation	estimation	NN
cord-002542-f7l4ty2j	333	9	in	in	IN
cord-002542-f7l4ty2j	333	10	the	the	DT
cord-002542-f7l4ty2j	333	11	potential	potential	JJ
cord-002542-f7l4ty2j	333	12	number	number	NN
cord-002542-f7l4ty2j	333	13	of	of	IN
cord-002542-f7l4ty2j	333	14	unique	unique	JJ
cord-002542-f7l4ty2j	333	15	structural	structural	JJ
cord-002542-f7l4ty2j	333	16	variants	variant	NNS
cord-002542-f7l4ty2j	333	17	.	.	.
cord-002542-f7l4ty2j	334	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	334	2	we	-PRON-	PRP
cord-002542-f7l4ty2j	334	3	filtered	filter	VBD
cord-002542-f7l4ty2j	334	4	datasets	dataset	NNS
cord-002542-f7l4ty2j	334	5	by	by	IN
cord-002542-f7l4ty2j	334	6	requiring	require	VBG
cord-002542-f7l4ty2j	334	7	genomes	genome	NNS
cord-002542-f7l4ty2j	334	8	to	to	TO
cord-002542-f7l4ty2j	334	9	be	be	VB
cord-002542-f7l4ty2j	334	10	represented	represent	VBN
cord-002542-f7l4ty2j	334	11	by	by	IN
cord-002542-f7l4ty2j	334	12	three	three	CD
cord-002542-f7l4ty2j	334	13	or	or	CC
cord-002542-f7l4ty2j	334	14	more	more	JJR
cord-002542-f7l4ty2j	334	15	reads	read	NNS
cord-002542-f7l4ty2j	334	16	.	.	.
cord-002542-f7l4ty2j	335	1	While	while	IN
cord-002542-f7l4ty2j	335	2	removing	remove	VBG
cord-002542-f7l4ty2j	335	3	a	a	DT
cord-002542-f7l4ty2j	335	4	lot	lot	NN
cord-002542-f7l4ty2j	335	5	of	of	IN
cord-002542-f7l4ty2j	335	6	noise	noise	NN
cord-002542-f7l4ty2j	335	7	,	,	,
cord-002542-f7l4ty2j	335	8	this	this	DT
cord-002542-f7l4ty2j	335	9	has	have	VBZ
cord-002542-f7l4ty2j	335	10	the	the	DT
cord-002542-f7l4ty2j	335	11	drawback	drawback	NN
cord-002542-f7l4ty2j	335	12	that	that	IN
cord-002542-f7l4ty2j	335	13	we	-PRON-	PRP
cord-002542-f7l4ty2j	335	14	might	may	MD
cord-002542-f7l4ty2j	335	15	be	be	VB
cord-002542-f7l4ty2j	335	16	losing	lose	VBG
cord-002542-f7l4ty2j	335	17	rare	rare	JJ
cord-002542-f7l4ty2j	335	18	defective	defective	JJ
cord-002542-f7l4ty2j	335	19	RNAs	rna	NNS
cord-002542-f7l4ty2j	335	20	.	.	.
cord-002542-f7l4ty2j	336	1	Stacked	stack	VBN
cord-002542-f7l4ty2j	336	2	area	area	NN
cord-002542-f7l4ty2j	336	3	plots	plot	NNS
cord-002542-f7l4ty2j	336	4	for	for	IN
cord-002542-f7l4ty2j	336	5	genomes	genome	NNS
cord-002542-f7l4ty2j	336	6	represented	represent	VBN
cord-002542-f7l4ty2j	336	7	by	by	IN
cord-002542-f7l4ty2j	336	8	three	three	CD
cord-002542-f7l4ty2j	336	9	or	or	CC
cord-002542-f7l4ty2j	336	10	more	more	JJR
cord-002542-f7l4ty2j	336	11	reads	read	NNS
cord-002542-f7l4ty2j	336	12	are	be	VBP
cord-002542-f7l4ty2j	336	13	shown	show	VBN
cord-002542-f7l4ty2j	336	14	in	in	IN
cord-002542-f7l4ty2j	336	15	The	the	DT
cord-002542-f7l4ty2j	336	16	stacked	stack	VBN
cord-002542-f7l4ty2j	336	17	area	area	NN
cord-002542-f7l4ty2j	336	18	plot	plot	NN
cord-002542-f7l4ty2j	336	19	for	for	IN
cord-002542-f7l4ty2j	336	20	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	336	21	(	(	-LRB-
cord-002542-f7l4ty2j	336	22	Fig	Fig	NNP
cord-002542-f7l4ty2j	336	23	6A	6a	CD
cord-002542-f7l4ty2j	336	24	)	)	-RRB-
cord-002542-f7l4ty2j	336	25	shows	show	VBZ
cord-002542-f7l4ty2j	336	26	that	that	IN
cord-002542-f7l4ty2j	336	27	the	the	DT
cord-002542-f7l4ty2j	336	28	composition	composition	NN
cord-002542-f7l4ty2j	336	29	of	of	IN
cord-002542-f7l4ty2j	336	30	DI	DI	NNP
cord-002542-f7l4ty2j	336	31	-	-	HYPH
cord-002542-f7l4ty2j	336	32	RNAs	rna	NNS
cord-002542-f7l4ty2j	336	33	in	in	IN
cord-002542-f7l4ty2j	336	34	the	the	DT
cord-002542-f7l4ty2j	336	35	viral	viral	JJ
cord-002542-f7l4ty2j	336	36	population	population	NN
cord-002542-f7l4ty2j	336	37	changes	change	VBZ
cord-002542-f7l4ty2j	336	38	over	over	IN
cord-002542-f7l4ty2j	336	39	time	time	NN
cord-002542-f7l4ty2j	336	40	and	and	CC
cord-002542-f7l4ty2j	336	41	new	new	JJ
cord-002542-f7l4ty2j	336	42	species	specie	NNS
cord-002542-f7l4ty2j	336	43	appear	appear	VBP
cord-002542-f7l4ty2j	336	44	at	at	IN
cord-002542-f7l4ty2j	336	45	each	each	DT
cord-002542-f7l4ty2j	336	46	passage	passage	NN
cord-002542-f7l4ty2j	336	47	.	.	.
cord-002542-f7l4ty2j	337	1	For	for	IN
cord-002542-f7l4ty2j	337	2	example	example	NN
cord-002542-f7l4ty2j	337	3	,	,	,
cord-002542-f7l4ty2j	337	4	the	the	DT
cord-002542-f7l4ty2j	337	5	most	most	RBS
cord-002542-f7l4ty2j	337	6	abundant	abundant	JJ
cord-002542-f7l4ty2j	337	7	defective	defective	JJ
cord-002542-f7l4ty2j	337	8	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	337	9	species	specie	NNS
cord-002542-f7l4ty2j	337	10	in	in	IN
cord-002542-f7l4ty2j	337	11	passage	passage	NN
cord-002542-f7l4ty2j	337	12	5	5	CD
cord-002542-f7l4ty2j	337	13	is	be	VBZ
cord-002542-f7l4ty2j	337	14	'	'	''
cord-002542-f7l4ty2j	337	15	1_317	1_317	CD
cord-002542-f7l4ty2j	337	16	^	^	:
cord-002542-f7l4ty2j	337	17	1091_1242	1091_1242	CD
cord-002542-f7l4ty2j	337	18	^	^	:
cord-002542-f7l4ty2j	337	19	2301_3107	2301_3107	CD
cord-002542-f7l4ty2j	337	20	'	'	''
cord-002542-f7l4ty2j	337	21	but	but	CC
cord-002542-f7l4ty2j	337	22	reduces	reduce	VBZ
cord-002542-f7l4ty2j	337	23	in	in	IN
cord-002542-f7l4ty2j	337	24	relative	relative	JJ
cord-002542-f7l4ty2j	337	25	frequency	frequency	NN
cord-002542-f7l4ty2j	337	26	in	in	IN
cord-002542-f7l4ty2j	337	27	later	later	JJ
cord-002542-f7l4ty2j	337	28	passages	passage	NNS
cord-002542-f7l4ty2j	337	29	.	.	.
cord-002542-f7l4ty2j	338	1	The	the	DT
cord-002542-f7l4ty2j	338	2	most	most	RBS
cord-002542-f7l4ty2j	338	3	abundant	abundant	JJ
cord-002542-f7l4ty2j	338	4	species	specie	NNS
cord-002542-f7l4ty2j	338	5	in	in	IN
cord-002542-f7l4ty2j	338	6	the	the	DT
cord-002542-f7l4ty2j	338	7	final	final	JJ
cord-002542-f7l4ty2j	338	8	passage	passage	NN
cord-002542-f7l4ty2j	338	9	9	9	CD
cord-002542-f7l4ty2j	338	10	is	be	VBZ
cord-002542-f7l4ty2j	338	11	'	'	``
cord-002542-f7l4ty2j	338	12	1_313	1_313	CD
cord-002542-f7l4ty2j	338	13	^	^	NFP
cord-002542-f7l4ty2j	338	14	941_1241	941_1241	CD
cord-002542-f7l4ty2j	338	15	^	^	:
cord-002542-f7l4ty2j	338	16	2325_3107	2325_3107	CD
cord-002542-f7l4ty2j	338	17	'	'	''
cord-002542-f7l4ty2j	338	18	,	,	,
cord-002542-f7l4ty2j	338	19	which	which	WDT
cord-002542-f7l4ty2j	338	20	appears	appear	VBZ
cord-002542-f7l4ty2j	338	21	at	at	IN
cord-002542-f7l4ty2j	338	22	low	low	JJ
cord-002542-f7l4ty2j	338	23	levels	level	NNS
cord-002542-f7l4ty2j	338	24	as	as	RB
cord-002542-f7l4ty2j	338	25	early	early	RB
cord-002542-f7l4ty2j	338	26	as	as	IN
cord-002542-f7l4ty2j	338	27	passage	passage	NN
cord-002542-f7l4ty2j	338	28	2	2	CD
cord-002542-f7l4ty2j	338	29	,	,	,
cord-002542-f7l4ty2j	338	30	but	but	CC
cord-002542-f7l4ty2j	338	31	does	do	VBZ
cord-002542-f7l4ty2j	338	32	not	not	RB
cord-002542-f7l4ty2j	338	33	begin	begin	VB
cord-002542-f7l4ty2j	338	34	to	to	TO
cord-002542-f7l4ty2j	338	35	accumulate	accumulate	VB
cord-002542-f7l4ty2j	338	36	until	until	IN
cord-002542-f7l4ty2j	338	37	passage	passage	NN
cord-002542-f7l4ty2j	338	38	6	6	CD
cord-002542-f7l4ty2j	338	39	(	(	-LRB-
cord-002542-f7l4ty2j	338	40	S2	S2	NNP
cord-002542-f7l4ty2j	338	41	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	338	42	)	)	-RRB-
cord-002542-f7l4ty2j	338	43	.	.	.
cord-002542-f7l4ty2j	339	1	Why	why	WRB
cord-002542-f7l4ty2j	339	2	this	this	DT
cord-002542-f7l4ty2j	339	3	DI	DI	NNP
cord-002542-f7l4ty2j	339	4	-	-	HYPH
cord-002542-f7l4ty2j	339	5	RNA	RNA	NNP
cord-002542-f7l4ty2j	339	6	only	only	RB
cord-002542-f7l4ty2j	339	7	begins	begin	VBZ
cord-002542-f7l4ty2j	339	8	to	to	TO
cord-002542-f7l4ty2j	339	9	accumulate	accumulate	VB
cord-002542-f7l4ty2j	339	10	at	at	IN
cord-002542-f7l4ty2j	339	11	later	later	JJ
cord-002542-f7l4ty2j	339	12	passages	passage	NNS
cord-002542-f7l4ty2j	339	13	despite	despite	IN
cord-002542-f7l4ty2j	339	14	being	be	VBG
cord-002542-f7l4ty2j	339	15	present	present	JJ
cord-002542-f7l4ty2j	339	16	in	in	IN
cord-002542-f7l4ty2j	339	17	the	the	DT
cord-002542-f7l4ty2j	339	18	early	early	JJ
cord-002542-f7l4ty2j	339	19	passages	passage	NNS
cord-002542-f7l4ty2j	339	20	is	be	VBZ
cord-002542-f7l4ty2j	339	21	not	not	RB
cord-002542-f7l4ty2j	339	22	clear	clear	JJ
cord-002542-f7l4ty2j	339	23	.	.	.
cord-002542-f7l4ty2j	340	1	The	the	DT
cord-002542-f7l4ty2j	340	2	'	'	``
cord-002542-f7l4ty2j	340	3	complex	complex	JJ
cord-002542-f7l4ty2j	340	4	DI	DI	NNP
cord-002542-f7l4ty2j	340	5	-	-	HYPH
cord-002542-f7l4ty2j	340	6	RNA	RNA	NNP
cord-002542-f7l4ty2j	340	7	'	'	''
cord-002542-f7l4ty2j	340	8	that	that	WDT
cord-002542-f7l4ty2j	340	9	deletes	delete	VBZ
cord-002542-f7l4ty2j	340	10	the	the	DT
cord-002542-f7l4ty2j	340	11	PSCE	PSCE	NNPS
cord-002542-f7l4ty2j	340	12	in	in	IN
cord-002542-f7l4ty2j	340	13	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	340	14	referred	refer	VBD
cord-002542-f7l4ty2j	340	15	to	to	IN
cord-002542-f7l4ty2j	340	16	in	in	IN
cord-002542-f7l4ty2j	340	17	the	the	DT
cord-002542-f7l4ty2j	340	18	previous	previous	JJ
cord-002542-f7l4ty2j	340	19	section	section	NN
cord-002542-f7l4ty2j	340	20	(	(	-LRB-
cord-002542-f7l4ty2j	340	21	'	'	``
cord-002542-f7l4ty2j	340	22	1_342	1_342	CD
cord-002542-f7l4ty2j	340	23	^	^	NFP
cord-002542-f7l4ty2j	340	24	1083_1245	1083_1245	CD
cord-002542-f7l4ty2j	340	25	^	^	:
cord-002542-f7l4ty2j	340	26	2514_3107	2514_3107	NNP
cord-002542-f7l4ty2j	340	27	'	'	''
cord-002542-f7l4ty2j	340	28	)	)	-RRB-
cord-002542-f7l4ty2j	340	29	is	be	VBZ
cord-002542-f7l4ty2j	340	30	also	also	RB
cord-002542-f7l4ty2j	340	31	observed	observe	VBN
cord-002542-f7l4ty2j	340	32	(	(	-LRB-
cord-002542-f7l4ty2j	340	33	annotated	annotate	VBN
cord-002542-f7l4ty2j	340	34	in	in	IN
cord-002542-f7l4ty2j	340	35	Fig	Fig	NNP
cord-002542-f7l4ty2j	340	36	6A	6a	CD
cord-002542-f7l4ty2j	340	37	)	)	-RRB-
cord-002542-f7l4ty2j	340	38	first	first	RB
cord-002542-f7l4ty2j	340	39	appearing	appear	VBG
cord-002542-f7l4ty2j	340	40	at	at	IN
cord-002542-f7l4ty2j	340	41	passage	passage	NN
cord-002542-f7l4ty2j	340	42	5	5	CD
cord-002542-f7l4ty2j	340	43	.	.	.
cord-002542-f7l4ty2j	341	1	As	as	IN
cord-002542-f7l4ty2j	341	2	can	can	MD
cord-002542-f7l4ty2j	341	3	be	be	VB
cord-002542-f7l4ty2j	341	4	seen	see	VBN
cord-002542-f7l4ty2j	341	5	in	in	IN
cord-002542-f7l4ty2j	341	6	the	the	DT
cord-002542-f7l4ty2j	341	7	stacked	stack	VBN
cord-002542-f7l4ty2j	341	8	area	area	NN
cord-002542-f7l4ty2j	341	9	plot	plot	NN
cord-002542-f7l4ty2j	341	10	for	for	IN
cord-002542-f7l4ty2j	341	11	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	341	12	(	(	-LRB-
cord-002542-f7l4ty2j	341	13	Fig	Fig	NNP
cord-002542-f7l4ty2j	341	14	6B	6b	CD
cord-002542-f7l4ty2j	341	15	)	)	-RRB-
cord-002542-f7l4ty2j	341	16	,	,	,
cord-002542-f7l4ty2j	341	17	the	the	DT
cord-002542-f7l4ty2j	341	18	general	general	JJ
cord-002542-f7l4ty2j	341	19	composition	composition	NN
cord-002542-f7l4ty2j	341	20	of	of	IN
cord-002542-f7l4ty2j	341	21	DI	DI	NNP
cord-002542-f7l4ty2j	341	22	-	-	HYPH
cord-002542-f7l4ty2j	341	23	RNA	RNA	NNP
cord-002542-f7l4ty2j	341	24	species	specie	NNS
cord-002542-f7l4ty2j	341	25	is	be	VBZ
cord-002542-f7l4ty2j	341	26	established	establish	VBN
cord-002542-f7l4ty2j	341	27	at	at	IN
cord-002542-f7l4ty2j	341	28	passages	passage	NNS
cord-002542-f7l4ty2j	341	29	4	4	CD
cord-002542-f7l4ty2j	341	30	-	-	SYM
cord-002542-f7l4ty2j	341	31	5	5	CD
cord-002542-f7l4ty2j	341	32	.	.	.
cord-002542-f7l4ty2j	342	1	Subsequently	subsequently	RB
cord-002542-f7l4ty2j	342	2	,	,	,
cord-002542-f7l4ty2j	342	3	the	the	DT
cord-002542-f7l4ty2j	342	4	relative	relative	JJ
cord-002542-f7l4ty2j	342	5	frequencies	frequency	NNS
cord-002542-f7l4ty2j	342	6	of	of	IN
cord-002542-f7l4ty2j	342	7	the	the	DT
cord-002542-f7l4ty2j	342	8	DI	DI	NNP
cord-002542-f7l4ty2j	342	9	-	-	HYPH
cord-002542-f7l4ty2j	342	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	342	11	fluctuate	fluctuate	VBP
cord-002542-f7l4ty2j	342	12	but	but	CC
cord-002542-f7l4ty2j	342	13	the	the	DT
cord-002542-f7l4ty2j	342	14	overall	overall	JJ
cord-002542-f7l4ty2j	342	15	diversity	diversity	NN
cord-002542-f7l4ty2j	342	16	changes	change	VBZ
cord-002542-f7l4ty2j	342	17	little	little	JJ
cord-002542-f7l4ty2j	342	18	with	with	IN
cord-002542-f7l4ty2j	342	19	few	few	JJ
cord-002542-f7l4ty2j	342	20	new	new	JJ
cord-002542-f7l4ty2j	342	21	species	specie	NNS
cord-002542-f7l4ty2j	342	22	appearing	appear	VBG
cord-002542-f7l4ty2j	342	23	after	after	IN
cord-002542-f7l4ty2j	342	24	passage	passage	NN
cord-002542-f7l4ty2j	342	25	4	4	CD
cord-002542-f7l4ty2j	342	26	.	.	.
cord-002542-f7l4ty2j	343	1	This	this	DT
cord-002542-f7l4ty2j	343	2	is	be	VBZ
cord-002542-f7l4ty2j	343	3	also	also	RB
cord-002542-f7l4ty2j	343	4	observed	observe	VBN
cord-002542-f7l4ty2j	343	5	when	when	WRB
cord-002542-f7l4ty2j	343	6	calculating	calculate	VBG
cord-002542-f7l4ty2j	343	7	the	the	DT
cord-002542-f7l4ty2j	343	8	Shannon	Shannon	NNP
cord-002542-f7l4ty2j	343	9	Diversity	Diversity	NNP
cord-002542-f7l4ty2j	343	10	index	index	NN
cord-002542-f7l4ty2j	343	11	(	(	-LRB-
cord-002542-f7l4ty2j	343	12	Fig	Fig	NNP
cord-002542-f7l4ty2j	343	13	5B	5b	NN
cord-002542-f7l4ty2j	343	14	)	)	-RRB-
cord-002542-f7l4ty2j	343	15	whereby	whereby	WRB
cord-002542-f7l4ty2j	343	16	entropy	entropy	NN
cord-002542-f7l4ty2j	343	17	reaches	reach	VBZ
cord-002542-f7l4ty2j	343	18	a	a	DT
cord-002542-f7l4ty2j	343	19	maximum	maximum	NN
cord-002542-f7l4ty2j	343	20	at	at	IN
cord-002542-f7l4ty2j	343	21	passage	passage	NN
cord-002542-f7l4ty2j	343	22	5	5	CD
cord-002542-f7l4ty2j	343	23	and	and	CC
cord-002542-f7l4ty2j	343	24	decreases	decrease	VBZ
cord-002542-f7l4ty2j	343	25	thereafter	thereafter	RB
cord-002542-f7l4ty2j	343	26	.	.	.
cord-002542-f7l4ty2j	344	1	Interestingly	interestingly	RB
cord-002542-f7l4ty2j	344	2	,	,	,
cord-002542-f7l4ty2j	344	3	this	this	DT
cord-002542-f7l4ty2j	344	4	range	range	NN
cord-002542-f7l4ty2j	344	5	of	of	IN
cord-002542-f7l4ty2j	344	6	fluctuations	fluctuation	NNS
cord-002542-f7l4ty2j	344	7	resemble	resemble	VBP
cord-002542-f7l4ty2j	344	8	the	the	DT
cord-002542-f7l4ty2j	344	9	sinusoidal	sinusoidal	JJ
cord-002542-f7l4ty2j	344	10	patterns	pattern	NNS
cord-002542-f7l4ty2j	344	11	of	of	IN
cord-002542-f7l4ty2j	344	12	DI	DI	NNP
cord-002542-f7l4ty2j	344	13	-	-	HYPH
cord-002542-f7l4ty2j	344	14	RNA	RNA	NNP
cord-002542-f7l4ty2j	344	15	abundance	abundance	NN
cord-002542-f7l4ty2j	344	16	that	that	WDT
cord-002542-f7l4ty2j	344	17	have	have	VBP
cord-002542-f7l4ty2j	344	18	been	be	VBN
cord-002542-f7l4ty2j	344	19	observed	observe	VBN
cord-002542-f7l4ty2j	344	20	in	in	IN
cord-002542-f7l4ty2j	344	21	other	other	JJ
cord-002542-f7l4ty2j	344	22	studies	study	NNS
cord-002542-f7l4ty2j	344	23	of	of	IN
cord-002542-f7l4ty2j	344	24	RNA	RNA	NNP
cord-002542-f7l4ty2j	344	25	viruses	virus	NNS
cord-002542-f7l4ty2j	344	26	where	where	WRB
cord-002542-f7l4ty2j	344	27	the	the	DT
cord-002542-f7l4ty2j	344	28	ratio	ratio	NN
cord-002542-f7l4ty2j	344	29	of	of	IN
cord-002542-f7l4ty2j	344	30	the	the	DT
cord-002542-f7l4ty2j	344	31	frequency	frequency	NN
cord-002542-f7l4ty2j	344	32	of	of	IN
cord-002542-f7l4ty2j	344	33	DI	DI	NNP
cord-002542-f7l4ty2j	344	34	-	-	HYPH
cord-002542-f7l4ty2j	344	35	RNAs	rna	NNS
cord-002542-f7l4ty2j	344	36	to	to	IN
cord-002542-f7l4ty2j	344	37	wildtype	wildtype	NN
cord-002542-f7l4ty2j	344	38	genome	genome	NN
cord-002542-f7l4ty2j	344	39	has	have	VBZ
cord-002542-f7l4ty2j	344	40	been	be	VBN
cord-002542-f7l4ty2j	344	41	measured	measure	VBN
cord-002542-f7l4ty2j	344	42	through	through	IN
cord-002542-f7l4ty2j	344	43	longitudinal	longitudinal	JJ
cord-002542-f7l4ty2j	344	44	studies	study	NNS
cord-002542-f7l4ty2j	344	45	[	[	-LRB-
cord-002542-f7l4ty2j	344	46	67	67	CD
cord-002542-f7l4ty2j	344	47	]	]	-RRB-
cord-002542-f7l4ty2j	344	48	.	.	.
cord-002542-f7l4ty2j	345	1	The	the	DT
cord-002542-f7l4ty2j	345	2	reduction	reduction	NN
cord-002542-f7l4ty2j	345	3	in	in	IN
cord-002542-f7l4ty2j	345	4	full	full	JJ
cord-002542-f7l4ty2j	345	5	-	-	HYPH
cord-002542-f7l4ty2j	345	6	length	length	NN
cord-002542-f7l4ty2j	345	7	infectious	infectious	JJ
cord-002542-f7l4ty2j	345	8	viral	viral	JJ
cord-002542-f7l4ty2j	345	9	genomes	genome	NNS
cord-002542-f7l4ty2j	345	10	and	and	CC
cord-002542-f7l4ty2j	345	11	the	the	DT
cord-002542-f7l4ty2j	345	12	accumulation	accumulation	NN
cord-002542-f7l4ty2j	345	13	of	of	IN
cord-002542-f7l4ty2j	345	14	defective	defective	JJ
cord-002542-f7l4ty2j	345	15	RNAs	rna	NNS
cord-002542-f7l4ty2j	345	16	during	during	IN
cord-002542-f7l4ty2j	345	17	passaging	passaging	NN
cord-002542-f7l4ty2j	345	18	is	be	VBZ
cord-002542-f7l4ty2j	345	19	likely	likely	JJ
cord-002542-f7l4ty2j	345	20	to	to	TO
cord-002542-f7l4ty2j	345	21	correspond	correspond	VB
cord-002542-f7l4ty2j	345	22	to	to	IN
cord-002542-f7l4ty2j	345	23	a	a	DT
cord-002542-f7l4ty2j	345	24	decrease	decrease	NN
cord-002542-f7l4ty2j	345	25	in	in	IN
cord-002542-f7l4ty2j	345	26	the	the	DT
cord-002542-f7l4ty2j	345	27	specific	specific	JJ
cord-002542-f7l4ty2j	345	28	infectivity	infectivity	NN
cord-002542-f7l4ty2j	345	29	of	of	IN
cord-002542-f7l4ty2j	345	30	the	the	DT
cord-002542-f7l4ty2j	345	31	virus	virus	NN
cord-002542-f7l4ty2j	345	32	samples	sample	NNS
cord-002542-f7l4ty2j	345	33	.	.	.
cord-002542-f7l4ty2j	346	1	To	to	TO
cord-002542-f7l4ty2j	346	2	determine	determine	VB
cord-002542-f7l4ty2j	346	3	the	the	DT
cord-002542-f7l4ty2j	346	4	effect	effect	NN
cord-002542-f7l4ty2j	346	5	of	of	IN
cord-002542-f7l4ty2j	346	6	defective	defective	JJ
cord-002542-f7l4ty2j	346	7	RNAs	rna	NNS
cord-002542-f7l4ty2j	346	8	characterized	characterize	VBN
cord-002542-f7l4ty2j	346	9	by	by	IN
cord-002542-f7l4ty2j	346	10	combined	combine	VBN
cord-002542-f7l4ty2j	346	11	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	346	12	and	and	CC
cord-002542-f7l4ty2j	346	13	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	346	14	sequencing	sequencing	NN
cord-002542-f7l4ty2j	346	15	of	of	IN
cord-002542-f7l4ty2j	346	16	replicate	replicate	VBP
cord-002542-f7l4ty2j	346	17	2	2	CD
cord-002542-f7l4ty2j	346	18	upon	upon	IN
cord-002542-f7l4ty2j	346	19	specific	specific	JJ
cord-002542-f7l4ty2j	346	20	infectivity	infectivity	NN
cord-002542-f7l4ty2j	346	21	,	,	,
cord-002542-f7l4ty2j	346	22	we	-PRON-	PRP
cord-002542-f7l4ty2j	346	23	performed	perform	VBD
cord-002542-f7l4ty2j	346	24	50	50	CD
cord-002542-f7l4ty2j	346	25	%	%	NN
cord-002542-f7l4ty2j	346	26	tissue	tissue	NN
cord-002542-f7l4ty2j	346	27	culture	culture	NN
cord-002542-f7l4ty2j	346	28	infectious	infectious	JJ
cord-002542-f7l4ty2j	346	29	dose	dose	NN
cord-002542-f7l4ty2j	347	1	(	(	-LRB-
cord-002542-f7l4ty2j	347	2	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	347	3	)	)	-RRB-
cord-002542-f7l4ty2j	347	4	assays	assay	NNS
cord-002542-f7l4ty2j	347	5	for	for	IN
cord-002542-f7l4ty2j	347	6	each	each	DT
cord-002542-f7l4ty2j	347	7	passage	passage	NN
cord-002542-f7l4ty2j	347	8	1	1	CD
cord-002542-f7l4ty2j	347	9	-	-	SYM
cord-002542-f7l4ty2j	347	10	9	9	CD
cord-002542-f7l4ty2j	347	11	for	for	IN
cord-002542-f7l4ty2j	347	12	both	both	CC
cord-002542-f7l4ty2j	347	13	the	the	DT
cord-002542-f7l4ty2j	347	14	original	original	JJ
cord-002542-f7l4ty2j	347	15	inoculum	inoculum	NN
cord-002542-f7l4ty2j	347	16	used	use	VBN
cord-002542-f7l4ty2j	347	17	to	to	TO
cord-002542-f7l4ty2j	347	18	infect	infect	VB
cord-002542-f7l4ty2j	347	19	each	each	DT
cord-002542-f7l4ty2j	347	20	sample	sample	NN
cord-002542-f7l4ty2j	347	21	and	and	CC
cord-002542-f7l4ty2j	347	22	for	for	IN
cord-002542-f7l4ty2j	347	23	the	the	DT
cord-002542-f7l4ty2j	347	24	particles	particle	NNS
cord-002542-f7l4ty2j	347	25	purified	purify	VBN
cord-002542-f7l4ty2j	347	26	from	from	IN
cord-002542-f7l4ty2j	347	27	each	each	DT
cord-002542-f7l4ty2j	347	28	passage	passage	NN
cord-002542-f7l4ty2j	347	29	[	[	-LRB-
cord-002542-f7l4ty2j	347	30	51	51	CD
cord-002542-f7l4ty2j	347	31	]	]	-RRB-
cord-002542-f7l4ty2j	347	32	.	.	.
cord-002542-f7l4ty2j	348	1	The	the	DT
cord-002542-f7l4ty2j	348	2	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	348	3	assay	assay	NN
cord-002542-f7l4ty2j	348	4	is	be	VBZ
cord-002542-f7l4ty2j	348	5	used	use	VBN
cord-002542-f7l4ty2j	348	6	to	to	TO
cord-002542-f7l4ty2j	348	7	determine	determine	VB
cord-002542-f7l4ty2j	348	8	the	the	DT
cord-002542-f7l4ty2j	348	9	dose	dose	NN
cord-002542-f7l4ty2j	348	10	required	require	VBN
cord-002542-f7l4ty2j	348	11	to	to	TO
cord-002542-f7l4ty2j	348	12	give	give	VB
cord-002542-f7l4ty2j	348	13	a	a	DT
cord-002542-f7l4ty2j	348	14	50	50	CD
cord-002542-f7l4ty2j	348	15	%	%	NN
cord-002542-f7l4ty2j	348	16	chance	chance	NN
cord-002542-f7l4ty2j	348	17	that	that	IN
cord-002542-f7l4ty2j	348	18	cells	cell	NNS
cord-002542-f7l4ty2j	348	19	in	in	IN
cord-002542-f7l4ty2j	348	20	culture	culture	NN
cord-002542-f7l4ty2j	348	21	will	will	MD
cord-002542-f7l4ty2j	348	22	be	be	VB
cord-002542-f7l4ty2j	348	23	successfully	successfully	RB
cord-002542-f7l4ty2j	348	24	infected	infect	VBN
cord-002542-f7l4ty2j	348	25	as	as	IN
cord-002542-f7l4ty2j	348	26	determined	determine	VBN
cord-002542-f7l4ty2j	348	27	by	by	IN
cord-002542-f7l4ty2j	348	28	CPE	CPE	NNP
cord-002542-f7l4ty2j	348	29	and	and	CC
cord-002542-f7l4ty2j	348	30	is	be	VBZ
cord-002542-f7l4ty2j	348	31	typically	typically	RB
cord-002542-f7l4ty2j	348	32	used	use	VBN
cord-002542-f7l4ty2j	348	33	to	to	TO
cord-002542-f7l4ty2j	348	34	determine	determine	VB
cord-002542-f7l4ty2j	348	35	viral	viral	JJ
cord-002542-f7l4ty2j	348	36	titer	titer	NN
cord-002542-f7l4ty2j	348	37	and	and	CC
cord-002542-f7l4ty2j	348	38	the	the	DT
cord-002542-f7l4ty2j	348	39	effective	effective	JJ
cord-002542-f7l4ty2j	348	40	MOI	MOI	NNP
cord-002542-f7l4ty2j	348	41	of	of	IN
cord-002542-f7l4ty2j	348	42	the	the	DT
cord-002542-f7l4ty2j	348	43	inocula	inocula	NNP
cord-002542-f7l4ty2j	348	44	transferred	transfer	VBN
cord-002542-f7l4ty2j	348	45	from	from	IN
cord-002542-f7l4ty2j	348	46	passage	passage	NN
cord-002542-f7l4ty2j	348	47	to	to	IN
cord-002542-f7l4ty2j	348	48	passage	passage	NN
cord-002542-f7l4ty2j	348	49	.	.	.
cord-002542-f7l4ty2j	349	1	The	the	DT
cord-002542-f7l4ty2j	349	2	results	result	NNS
cord-002542-f7l4ty2j	349	3	from	from	IN
cord-002542-f7l4ty2j	349	4	the	the	DT
cord-002542-f7l4ty2j	349	5	TCID50	tcid50	CD
cord-002542-f7l4ty2j	349	6	assay	assay	NN
cord-002542-f7l4ty2j	349	7	for	for	IN
cord-002542-f7l4ty2j	349	8	each	each	DT
cord-002542-f7l4ty2j	349	9	passage	passage	NN
cord-002542-f7l4ty2j	349	10	are	be	VBP
cord-002542-f7l4ty2j	349	11	shown	show	VBN
cord-002542-f7l4ty2j	349	12	in	in	IN
cord-002542-f7l4ty2j	349	13	Fig	Fig	NNP
cord-002542-f7l4ty2j	349	14	7A	7a	NN
cord-002542-f7l4ty2j	349	15	and	and	CC
cord-002542-f7l4ty2j	349	16	7B	7b	NN
cord-002542-f7l4ty2j	349	17	.	.	.
cord-002542-f7l4ty2j	350	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	350	2	found	find	VBD
cord-002542-f7l4ty2j	350	3	that	that	IN
cord-002542-f7l4ty2j	350	4	the	the	DT
cord-002542-f7l4ty2j	350	5	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	350	6	value	value	NN
cord-002542-f7l4ty2j	350	7	(	(	-LRB-
cord-002542-f7l4ty2j	350	8	and	and	CC
cord-002542-f7l4ty2j	350	9	thus	thus	RB
cord-002542-f7l4ty2j	350	10	PFUs(Plaque	PFUs(Plaque	NNP
cord-002542-f7l4ty2j	350	11	Forming	Forming	NNP
cord-002542-f7l4ty2j	350	12	Units)/ml	Units)/ml	NNS
cord-002542-f7l4ty2j	350	13	)	)	-RRB-
cord-002542-f7l4ty2j	350	14	drops	drop	VBZ
cord-002542-f7l4ty2j	350	15	considerably	considerably	RB
cord-002542-f7l4ty2j	350	16	during	during	IN
cord-002542-f7l4ty2j	350	17	passaging	passage	VBG
cord-002542-f7l4ty2j	350	18	by	by	IN
cord-002542-f7l4ty2j	350	19	over	over	IN
cord-002542-f7l4ty2j	350	20	four	four	CD
cord-002542-f7l4ty2j	350	21	orders	order	NNS
cord-002542-f7l4ty2j	350	22	of	of	IN
cord-002542-f7l4ty2j	350	23	magnitude	magnitude	NN
cord-002542-f7l4ty2j	350	24	.	.	.
cord-002542-f7l4ty2j	351	1	The	the	DT
cord-002542-f7l4ty2j	351	2	corresponding	corresponding	JJ
cord-002542-f7l4ty2j	351	3	effective	effective	JJ
cord-002542-f7l4ty2j	351	4	MOI	MOI	NNP
cord-002542-f7l4ty2j	351	5	(	(	-LRB-
cord-002542-f7l4ty2j	351	6	PFUs	pfus	NN
cord-002542-f7l4ty2j	351	7	per	per	IN
cord-002542-f7l4ty2j	351	8	cell	cell	NN
cord-002542-f7l4ty2j	351	9	)	)	-RRB-
cord-002542-f7l4ty2j	351	10	also	also	RB
cord-002542-f7l4ty2j	351	11	drops	drop	VBZ
cord-002542-f7l4ty2j	351	12	from	from	IN
cord-002542-f7l4ty2j	351	13	38.5	38.5	CD
cord-002542-f7l4ty2j	351	14	to	to	IN
cord-002542-f7l4ty2j	351	15	0.0003	0.0003	CD
cord-002542-f7l4ty2j	351	16	during	during	IN
cord-002542-f7l4ty2j	351	17	passaging	passaging	NN
cord-002542-f7l4ty2j	351	18	(	(	-LRB-
cord-002542-f7l4ty2j	351	19	Fig	Fig	NNP
cord-002542-f7l4ty2j	351	20	7B	7b	NN
cord-002542-f7l4ty2j	351	21	)	)	-RRB-
cord-002542-f7l4ty2j	351	22	.	.	.
cord-002542-f7l4ty2j	352	1	and	and	CC
cord-002542-f7l4ty2j	352	2	(	(	-LRB-
cord-002542-f7l4ty2j	352	3	B	b	NN
cord-002542-f7l4ty2j	352	4	)	)	-RRB-
cord-002542-f7l4ty2j	352	5	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	352	6	.	.	.
cord-002542-f7l4ty2j	353	1	The	the	DT
cord-002542-f7l4ty2j	353	2	passage	passage	NN
cord-002542-f7l4ty2j	353	3	number	number	NN
cord-002542-f7l4ty2j	353	4	is	be	VBZ
cord-002542-f7l4ty2j	353	5	indicated	indicate	VBN
cord-002542-f7l4ty2j	353	6	on	on	IN
cord-002542-f7l4ty2j	353	7	the	the	DT
cord-002542-f7l4ty2j	353	8	x	x	NN
cord-002542-f7l4ty2j	353	9	-	-	HYPH
cord-002542-f7l4ty2j	353	10	axis	axis	NN
cord-002542-f7l4ty2j	353	11	and	and	CC
cord-002542-f7l4ty2j	353	12	the	the	DT
cord-002542-f7l4ty2j	353	13	stacked	stacked	JJ
cord-002542-f7l4ty2j	353	14	frequencies	frequency	NNS
cord-002542-f7l4ty2j	353	15	of	of	IN
cord-002542-f7l4ty2j	353	16	each	each	DT
cord-002542-f7l4ty2j	353	17	detected	detect	VBN
cord-002542-f7l4ty2j	353	18	defective	defective	JJ
cord-002542-f7l4ty2j	353	19	RNA	RNA	NNP
cord-002542-f7l4ty2j	353	20	is	be	VBZ
cord-002542-f7l4ty2j	353	21	shown	show	VBN
cord-002542-f7l4ty2j	353	22	in	in	IN
cord-002542-f7l4ty2j	353	23	the	the	DT
cord-002542-f7l4ty2j	353	24	y	y	NN
cord-002542-f7l4ty2j	353	25	-	-	HYPH
cord-002542-f7l4ty2j	353	26	axis	axis	NN
cord-002542-f7l4ty2j	353	27	.	.	.
cord-002542-f7l4ty2j	354	1	Each	each	DT
cord-002542-f7l4ty2j	354	2	non	non	JJ
cord-002542-f7l4ty2j	354	3	-	-	JJ
cord-002542-f7l4ty2j	354	4	contiguous	contiguous	JJ
cord-002542-f7l4ty2j	354	5	color	color	NN
cord-002542-f7l4ty2j	354	6	represents	represent	VBZ
cord-002542-f7l4ty2j	354	7	a	a	DT
cord-002542-f7l4ty2j	354	8	specific	specific	JJ
cord-002542-f7l4ty2j	354	9	genome	genome	NN
cord-002542-f7l4ty2j	354	10	characterized	characterize	VBN
cord-002542-f7l4ty2j	354	11	by	by	IN
cord-002542-f7l4ty2j	354	12	MinION	MinION	VBG
cord-002542-f7l4ty2j	354	13	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	354	14	sequencing	sequencing	NN
cord-002542-f7l4ty2j	354	15	.	.	.
cord-002542-f7l4ty2j	355	1	Wild	wild	JJ
cord-002542-f7l4ty2j	355	2	-	-	HYPH
cord-002542-f7l4ty2j	355	3	type	type	NN
cord-002542-f7l4ty2j	355	4	genomes	genome	NNS
cord-002542-f7l4ty2j	355	5	are	be	VBP
cord-002542-f7l4ty2j	355	6	colored	color	VBN
cord-002542-f7l4ty2j	355	7	green	green	JJ
cord-002542-f7l4ty2j	355	8	,	,	,
cord-002542-f7l4ty2j	355	9	genomes	genome	NNS
cord-002542-f7l4ty2j	355	10	with	with	IN
cord-002542-f7l4ty2j	355	11	one	one	CD
cord-002542-f7l4ty2j	355	12	deletion	deletion	NN
cord-002542-f7l4ty2j	355	13	are	be	VBP
cord-002542-f7l4ty2j	355	14	colored	color	VBN
cord-002542-f7l4ty2j	355	15	in	in	IN
cord-002542-f7l4ty2j	355	16	shades	shade	NNS
cord-002542-f7l4ty2j	355	17	of	of	IN
cord-002542-f7l4ty2j	355	18	blue	blue	JJ
cord-002542-f7l4ty2j	355	19	,	,	,
cord-002542-f7l4ty2j	355	20	and	and	CC
cord-002542-f7l4ty2j	355	21	genomes	genome	NNS
cord-002542-f7l4ty2j	355	22	with	with	IN
cord-002542-f7l4ty2j	355	23	two	two	CD
cord-002542-f7l4ty2j	355	24	or	or	CC
cord-002542-f7l4ty2j	355	25	more	more	JJR
cord-002542-f7l4ty2j	355	26	deletions	deletion	NNS
cord-002542-f7l4ty2j	355	27	are	be	VBP
cord-002542-f7l4ty2j	355	28	colored	color	VBN
cord-002542-f7l4ty2j	355	29	in	in	IN
cord-002542-f7l4ty2j	355	30	shades	shade	NNS
cord-002542-f7l4ty2j	355	31	of	of	IN
cord-002542-f7l4ty2j	355	32	orange	orange	NN
cord-002542-f7l4ty2j	355	33	(	(	-LRB-
cord-002542-f7l4ty2j	355	34	using	use	VBG
cord-002542-f7l4ty2j	355	35	the	the	DT
cord-002542-f7l4ty2j	355	36	same	same	JJ
cord-002542-f7l4ty2j	355	37	color	color	NN
cord-002542-f7l4ty2j	355	38	scheme	scheme	NN
cord-002542-f7l4ty2j	355	39	as	as	IN
cord-002542-f7l4ty2j	355	40	in	in	IN
cord-002542-f7l4ty2j	355	41	Fig	Fig	NNP
cord-002542-f7l4ty2j	355	42	5B	5b	NN
cord-002542-f7l4ty2j	355	43	)	)	-RRB-
cord-002542-f7l4ty2j	355	44	.	.	.
cord-002542-f7l4ty2j	356	1	Raw	raw	JJ
cord-002542-f7l4ty2j	356	2	data	datum	NNS
cord-002542-f7l4ty2j	356	3	and	and	CC
cord-002542-f7l4ty2j	356	4	annotations	annotation	NNS
cord-002542-f7l4ty2j	356	5	are	be	VBP
cord-002542-f7l4ty2j	356	6	in	in	IN
cord-002542-f7l4ty2j	356	7	S2	S2	NNP
cord-002542-f7l4ty2j	356	8	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	356	9	.	.	.
cord-002542-f7l4ty2j	357	1	To	to	TO
cord-002542-f7l4ty2j	357	2	determine	determine	VB
cord-002542-f7l4ty2j	357	3	whether	whether	IN
cord-002542-f7l4ty2j	357	4	the	the	DT
cord-002542-f7l4ty2j	357	5	drop	drop	NN
cord-002542-f7l4ty2j	357	6	in	in	IN
cord-002542-f7l4ty2j	357	7	effective	effective	JJ
cord-002542-f7l4ty2j	357	8	MOI	MOI	NNP
cord-002542-f7l4ty2j	357	9	was	be	VBD
cord-002542-f7l4ty2j	357	10	driven	drive	VBN
cord-002542-f7l4ty2j	357	11	by	by	IN
cord-002542-f7l4ty2j	357	12	reduced	reduce	VBN
cord-002542-f7l4ty2j	357	13	total	total	JJ
cord-002542-f7l4ty2j	357	14	particle	particle	NN
cord-002542-f7l4ty2j	357	15	yield	yield	NN
cord-002542-f7l4ty2j	357	16	or	or	CC
cord-002542-f7l4ty2j	357	17	from	from	IN
cord-002542-f7l4ty2j	357	18	reduced	reduce	VBN
cord-002542-f7l4ty2j	357	19	specific	specific	JJ
cord-002542-f7l4ty2j	357	20	infectivity	infectivity	NN
cord-002542-f7l4ty2j	357	21	(	(	-LRB-
cord-002542-f7l4ty2j	357	22	i.e.	i.e.	FW
cord-002542-f7l4ty2j	357	23	virus	virus	NN
cord-002542-f7l4ty2j	357	24	particles	particle	NNS
cord-002542-f7l4ty2j	357	25	per	per	IN
cord-002542-f7l4ty2j	357	26	PFU	pfu	NN
cord-002542-f7l4ty2j	357	27	)	)	-RRB-
cord-002542-f7l4ty2j	357	28	,	,	,
cord-002542-f7l4ty2j	357	29	we	-PRON-	PRP
cord-002542-f7l4ty2j	357	30	also	also	RB
cord-002542-f7l4ty2j	357	31	performed	perform	VBD
cord-002542-f7l4ty2j	357	32	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	357	33	analysis	analysis	NN
cord-002542-f7l4ty2j	357	34	of	of	IN
cord-002542-f7l4ty2j	357	35	our	-PRON-	PRP$
cord-002542-f7l4ty2j	357	36	purified	purify	VBN
cord-002542-f7l4ty2j	357	37	and	and	CC
cord-002542-f7l4ty2j	357	38	quantified	quantify	VBN
cord-002542-f7l4ty2j	357	39	virus	virus	NN
cord-002542-f7l4ty2j	357	40	stocks	stock	NNS
cord-002542-f7l4ty2j	357	41	(	(	-LRB-
cord-002542-f7l4ty2j	357	42	described	describe	VBN
cord-002542-f7l4ty2j	357	43	in	in	IN
cord-002542-f7l4ty2j	357	44	methods	method	NNS
cord-002542-f7l4ty2j	357	45	)	)	-RRB-
cord-002542-f7l4ty2j	357	46	.	.	.
cord-002542-f7l4ty2j	358	1	This	this	DT
cord-002542-f7l4ty2j	358	2	allowed	allow	VBD
cord-002542-f7l4ty2j	358	3	us	-PRON-	PRP
cord-002542-f7l4ty2j	358	4	to	to	IN
cord-002542-f7l4ty2j	358	5	Pathways	pathway	NNS
cord-002542-f7l4ty2j	358	6	of	of	IN
cord-002542-f7l4ty2j	358	7	FHV	FHV	NNP
cord-002542-f7l4ty2j	358	8	defective	defective	JJ
cord-002542-f7l4ty2j	358	9	RNA	RNA	NNP
cord-002542-f7l4ty2j	358	10	evolution	evolution	NN
cord-002542-f7l4ty2j	358	11	by	by	IN
cord-002542-f7l4ty2j	358	12	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	358	13	and	and	CC
cord-002542-f7l4ty2j	358	14	the	the	DT
cord-002542-f7l4ty2j	358	15	MinION	minion	NN
cord-002542-f7l4ty2j	358	16	determine	determine	VBP
cord-002542-f7l4ty2j	358	17	and	and	CC
cord-002542-f7l4ty2j	358	18	normalize	normalize	VB
cord-002542-f7l4ty2j	358	19	the	the	DT
cord-002542-f7l4ty2j	358	20	number	number	NN
cord-002542-f7l4ty2j	358	21	of	of	IN
cord-002542-f7l4ty2j	358	22	virus	virus	NN
cord-002542-f7l4ty2j	358	23	particles	particle	NNS
cord-002542-f7l4ty2j	358	24	delivered	deliver	VBN
cord-002542-f7l4ty2j	358	25	per	per	IN
cord-002542-f7l4ty2j	358	26	cell	cell	NN
cord-002542-f7l4ty2j	358	27	between	between	IN
cord-002542-f7l4ty2j	358	28	each	each	DT
cord-002542-f7l4ty2j	358	29	passage	passage	NN
cord-002542-f7l4ty2j	358	30	.	.	.
cord-002542-f7l4ty2j	359	1	As	as	IN
cord-002542-f7l4ty2j	359	2	the	the	DT
cord-002542-f7l4ty2j	359	3	particle	particle	NN
cord-002542-f7l4ty2j	359	4	-	-	HYPH
cord-002542-f7l4ty2j	359	5	per	per	IN
cord-002542-f7l4ty2j	359	6	-	-	HYPH
cord-002542-f7l4ty2j	359	7	PFU	pfu	NN
cord-002542-f7l4ty2j	359	8	ratio	ratio	NN
cord-002542-f7l4ty2j	359	9	has	have	VBZ
cord-002542-f7l4ty2j	359	10	previously	previously	RB
cord-002542-f7l4ty2j	359	11	been	be	VBN
cord-002542-f7l4ty2j	359	12	estimated	estimate	VBN
cord-002542-f7l4ty2j	359	13	at	at	IN
cord-002542-f7l4ty2j	359	14	300	300	CD
cord-002542-f7l4ty2j	359	15	-	-	SYM
cord-002542-f7l4ty2j	359	16	400	400	CD
cord-002542-f7l4ty2j	359	17	particles	particle	NNS
cord-002542-f7l4ty2j	359	18	-	-	HYPH
cord-002542-f7l4ty2j	359	19	per	per	FW
cord-002542-f7l4ty2j	359	20	-	-	HYPH
cord-002542-f7l4ty2j	359	21	PFU	pfu	NN
cord-002542-f7l4ty2j	359	22	[	[	-LRB-
cord-002542-f7l4ty2j	359	23	26	26	CD
cord-002542-f7l4ty2j	359	24	,	,	,
cord-002542-f7l4ty2j	359	25	52	52	CD
cord-002542-f7l4ty2j	359	26	]	]	-RRB-
cord-002542-f7l4ty2j	359	27	we	-PRON-	PRP
cord-002542-f7l4ty2j	359	28	setup	setup	VBP
cord-002542-f7l4ty2j	359	29	our	-PRON-	PRP$
cord-002542-f7l4ty2j	359	30	assay	assay	NN
cord-002542-f7l4ty2j	359	31	beginning	begin	VBG
cord-002542-f7l4ty2j	359	32	with	with	IN
cord-002542-f7l4ty2j	359	33	300'000	300'000	CD
cord-002542-f7l4ty2j	359	34	particles	particle	NNS
cord-002542-f7l4ty2j	359	35	per	per	IN
cord-002542-f7l4ty2j	359	36	cell	cell	NN
cord-002542-f7l4ty2j	359	37	in	in	IN
cord-002542-f7l4ty2j	359	38	96	96	CD
cord-002542-f7l4ty2j	359	39	well	well	JJ
cord-002542-f7l4ty2j	359	40	format	format	NN
cord-002542-f7l4ty2j	359	41	and	and	CC
cord-002542-f7l4ty2j	359	42	performed	perform	VBD
cord-002542-f7l4ty2j	359	43	8	8	CD
cord-002542-f7l4ty2j	359	44	10-fold	10-fold	JJ
cord-002542-f7l4ty2j	359	45	serial	serial	JJ
cord-002542-f7l4ty2j	359	46	dilutions	dilution	NNS
cord-002542-f7l4ty2j	359	47	.	.	.
cord-002542-f7l4ty2j	360	1	In	in	IN
cord-002542-f7l4ty2j	360	2	this	this	DT
cord-002542-f7l4ty2j	360	3	assay	assay	NN
cord-002542-f7l4ty2j	360	4	,	,	,
cord-002542-f7l4ty2j	360	5	we	-PRON-	PRP
cord-002542-f7l4ty2j	360	6	found	find	VBD
cord-002542-f7l4ty2j	360	7	that	that	IN
cord-002542-f7l4ty2j	360	8	the	the	DT
cord-002542-f7l4ty2j	360	9	number	number	NN
cord-002542-f7l4ty2j	360	10	of	of	IN
cord-002542-f7l4ty2j	360	11	viral	viral	JJ
cord-002542-f7l4ty2j	360	12	particles	particle	NNS
cord-002542-f7l4ty2j	360	13	required	require	VBN
cord-002542-f7l4ty2j	360	14	to	to	TO
cord-002542-f7l4ty2j	360	15	induce	induce	VB
cord-002542-f7l4ty2j	360	16	CPE	CPE	NNP
cord-002542-f7l4ty2j	360	17	decreased	decrease	VBD
cord-002542-f7l4ty2j	360	18	by	by	IN
cord-002542-f7l4ty2j	360	19	over	over	IN
cord-002542-f7l4ty2j	360	20	400-fold	400-fold	CD
cord-002542-f7l4ty2j	360	21	during	during	IN
cord-002542-f7l4ty2j	360	22	passaging	passaging	NN
cord-002542-f7l4ty2j	360	23	(	(	-LRB-
cord-002542-f7l4ty2j	360	24	Fig	Fig	NNP
cord-002542-f7l4ty2j	360	25	7A	7a	NN
cord-002542-f7l4ty2j	360	26	)	)	-RRB-
cord-002542-f7l4ty2j	360	27	with	with	IN
cord-002542-f7l4ty2j	360	28	a	a	DT
cord-002542-f7l4ty2j	360	29	trend	trend	NN
cord-002542-f7l4ty2j	360	30	very	very	RB
cord-002542-f7l4ty2j	360	31	similar	similar	JJ
cord-002542-f7l4ty2j	360	32	to	to	IN
cord-002542-f7l4ty2j	360	33	that	that	DT
cord-002542-f7l4ty2j	360	34	for	for	IN
cord-002542-f7l4ty2j	360	35	the	the	DT
cord-002542-f7l4ty2j	360	36	unpurified	unpurified	JJ
cord-002542-f7l4ty2j	360	37	inocula	inocula	NNP
cord-002542-f7l4ty2j	360	38	.	.	.
cord-002542-f7l4ty2j	361	1	Together	together	RB
cord-002542-f7l4ty2j	361	2	,	,	,
cord-002542-f7l4ty2j	361	3	these	these	DT
cord-002542-f7l4ty2j	361	4	data	datum	NNS
cord-002542-f7l4ty2j	361	5	indicate	indicate	VBP
cord-002542-f7l4ty2j	361	6	virus	virus	NN
cord-002542-f7l4ty2j	361	7	specific	specific	JJ
cord-002542-f7l4ty2j	361	8	infectivity	infectivity	NN
cord-002542-f7l4ty2j	361	9	drops	drop	VBZ
cord-002542-f7l4ty2j	361	10	with	with	IN
cord-002542-f7l4ty2j	361	11	a	a	DT
cord-002542-f7l4ty2j	361	12	corresponding	corresponding	JJ
cord-002542-f7l4ty2j	361	13	increase	increase	NN
cord-002542-f7l4ty2j	361	14	in	in	IN
cord-002542-f7l4ty2j	361	15	the	the	DT
cord-002542-f7l4ty2j	361	16	defective	defective	JJ
cord-002542-f7l4ty2j	361	17	RNA	RNA	NNP
cord-002542-f7l4ty2j	361	18	population	population	NN
cord-002542-f7l4ty2j	361	19	.	.	.
cord-002542-f7l4ty2j	362	1	There	there	EX
cord-002542-f7l4ty2j	362	2	was	be	VBD
cord-002542-f7l4ty2j	362	3	an	an	DT
cord-002542-f7l4ty2j	362	4	exception	exception	NN
cord-002542-f7l4ty2j	362	5	at	at	IN
cord-002542-f7l4ty2j	362	6	passage	passage	NN
cord-002542-f7l4ty2j	362	7	7	7	CD
cord-002542-f7l4ty2j	363	1	where	where	WRB
cord-002542-f7l4ty2j	363	2	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	364	1	actually	actually	RB
cord-002542-f7l4ty2j	364	2	increased~5	increased~5	NNP
cord-002542-f7l4ty2j	364	3	fold	fold	VB
cord-002542-f7l4ty2j	364	4	from	from	IN
cord-002542-f7l4ty2j	364	5	the	the	DT
cord-002542-f7l4ty2j	364	6	previous	previous	JJ
cord-002542-f7l4ty2j	364	7	passage	passage	NN
cord-002542-f7l4ty2j	364	8	.	.	.
cord-002542-f7l4ty2j	365	1	This	this	DT
cord-002542-f7l4ty2j	365	2	could	could	MD
cord-002542-f7l4ty2j	365	3	be	be	VB
cord-002542-f7l4ty2j	365	4	correlated	correlate	VBN
cord-002542-f7l4ty2j	365	5	to	to	IN
cord-002542-f7l4ty2j	365	6	our	-PRON-	PRP$
cord-002542-f7l4ty2j	365	7	observation	observation	NN
cord-002542-f7l4ty2j	365	8	of	of	IN
cord-002542-f7l4ty2j	365	9	a	a	DT
cord-002542-f7l4ty2j	365	10	decrease	decrease	NN
cord-002542-f7l4ty2j	365	11	in	in	IN
cord-002542-f7l4ty2j	365	12	the	the	DT
cord-002542-f7l4ty2j	365	13	amount	amount	NN
cord-002542-f7l4ty2j	365	14	of	of	IN
cord-002542-f7l4ty2j	365	15	defective	defective	JJ
cord-002542-f7l4ty2j	365	16	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	365	17	species	specie	NNS
cord-002542-f7l4ty2j	365	18	in	in	IN
cord-002542-f7l4ty2j	365	19	the	the	DT
cord-002542-f7l4ty2j	365	20	MinION	minion	NN
cord-002542-f7l4ty2j	365	21	analysis	analysis	NN
cord-002542-f7l4ty2j	365	22	(	(	-LRB-
cord-002542-f7l4ty2j	365	23	Figs	Figs	NNP
cord-002542-f7l4ty2j	365	24	5B	5b	NN
cord-002542-f7l4ty2j	365	25	and	and	CC
cord-002542-f7l4ty2j	365	26	6B	6b	CD
cord-002542-f7l4ty2j	365	27	)	)	-RRB-
cord-002542-f7l4ty2j	365	28	.	.	.
cord-002542-f7l4ty2j	366	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	366	2	further	further	RB
cord-002542-f7l4ty2j	366	3	characterized	characterize	VBD
cord-002542-f7l4ty2j	366	4	each	each	DT
cord-002542-f7l4ty2j	366	5	well	well	NN
cord-002542-f7l4ty2j	366	6	of	of	IN
cord-002542-f7l4ty2j	366	7	the	the	DT
cord-002542-f7l4ty2j	366	8	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	366	9	assay	assay	NN
cord-002542-f7l4ty2j	366	10	of	of	IN
cord-002542-f7l4ty2j	366	11	our	-PRON-	PRP$
cord-002542-f7l4ty2j	366	12	purified	purify	VBN
cord-002542-f7l4ty2j	366	13	particles	particle	NNS
cord-002542-f7l4ty2j	366	14	using	use	VBG
cord-002542-f7l4ty2j	366	15	flowcytometry	flowcytometry	NN
cord-002542-f7l4ty2j	366	16	to	to	TO
cord-002542-f7l4ty2j	366	17	give	give	VB
cord-002542-f7l4ty2j	366	18	a	a	DT
cord-002542-f7l4ty2j	366	19	quantitative	quantitative	JJ
cord-002542-f7l4ty2j	366	20	assessment	assessment	NN
cord-002542-f7l4ty2j	366	21	of	of	IN
cord-002542-f7l4ty2j	366	22	cell	cell	NN
cord-002542-f7l4ty2j	366	23	survival	survival	NN
cord-002542-f7l4ty2j	366	24	and	and	CC
cord-002542-f7l4ty2j	366	25	death	death	NN
cord-002542-f7l4ty2j	366	26	in	in	IN
cord-002542-f7l4ty2j	366	27	response	response	NN
cord-002542-f7l4ty2j	366	28	to	to	IN
cord-002542-f7l4ty2j	366	29	virus	virus	NN
cord-002542-f7l4ty2j	366	30	dose	dose	NN
cord-002542-f7l4ty2j	366	31	.	.	.
cord-002542-f7l4ty2j	367	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	367	2	calculated	calculate	VBD
cord-002542-f7l4ty2j	367	3	the	the	DT
cord-002542-f7l4ty2j	367	4	number	number	NN
cord-002542-f7l4ty2j	367	5	of	of	IN
cord-002542-f7l4ty2j	367	6	live	live	JJ
cord-002542-f7l4ty2j	367	7	cells	cell	NNS
cord-002542-f7l4ty2j	367	8	that	that	WDT
cord-002542-f7l4ty2j	367	9	remained	remain	VBD
cord-002542-f7l4ty2j	367	10	after	after	IN
cord-002542-f7l4ty2j	367	11	infection	infection	NN
cord-002542-f7l4ty2j	367	12	at	at	IN
cord-002542-f7l4ty2j	367	13	each	each	DT
cord-002542-f7l4ty2j	367	14	dilution	dilution	NN
cord-002542-f7l4ty2j	367	15	and	and	CC
cord-002542-f7l4ty2j	367	16	for	for	IN
cord-002542-f7l4ty2j	367	17	each	each	DT
cord-002542-f7l4ty2j	367	18	passage	passage	NN
cord-002542-f7l4ty2j	368	1	(	(	-LRB-
cord-002542-f7l4ty2j	368	2	Fig	Fig	NNP
cord-002542-f7l4ty2j	368	3	7C	7C	NNP
cord-002542-f7l4ty2j	368	4	and	and	CC
cord-002542-f7l4ty2j	368	5	S7	S7	NNP
cord-002542-f7l4ty2j	368	6	Fig	Fig	NNP
cord-002542-f7l4ty2j	368	7	)	)	-RRB-
cord-002542-f7l4ty2j	368	8	.	.	.
cord-002542-f7l4ty2j	369	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	369	2	observed	observe	VBD
cord-002542-f7l4ty2j	369	3	a	a	DT
cord-002542-f7l4ty2j	369	4	reduced	reduced	JJ
cord-002542-f7l4ty2j	369	5	overall	overall	JJ
cord-002542-f7l4ty2j	369	6	CPE	CPE	NNP
cord-002542-f7l4ty2j	369	7	in	in	IN
cord-002542-f7l4ty2j	369	8	later	later	JJ
cord-002542-f7l4ty2j	369	9	passages	passage	NNS
cord-002542-f7l4ty2j	369	10	at	at	IN
cord-002542-f7l4ty2j	369	11	the	the	DT
cord-002542-f7l4ty2j	369	12	highest	high	JJS
cord-002542-f7l4ty2j	369	13	virus	virus	NN
cord-002542-f7l4ty2j	369	14	dose	dose	NN
cord-002542-f7l4ty2j	369	15	as	as	RB
cord-002542-f7l4ty2j	369	16	well	well	RB
cord-002542-f7l4ty2j	369	17	as	as	IN
cord-002542-f7l4ty2j	369	18	an	an	DT
cord-002542-f7l4ty2j	369	19	increase	increase	NN
cord-002542-f7l4ty2j	369	20	in	in	IN
cord-002542-f7l4ty2j	369	21	the	the	DT
cord-002542-f7l4ty2j	369	22	number	number	NN
cord-002542-f7l4ty2j	369	23	of	of	IN
cord-002542-f7l4ty2j	369	24	viral	viral	JJ
cord-002542-f7l4ty2j	369	25	particles	particle	NNS
cord-002542-f7l4ty2j	369	26	require	require	VBP
cord-002542-f7l4ty2j	369	27	to	to	TO
cord-002542-f7l4ty2j	369	28	induce	induce	VB
cord-002542-f7l4ty2j	369	29	the	the	DT
cord-002542-f7l4ty2j	369	30	same	same	JJ
cord-002542-f7l4ty2j	369	31	amount	amount	NN
cord-002542-f7l4ty2j	369	32	of	of	IN
cord-002542-f7l4ty2j	369	33	CPE	CPE	NNP
cord-002542-f7l4ty2j	369	34	(	(	-LRB-
cord-002542-f7l4ty2j	369	35	Fig	Fig	NNP
cord-002542-f7l4ty2j	369	36	7C	7C	NNP
cord-002542-f7l4ty2j	369	37	)	)	-RRB-
cord-002542-f7l4ty2j	369	38	.	.	.
cord-002542-f7l4ty2j	370	1	Together	together	RB
cord-002542-f7l4ty2j	370	2	these	these	DT
cord-002542-f7l4ty2j	370	3	trends	trend	NNS
cord-002542-f7l4ty2j	370	4	reflect	reflect	VBP
cord-002542-f7l4ty2j	370	5	a	a	DT
cord-002542-f7l4ty2j	370	6	reduced	reduce	VBN
cord-002542-f7l4ty2j	370	7	specific	specific	JJ
cord-002542-f7l4ty2j	370	8	infectivity	infectivity	NN
cord-002542-f7l4ty2j	370	9	during	during	IN
cord-002542-f7l4ty2j	370	10	viral	viral	JJ
cord-002542-f7l4ty2j	370	11	passaging	passaging	NN
cord-002542-f7l4ty2j	370	12	,	,	,
cord-002542-f7l4ty2j	370	13	in	in	IN
cord-002542-f7l4ty2j	370	14	agreement	agreement	NN
cord-002542-f7l4ty2j	370	15	with	with	IN
cord-002542-f7l4ty2j	370	16	our	-PRON-	PRP$
cord-002542-f7l4ty2j	370	17	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	370	18	assays	assay	NNS
cord-002542-f7l4ty2j	370	19	.	.	.
cord-002542-f7l4ty2j	371	1	Interestingly	interestingly	RB
cord-002542-f7l4ty2j	371	2	however	however	RB
cord-002542-f7l4ty2j	371	3	,	,	,
cord-002542-f7l4ty2j	371	4	for	for	IN
cord-002542-f7l4ty2j	371	5	the	the	DT
cord-002542-f7l4ty2j	371	6	highest	high	JJS
cord-002542-f7l4ty2j	371	7	particle	particle	NN
cord-002542-f7l4ty2j	371	8	concentrations	concentration	NNS
cord-002542-f7l4ty2j	371	9	in	in	IN
cord-002542-f7l4ty2j	371	10	passages	passage	NNS
cord-002542-f7l4ty2j	371	11	8	8	CD
cord-002542-f7l4ty2j	371	12	and	and	CC
cord-002542-f7l4ty2j	371	13	9	9	CD
cord-002542-f7l4ty2j	371	14	,	,	,
cord-002542-f7l4ty2j	371	15	we	-PRON-	PRP
cord-002542-f7l4ty2j	371	16	saw	see	VBD
cord-002542-f7l4ty2j	371	17	less	less	JJR
cord-002542-f7l4ty2j	371	18	cell	cell	NN
cord-002542-f7l4ty2j	371	19	death	death	NN
cord-002542-f7l4ty2j	371	20	at	at	IN
cord-002542-f7l4ty2j	371	21	the	the	DT
cord-002542-f7l4ty2j	371	22	highest	high	JJS
cord-002542-f7l4ty2j	371	23	doses	dose	NNS
cord-002542-f7l4ty2j	371	24	(	(	-LRB-
cord-002542-f7l4ty2j	371	25	300,000	300,000	CD
cord-002542-f7l4ty2j	371	26	and	and	CC
cord-002542-f7l4ty2j	371	27	30,000	30,000	CD
cord-002542-f7l4ty2j	371	28	particles	particle	NNS
cord-002542-f7l4ty2j	371	29	per	per	IN
cord-002542-f7l4ty2j	371	30	cell	cell	NN
cord-002542-f7l4ty2j	371	31	)	)	-RRB-
cord-002542-f7l4ty2j	371	32	than	than	IN
cord-002542-f7l4ty2j	371	33	for	for	IN
cord-002542-f7l4ty2j	371	34	cells	cell	NNS
cord-002542-f7l4ty2j	371	35	infected	infect	VBN
cord-002542-f7l4ty2j	371	36	with	with	IN
cord-002542-f7l4ty2j	371	37	the	the	DT
cord-002542-f7l4ty2j	371	38	same	same	JJ
cord-002542-f7l4ty2j	371	39	inoculum	inoculum	NN
cord-002542-f7l4ty2j	371	40	(	(	-LRB-
cord-002542-f7l4ty2j	371	41	and	and	CC
cord-002542-f7l4ty2j	371	42	therefore	therefore	RB
cord-002542-f7l4ty2j	371	43	same	same	JJ
cord-002542-f7l4ty2j	371	44	ratio	ratio	NN
cord-002542-f7l4ty2j	371	45	of	of	IN
cord-002542-f7l4ty2j	371	46	full	full	JJ
cord-002542-f7l4ty2j	371	47	-	-	HYPH
cord-002542-f7l4ty2j	371	48	length	length	NN
cord-002542-f7l4ty2j	371	49	to	to	IN
cord-002542-f7l4ty2j	371	50	defective	defective	JJ
cord-002542-f7l4ty2j	371	51	RNAs	rna	NNS
cord-002542-f7l4ty2j	371	52	)	)	-RRB-
cord-002542-f7l4ty2j	371	53	but	but	CC
cord-002542-f7l4ty2j	371	54	at	at	IN
cord-002542-f7l4ty2j	371	55	a	a	DT
cord-002542-f7l4ty2j	371	56	lower	low	JJR
cord-002542-f7l4ty2j	371	57	dose	dose	NN
cord-002542-f7l4ty2j	371	58	(	(	-LRB-
cord-002542-f7l4ty2j	371	59	3,000	3,000	CD
cord-002542-f7l4ty2j	371	60	-	-	SYM
cord-002542-f7l4ty2j	371	61	30	30	CD
cord-002542-f7l4ty2j	371	62	particles	particle	NNS
cord-002542-f7l4ty2j	371	63	per	per	IN
cord-002542-f7l4ty2j	371	64	cell	cell	NN
cord-002542-f7l4ty2j	371	65	)	)	-RRB-
cord-002542-f7l4ty2j	371	66	.	.	.
cord-002542-f7l4ty2j	372	1	This	this	DT
cord-002542-f7l4ty2j	372	2	observation	observation	NN
cord-002542-f7l4ty2j	372	3	indicates	indicate	VBZ
cord-002542-f7l4ty2j	372	4	the	the	DT
cord-002542-f7l4ty2j	372	5	protection	protection	NN
cord-002542-f7l4ty2j	372	6	of	of	IN
cord-002542-f7l4ty2j	372	7	cells	cell	NNS
cord-002542-f7l4ty2j	372	8	from	from	IN
cord-002542-f7l4ty2j	372	9	infection	infection	NN
cord-002542-f7l4ty2j	372	10	and/or	and/or	CC
cord-002542-f7l4ty2j	372	11	CPE	CPE	NNP
cord-002542-f7l4ty2j	372	12	when	when	WRB
cord-002542-f7l4ty2j	372	13	supplied	supply	VBN
cord-002542-f7l4ty2j	372	14	with	with	IN
cord-002542-f7l4ty2j	372	15	a	a	DT
cord-002542-f7l4ty2j	372	16	large	large	JJ
cord-002542-f7l4ty2j	372	17	dose	dose	NN
cord-002542-f7l4ty2j	372	18	of	of	IN
cord-002542-f7l4ty2j	372	19	viral	viral	JJ
cord-002542-f7l4ty2j	372	20	particles	particle	NNS
cord-002542-f7l4ty2j	372	21	that	that	WDT
cord-002542-f7l4ty2j	372	22	contain	contain	VBP
cord-002542-f7l4ty2j	372	23	a	a	DT
cord-002542-f7l4ty2j	372	24	large	large	JJ
cord-002542-f7l4ty2j	372	25	proportion	proportion	NN
cord-002542-f7l4ty2j	372	26	of	of	IN
cord-002542-f7l4ty2j	372	27	DI	DI	NNP
cord-002542-f7l4ty2j	372	28	-	-	HYPH
cord-002542-f7l4ty2j	372	29	RNAs	rna	NNS
cord-002542-f7l4ty2j	372	30	.	.	.
cord-002542-f7l4ty2j	373	1	In	in	IN
cord-002542-f7l4ty2j	373	2	this	this	DT
cord-002542-f7l4ty2j	373	3	manuscript	manuscript	NN
cord-002542-f7l4ty2j	373	4	,	,	,
cord-002542-f7l4ty2j	373	5	we	-PRON-	PRP
cord-002542-f7l4ty2j	373	6	sought	seek	VBD
cord-002542-f7l4ty2j	373	7	to	to	TO
cord-002542-f7l4ty2j	373	8	provide	provide	VB
cord-002542-f7l4ty2j	373	9	a	a	DT
cord-002542-f7l4ty2j	373	10	thorough	thorough	JJ
cord-002542-f7l4ty2j	373	11	and	and	CC
cord-002542-f7l4ty2j	373	12	comprehensive	comprehensive	JJ
cord-002542-f7l4ty2j	373	13	analysis	analysis	NN
cord-002542-f7l4ty2j	373	14	of	of	IN
cord-002542-f7l4ty2j	373	15	the	the	DT
cord-002542-f7l4ty2j	373	16	frequency	frequency	NN
cord-002542-f7l4ty2j	373	17	and	and	CC
cord-002542-f7l4ty2j	373	18	identity	identity	NN
cord-002542-f7l4ty2j	373	19	of	of	IN
cord-002542-f7l4ty2j	373	20	recombination	recombination	NN
cord-002542-f7l4ty2j	373	21	events	event	NNS
cord-002542-f7l4ty2j	373	22	present	present	JJ
cord-002542-f7l4ty2j	373	23	during	during	IN
cord-002542-f7l4ty2j	373	24	the	the	DT
cord-002542-f7l4ty2j	373	25	serial	serial	JJ
cord-002542-f7l4ty2j	373	26	passaging	passaging	NN
cord-002542-f7l4ty2j	373	27	of	of	IN
cord-002542-f7l4ty2j	373	28	Flock	Flock	NNP
cord-002542-f7l4ty2j	373	29	House	House	NNP
cord-002542-f7l4ty2j	373	30	virus	virus	NN
cord-002542-f7l4ty2j	373	31	in	in	IN
cord-002542-f7l4ty2j	373	32	cell	cell	NN
cord-002542-f7l4ty2j	373	33	culture	culture	NN
cord-002542-f7l4ty2j	373	34	in	in	IN
cord-002542-f7l4ty2j	373	35	order	order	NN
cord-002542-f7l4ty2j	373	36	to	to	TO
cord-002542-f7l4ty2j	373	37	elucidate	elucidate	VB
cord-002542-f7l4ty2j	373	38	the	the	DT
cord-002542-f7l4ty2j	373	39	pathways	pathway	NNS
cord-002542-f7l4ty2j	373	40	and	and	CC
cord-002542-f7l4ty2j	373	41	mechanism	mechanism	NN
cord-002542-f7l4ty2j	373	42	of	of	IN
cord-002542-f7l4ty2j	373	43	DI	DI	NNP
cord-002542-f7l4ty2j	373	44	-	-	HYPH
cord-002542-f7l4ty2j	373	45	RNA	RNA	NNP
cord-002542-f7l4ty2j	373	46	emergence	emergence	NN
cord-002542-f7l4ty2j	373	47	and	and	CC
cord-002542-f7l4ty2j	373	48	evolution	evolution	NN
cord-002542-f7l4ty2j	373	49	.	.	.
cord-002542-f7l4ty2j	374	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	374	2	began	begin	VBD
cord-002542-f7l4ty2j	374	3	with	with	IN
cord-002542-f7l4ty2j	374	4	a	a	DT
cord-002542-f7l4ty2j	374	5	homogenous	homogenous	JJ
cord-002542-f7l4ty2j	374	6	inoculum	inoculum	NN
cord-002542-f7l4ty2j	374	7	derived	derive	VBN
cord-002542-f7l4ty2j	374	8	from	from	IN
cord-002542-f7l4ty2j	374	9	plasmid	plasmid	NN
cord-002542-f7l4ty2j	374	10	cDNAs	cdna	NNS
cord-002542-f7l4ty2j	374	11	of	of	IN
cord-002542-f7l4ty2j	374	12	each	each	DT
cord-002542-f7l4ty2j	374	13	of	of	IN
cord-002542-f7l4ty2j	374	14	the	the	DT
cord-002542-f7l4ty2j	374	15	FHV	FHV	NNP
cord-002542-f7l4ty2j	374	16	genomes	genome	NNS
cord-002542-f7l4ty2j	374	17	.	.	.
cord-002542-f7l4ty2j	375	1	In	in	IN
cord-002542-f7l4ty2j	375	2	the	the	DT
cord-002542-f7l4ty2j	375	3	inoculum	inoculum	NN
cord-002542-f7l4ty2j	375	4	and	and	CC
cord-002542-f7l4ty2j	375	5	in	in	IN
cord-002542-f7l4ty2j	375	6	the	the	DT
cord-002542-f7l4ty2j	375	7	early	early	JJ
cord-002542-f7l4ty2j	375	8	passages	passage	NNS
cord-002542-f7l4ty2j	375	9	,	,	,
cord-002542-f7l4ty2j	375	10	we	-PRON-	PRP
cord-002542-f7l4ty2j	375	11	find	find	VBP
cord-002542-f7l4ty2j	375	12	a	a	DT
cord-002542-f7l4ty2j	375	13	wide	wide	JJ
cord-002542-f7l4ty2j	375	14	range	range	NN
cord-002542-f7l4ty2j	375	15	of	of	IN
cord-002542-f7l4ty2j	375	16	low	low	JJ
cord-002542-f7l4ty2j	375	17	-	-	HYPH
cord-002542-f7l4ty2j	375	18	frequency	frequency	NN
cord-002542-f7l4ty2j	375	19	recombination	recombination	NN
cord-002542-f7l4ty2j	375	20	events	event	NNS
cord-002542-f7l4ty2j	375	21	corresponding	correspond	VBG
cord-002542-f7l4ty2j	375	22	to	to	IN
cord-002542-f7l4ty2j	375	23	deletions	deletion	NNS
cord-002542-f7l4ty2j	375	24	and	and	CC
cord-002542-f7l4ty2j	375	25	duplications	duplication	NNS
cord-002542-f7l4ty2j	375	26	that	that	WDT
cord-002542-f7l4ty2j	375	27	are	be	VBP
cord-002542-f7l4ty2j	375	28	dispersed	disperse	VBN
cord-002542-f7l4ty2j	375	29	through	through	IN
cord-002542-f7l4ty2j	375	30	-	-	HYPH
cord-002542-f7l4ty2j	375	31	out	out	NN
cord-002542-f7l4ty2j	375	32	the	the	DT
cord-002542-f7l4ty2j	375	33	viral	viral	JJ
cord-002542-f7l4ty2j	375	34	genomic	genomic	JJ
cord-002542-f7l4ty2j	375	35	RNAs	rna	NNS
cord-002542-f7l4ty2j	375	36	.	.	.
cord-002542-f7l4ty2j	376	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	376	2	can	can	MD
cord-002542-f7l4ty2j	376	3	be	be	VB
cord-002542-f7l4ty2j	376	4	confident	confident	JJ
cord-002542-f7l4ty2j	376	5	that	that	IN
cord-002542-f7l4ty2j	376	6	these	these	DT
cord-002542-f7l4ty2j	376	7	species	specie	NNS
cord-002542-f7l4ty2j	376	8	do	do	VBP
cord-002542-f7l4ty2j	376	9	not	not	RB
cord-002542-f7l4ty2j	376	10	constitute	constitute	VB
cord-002542-f7l4ty2j	376	11	sequencing	sequencing	NN
cord-002542-f7l4ty2j	376	12	artifacts	artifact	NNS
cord-002542-f7l4ty2j	376	13	as	as	IN
cord-002542-f7l4ty2j	376	14	we	-PRON-	PRP
cord-002542-f7l4ty2j	376	15	made	make	VBD
cord-002542-f7l4ty2j	376	16	our	-PRON-	PRP$
cord-002542-f7l4ty2j	376	17	RNAseq	rnaseq	NN
cord-002542-f7l4ty2j	376	18	libraries	library	NNS
cord-002542-f7l4ty2j	376	19	using	use	VBG
cord-002542-f7l4ty2j	376	20	'	'	``
cord-002542-f7l4ty2j	376	21	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	376	22	'	'	''
cord-002542-f7l4ty2j	376	23	[	[	-LRB-
cord-002542-f7l4ty2j	376	24	35	35	CD
cord-002542-f7l4ty2j	376	25	]	]	-RRB-
cord-002542-f7l4ty2j	376	26	that	that	WDT
cord-002542-f7l4ty2j	376	27	has	have	VBZ
cord-002542-f7l4ty2j	376	28	previously	previously	RB
cord-002542-f7l4ty2j	376	29	been	be	VBN
cord-002542-f7l4ty2j	376	30	demonstrated	demonstrate	VBN
cord-002542-f7l4ty2j	376	31	to	to	TO
cord-002542-f7l4ty2j	376	32	reduce	reduce	VB
cord-002542-f7l4ty2j	376	33	artifactual	artifactual	JJ
cord-002542-f7l4ty2j	376	34	recombination	recombination	NN
cord-002542-f7l4ty2j	376	35	in	in	IN
cord-002542-f7l4ty2j	376	36	RNAseq	RNAseq	NNP
cord-002542-f7l4ty2j	376	37	data	datum	NNS
cord-002542-f7l4ty2j	376	38	to	to	IN
cord-002542-f7l4ty2j	376	39	fewer	few	JJR
cord-002542-f7l4ty2j	376	40	than	than	IN
cord-002542-f7l4ty2j	376	41	3	3	CD
cord-002542-f7l4ty2j	376	42	events	event	NNS
cord-002542-f7l4ty2j	376	43	per	per	IN
cord-002542-f7l4ty2j	376	44	million	million	CD
cord-002542-f7l4ty2j	376	45	reads	read	NNS
cord-002542-f7l4ty2j	376	46	.	.	.
cord-002542-f7l4ty2j	377	1	Further	further	JJ
cord-002542-f7l4ty2j	377	2	confidence	confidence	NN
cord-002542-f7l4ty2j	377	3	in	in	IN
cord-002542-f7l4ty2j	377	4	the	the	DT
cord-002542-f7l4ty2j	377	5	low	low	JJ
cord-002542-f7l4ty2j	377	6	rates	rate	NNS
cord-002542-f7l4ty2j	377	7	of	of	IN
cord-002542-f7l4ty2j	377	8	artifactual	artifactual	JJ
cord-002542-f7l4ty2j	377	9	recombination	recombination	NN
cord-002542-f7l4ty2j	377	10	in	in	IN
cord-002542-f7l4ty2j	377	11	our	-PRON-	PRP$
cord-002542-f7l4ty2j	377	12	study	study	NN
cord-002542-f7l4ty2j	377	13	is	be	VBZ
cord-002542-f7l4ty2j	377	14	provided	provide	VBN
cord-002542-f7l4ty2j	377	15	internally	internally	RB
cord-002542-f7l4ty2j	377	16	by	by	IN
cord-002542-f7l4ty2j	377	17	inspecting	inspect	VBG
cord-002542-f7l4ty2j	377	18	the	the	DT
cord-002542-f7l4ty2j	377	19	numbers	number	NNS
cord-002542-f7l4ty2j	377	20	of	of	IN
cord-002542-f7l4ty2j	377	21	inter	inter	JJ
cord-002542-f7l4ty2j	377	22	-	-	JJ
cord-002542-f7l4ty2j	377	23	RNA	rna	JJ
cord-002542-f7l4ty2j	377	24	recombination	recombination	NN
cord-002542-f7l4ty2j	377	25	events	event	NNS
cord-002542-f7l4ty2j	377	26	(	(	-LRB-
cord-002542-f7l4ty2j	377	27	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	377	28	to	to	IN
cord-002542-f7l4ty2j	377	29	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	377	30	and	and	CC
cord-002542-f7l4ty2j	377	31	vice	vice	NN
cord-002542-f7l4ty2j	377	32	versa	versa	RB
cord-002542-f7l4ty2j	377	33	)	)	-RRB-
cord-002542-f7l4ty2j	377	34	,	,	,
cord-002542-f7l4ty2j	377	35	which	which	WDT
cord-002542-f7l4ty2j	377	36	are	be	VBP
cord-002542-f7l4ty2j	377	37	always	always	RB
cord-002542-f7l4ty2j	377	38	low	low	JJ
cord-002542-f7l4ty2j	377	39	.	.	.
cord-002542-f7l4ty2j	378	1	Furthermore	furthermore	RB
cord-002542-f7l4ty2j	378	2	,	,	,
cord-002542-f7l4ty2j	378	3	the	the	DT
cord-002542-f7l4ty2j	378	4	majority	majority	NN
cord-002542-f7l4ty2j	378	5	of	of	IN
cord-002542-f7l4ty2j	378	6	the	the	DT
cord-002542-f7l4ty2j	378	7	detected	detect	VBN
cord-002542-f7l4ty2j	378	8	inter	inter	JJ
cord-002542-f7l4ty2j	378	9	-	-	JJ
cord-002542-f7l4ty2j	378	10	RNA	rna	JJ
cord-002542-f7l4ty2j	378	11	recombination	recombination	NN
cord-002542-f7l4ty2j	378	12	events	event	NNS
cord-002542-f7l4ty2j	378	13	correspond	correspond	VBP
cord-002542-f7l4ty2j	378	14	to	to	IN
cord-002542-f7l4ty2j	378	15	genomic	genomic	JJ
cord-002542-f7l4ty2j	378	16	RNA	RNA	NNP
cord-002542-f7l4ty2j	378	17	hetero	hetero	NNS
cord-002542-f7l4ty2j	378	18	-	-	HYPH
cord-002542-f7l4ty2j	378	19	and	and	CC
cord-002542-f7l4ty2j	378	20	homo	homo	NN
cord-002542-f7l4ty2j	378	21	-	-	HYPH
cord-002542-f7l4ty2j	378	22	dimers	dimer	NNS
cord-002542-f7l4ty2j	378	23	,	,	,
cord-002542-f7l4ty2j	378	24	which	which	WDT
cord-002542-f7l4ty2j	378	25	have	have	VBP
cord-002542-f7l4ty2j	378	26	previously	previously	RB
cord-002542-f7l4ty2j	378	27	been	be	VBN
cord-002542-f7l4ty2j	378	28	characterized	characterize	VBN
cord-002542-f7l4ty2j	378	29	as	as	IN
cord-002542-f7l4ty2j	378	30	replication	replication	NN
cord-002542-f7l4ty2j	378	31	intermediates	intermediate	NNS
cord-002542-f7l4ty2j	378	32	[	[	-LRB-
cord-002542-f7l4ty2j	378	33	65	65	CD
cord-002542-f7l4ty2j	378	34	]	]	-RRB-
cord-002542-f7l4ty2j	378	35	.	.	.
cord-002542-f7l4ty2j	379	1	Within	within	IN
cord-002542-f7l4ty2j	379	2	only	only	RB
cord-002542-f7l4ty2j	379	3	2	2	CD
cord-002542-f7l4ty2j	379	4	-	-	SYM
cord-002542-f7l4ty2j	379	5	3	3	CD
cord-002542-f7l4ty2j	379	6	passages	passage	NNS
cord-002542-f7l4ty2j	379	7	,	,	,
cord-002542-f7l4ty2j	379	8	however	however	RB
cord-002542-f7l4ty2j	379	9	,	,	,
cord-002542-f7l4ty2j	379	10	deletion	deletion	NN
cord-002542-f7l4ty2j	379	11	events	event	NNS
cord-002542-f7l4ty2j	379	12	similar	similar	JJ
cord-002542-f7l4ty2j	379	13	to	to	IN
cord-002542-f7l4ty2j	379	14	those	those	DT
cord-002542-f7l4ty2j	379	15	previously	previously	RB
cord-002542-f7l4ty2j	379	16	observed	observe	VBN
cord-002542-f7l4ty2j	379	17	in	in	IN
cord-002542-f7l4ty2j	379	18	DI	DI	NNP
cord-002542-f7l4ty2j	379	19	-	-	HYPH
cord-002542-f7l4ty2j	379	20	RNAs	rna	NNS
cord-002542-f7l4ty2j	379	21	appear	appear	VBP
cord-002542-f7l4ty2j	379	22	in	in	IN
cord-002542-f7l4ty2j	379	23	all	all	DT
cord-002542-f7l4ty2j	379	24	three	three	CD
cord-002542-f7l4ty2j	379	25	passaging	passaging	NN
cord-002542-f7l4ty2j	379	26	replicates	replicate	NNS
cord-002542-f7l4ty2j	379	27	.	.	.
cord-002542-f7l4ty2j	380	1	In	in	IN
cord-002542-f7l4ty2j	380	2	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	380	3	passages	passage	NNS
cord-002542-f7l4ty2j	380	4	,	,	,
cord-002542-f7l4ty2j	380	5	these	these	DT
cord-002542-f7l4ty2j	380	6	recombination	recombination	NN
cord-002542-f7l4ty2j	380	7	events	event	NNS
cord-002542-f7l4ty2j	380	8	begin	begin	VBP
cord-002542-f7l4ty2j	380	9	to	to	TO
cord-002542-f7l4ty2j	380	10	accumulate	accumulate	VB
cord-002542-f7l4ty2j	380	11	rapidly	rapidly	RB
cord-002542-f7l4ty2j	380	12	so	so	IN
cord-002542-f7l4ty2j	380	13	as	as	IN
cord-002542-f7l4ty2j	380	14	to	to	TO
cord-002542-f7l4ty2j	380	15	predominate	predominate	VB
cord-002542-f7l4ty2j	380	16	over	over	IN
cord-002542-f7l4ty2j	380	17	full	full	JJ
cord-002542-f7l4ty2j	380	18	-	-	HYPH
cord-002542-f7l4ty2j	380	19	length	length	NN
cord-002542-f7l4ty2j	380	20	viral	viral	JJ
cord-002542-f7l4ty2j	380	21	RNAs	rna	NNS
cord-002542-f7l4ty2j	380	22	.	.	.
cord-002542-f7l4ty2j	381	1	This	this	DT
cord-002542-f7l4ty2j	381	2	observation	observation	NN
cord-002542-f7l4ty2j	381	3	of	of	IN
cord-002542-f7l4ty2j	381	4	the	the	DT
cord-002542-f7l4ty2j	381	5	emergence	emergence	NN
cord-002542-f7l4ty2j	381	6	of	of	IN
cord-002542-f7l4ty2j	381	7	DI	DI	NNP
cord-002542-f7l4ty2j	381	8	-	-	HYPH
cord-002542-f7l4ty2j	381	9	RNA	RNA	NNP
cord-002542-f7l4ty2j	381	10	species	specie	NNS
cord-002542-f7l4ty2j	381	11	,	,	,
cord-002542-f7l4ty2j	381	12	followed	follow	VBN
cord-002542-f7l4ty2j	381	13	by	by	IN
cord-002542-f7l4ty2j	381	14	their	-PRON-	PRP$
cord-002542-f7l4ty2j	381	15	rapid	rapid	JJ
cord-002542-f7l4ty2j	381	16	accumulation	accumulation	NN
cord-002542-f7l4ty2j	381	17	is	be	VBZ
cord-002542-f7l4ty2j	381	18	consistent	consistent	JJ
cord-002542-f7l4ty2j	381	19	with	with	IN
cord-002542-f7l4ty2j	381	20	existing	exist	VBG
cord-002542-f7l4ty2j	381	21	theories	theory	NNS
cord-002542-f7l4ty2j	381	22	on	on	IN
cord-002542-f7l4ty2j	381	23	the	the	DT
cord-002542-f7l4ty2j	381	24	evolution	evolution	NN
cord-002542-f7l4ty2j	381	25	of	of	IN
cord-002542-f7l4ty2j	381	26	DI	DI	NNP
cord-002542-f7l4ty2j	381	27	-	-	HYPH
cord-002542-f7l4ty2j	381	28	RNAs	rna	NNS
cord-002542-f7l4ty2j	381	29	that	that	WDT
cord-002542-f7l4ty2j	381	30	postulate	postulate	VBP
cord-002542-f7l4ty2j	381	31	that	that	IN
cord-002542-f7l4ty2j	381	32	a	a	DT
cord-002542-f7l4ty2j	381	33	wide	wide	JJ
cord-002542-f7l4ty2j	381	34	range	range	NN
cord-002542-f7l4ty2j	381	35	of	of	IN
cord-002542-f7l4ty2j	381	36	potential	potential	JJ
cord-002542-f7l4ty2j	381	37	DI	DI	NNP
cord-002542-f7l4ty2j	381	38	-	-	HYPH
cord-002542-f7l4ty2j	381	39	RNA	RNA	NNP
cord-002542-f7l4ty2j	381	40	species	specie	NNS
cord-002542-f7l4ty2j	381	41	are	be	VBP
cord-002542-f7l4ty2j	381	42	generated	generate	VBN
cord-002542-f7l4ty2j	381	43	by	by	IN
cord-002542-f7l4ty2j	381	44	non	non	JJ
cord-002542-f7l4ty2j	381	45	-	-	JJ
cord-002542-f7l4ty2j	381	46	programmed	programmed	JJ
cord-002542-f7l4ty2j	381	47	RNA	rna	NN
cord-002542-f7l4ty2j	381	48	recombination	recombination	NN
cord-002542-f7l4ty2j	381	49	and	and	CC
cord-002542-f7l4ty2j	381	50	that	that	IN
cord-002542-f7l4ty2j	381	51	only	only	RB
cord-002542-f7l4ty2j	381	52	a	a	DT
cord-002542-f7l4ty2j	381	53	handful	handful	NN
cord-002542-f7l4ty2j	381	54	are	be	VBP
cord-002542-f7l4ty2j	381	55	successfully	successfully	RB
cord-002542-f7l4ty2j	381	56	replicated	replicate	VBN
cord-002542-f7l4ty2j	381	57	and	and	CC
cord-002542-f7l4ty2j	381	58	thus	thus	RB
cord-002542-f7l4ty2j	381	59	accumulate	accumulate	VB
cord-002542-f7l4ty2j	381	60	[	[	-LRB-
cord-002542-f7l4ty2j	381	61	9	9	CD
cord-002542-f7l4ty2j	381	62	]	]	-RRB-
cord-002542-f7l4ty2j	381	63	.	.	.
cord-002542-f7l4ty2j	382	1	While	while	IN
cord-002542-f7l4ty2j	382	2	the	the	DT
cord-002542-f7l4ty2j	382	3	short	short	RB
cord-002542-f7l4ty2j	382	4	-	-	HYPH
cord-002542-f7l4ty2j	382	5	read	read	NN
cord-002542-f7l4ty2j	382	6	data	datum	NNS
cord-002542-f7l4ty2j	382	7	provide	provide	VBP
cord-002542-f7l4ty2j	382	8	high	high	JJ
cord-002542-f7l4ty2j	382	9	-	-	HYPH
cord-002542-f7l4ty2j	382	10	resolution	resolution	NN
cord-002542-f7l4ty2j	382	11	characterization	characterization	NN
cord-002542-f7l4ty2j	382	12	of	of	IN
cord-002542-f7l4ty2j	382	13	individual	individual	JJ
cord-002542-f7l4ty2j	382	14	recombination	recombination	NN
cord-002542-f7l4ty2j	382	15	events	event	NNS
cord-002542-f7l4ty2j	382	16	,	,	,
cord-002542-f7l4ty2j	382	17	it	-PRON-	PRP
cord-002542-f7l4ty2j	382	18	is	be	VBZ
cord-002542-f7l4ty2j	382	19	through	through	IN
cord-002542-f7l4ty2j	382	20	the	the	DT
cord-002542-f7l4ty2j	382	21	use	use	NN
cord-002542-f7l4ty2j	382	22	of	of	IN
cord-002542-f7l4ty2j	382	23	the	the	DT
cord-002542-f7l4ty2j	382	24	Oxford	Oxford	NNP
cord-002542-f7l4ty2j	382	25	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	382	26	Technologies	Technologies	NNP
cord-002542-f7l4ty2j	382	27	(	(	-LRB-
cord-002542-f7l4ty2j	382	28	ONT	ONT	NNP
cord-002542-f7l4ty2j	382	29	)	)	-RRB-
cord-002542-f7l4ty2j	382	30	MinION	minion	FW
cord-002542-f7l4ty2j	382	31	that	that	IN
cord-002542-f7l4ty2j	382	32	we	-PRON-	PRP
cord-002542-f7l4ty2j	382	33	are	be	VBP
cord-002542-f7l4ty2j	382	34	able	able	JJ
cord-002542-f7l4ty2j	382	35	reconstitute	reconstitute	VB
cord-002542-f7l4ty2j	382	36	the	the	DT
cord-002542-f7l4ty2j	382	37	complex	complex	JJ
cord-002542-f7l4ty2j	382	38	full	full	JJ
cord-002542-f7l4ty2j	382	39	-	-	HYPH
cord-002542-f7l4ty2j	382	40	length	length	NN
cord-002542-f7l4ty2j	382	41	genomic	genomic	JJ
cord-002542-f7l4ty2j	382	42	landscape	landscape	NN
cord-002542-f7l4ty2j	382	43	of	of	IN
cord-002542-f7l4ty2j	382	44	FHV	FHV	NNP
cord-002542-f7l4ty2j	382	45	during	during	IN
cord-002542-f7l4ty2j	382	46	passaging	passaging	NN
cord-002542-f7l4ty2j	382	47	and	and	CC
cord-002542-f7l4ty2j	382	48	determine	determine	VB
cord-002542-f7l4ty2j	382	49	the	the	DT
cord-002542-f7l4ty2j	382	50	relative	relative	JJ
cord-002542-f7l4ty2j	382	51	abundances	abundance	NNS
cord-002542-f7l4ty2j	382	52	of	of	IN
cord-002542-f7l4ty2j	382	53	the	the	DT
cord-002542-f7l4ty2j	382	54	genomic	genomic	JJ
cord-002542-f7l4ty2j	382	55	RNAs	rna	NNS
cord-002542-f7l4ty2j	382	56	in	in	IN
cord-002542-f7l4ty2j	382	57	each	each	DT
cord-002542-f7l4ty2j	382	58	passage	passage	NN
cord-002542-f7l4ty2j	382	59	.	.	.
cord-002542-f7l4ty2j	383	1	As	as	IN
cord-002542-f7l4ty2j	383	2	a	a	DT
cord-002542-f7l4ty2j	383	3	result	result	NN
cord-002542-f7l4ty2j	383	4	,	,	,
cord-002542-f7l4ty2j	383	5	we	-PRON-	PRP
cord-002542-f7l4ty2j	383	6	were	be	VBD
cord-002542-f7l4ty2j	383	7	able	able	JJ
cord-002542-f7l4ty2j	383	8	to	to	TO
cord-002542-f7l4ty2j	383	9	determine	determine	VB
cord-002542-f7l4ty2j	383	10	that	that	DT
cord-002542-f7l4ty2j	383	11	by	by	IN
cord-002542-f7l4ty2j	383	12	the	the	DT
cord-002542-f7l4ty2j	383	13	final	final	JJ
cord-002542-f7l4ty2j	383	14	passage	passage	NN
cord-002542-f7l4ty2j	384	1	only~2	only~2	NNP
cord-002542-f7l4ty2j	385	1	%	%	NN
cord-002542-f7l4ty2j	385	2	of	of	IN
cord-002542-f7l4ty2j	385	3	the	the	DT
cord-002542-f7l4ty2j	385	4	mapped	map	VBN
cord-002542-f7l4ty2j	385	5	reads	read	NNS
cord-002542-f7l4ty2j	385	6	are	be	VBP
cord-002542-f7l4ty2j	385	7	full	full	JJ
cord-002542-f7l4ty2j	385	8	-	-	HYPH
cord-002542-f7l4ty2j	385	9	length	length	NN
cord-002542-f7l4ty2j	385	10	viral	viral	JJ
cord-002542-f7l4ty2j	385	11	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	385	12	,	,	,
cord-002542-f7l4ty2j	385	13	which	which	WDT
cord-002542-f7l4ty2j	385	14	corresponded	correspond	VBD
cord-002542-f7l4ty2j	385	15	with	with	IN
cord-002542-f7l4ty2j	385	16	a	a	DT
cord-002542-f7l4ty2j	385	17	large	large	JJ
cord-002542-f7l4ty2j	385	18	reduction	reduction	NN
cord-002542-f7l4ty2j	385	19	in	in	IN
cord-002542-f7l4ty2j	385	20	specific	specific	JJ
cord-002542-f7l4ty2j	385	21	infectivity	infectivity	NN
cord-002542-f7l4ty2j	385	22	.	.	.
cord-002542-f7l4ty2j	386	1	Additionally	additionally	RB
cord-002542-f7l4ty2j	386	2	,	,	,
cord-002542-f7l4ty2j	386	3	the	the	DT
cord-002542-f7l4ty2j	386	4	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	386	5	data	datum	NNS
cord-002542-f7l4ty2j	386	6	revealed	reveal	VBD
cord-002542-f7l4ty2j	386	7	complex	complex	JJ
cord-002542-f7l4ty2j	386	8	rearrangements	rearrangement	NNS
cord-002542-f7l4ty2j	386	9	of	of	IN
cord-002542-f7l4ty2j	386	10	RNA	RNA	NNP
cord-002542-f7l4ty2j	386	11	genomes	genome	NNS
cord-002542-f7l4ty2j	386	12	,	,	,
cord-002542-f7l4ty2j	386	13	including	include	VBG
cord-002542-f7l4ty2j	386	14	the	the	DT
cord-002542-f7l4ty2j	386	15	excision	excision	NN
cord-002542-f7l4ty2j	386	16	of	of	IN
cord-002542-f7l4ty2j	386	17	an	an	DT
cord-002542-f7l4ty2j	386	18	entire	entire	JJ
cord-002542-f7l4ty2j	386	19	functional	functional	JJ
cord-002542-f7l4ty2j	386	20	RNA	RNA	NNP
cord-002542-f7l4ty2j	386	21	motif	motif	NN
cord-002542-f7l4ty2j	386	22	and	and	CC
cord-002542-f7l4ty2j	386	23	its	-PRON-	PRP$
cord-002542-f7l4ty2j	386	24	reinsertion	reinsertion	NN
cord-002542-f7l4ty2j	386	25	in	in	IN
cord-002542-f7l4ty2j	386	26	the	the	DT
cord-002542-f7l4ty2j	386	27	5'UTR	5'utr	CD
cord-002542-f7l4ty2j	386	28	of	of	IN
cord-002542-f7l4ty2j	386	29	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	386	30	.	.	.
cord-002542-f7l4ty2j	387	1	The	the	DT
cord-002542-f7l4ty2j	387	2	variation	variation	NN
cord-002542-f7l4ty2j	387	3	in	in	IN
cord-002542-f7l4ty2j	387	4	recombination	recombination	NN
cord-002542-f7l4ty2j	387	5	boundaries	boundary	NNS
cord-002542-f7l4ty2j	387	6	of	of	IN
cord-002542-f7l4ty2j	387	7	the	the	DT
cord-002542-f7l4ty2j	387	8	DI	DI	NNP
cord-002542-f7l4ty2j	387	9	-	-	HYPH
cord-002542-f7l4ty2j	387	10	RNAs	RNAs	NNP
cord-002542-f7l4ty2j	387	11	suggests	suggest	VBZ
cord-002542-f7l4ty2j	387	12	that	that	IN
cord-002542-f7l4ty2j	387	13	a	a	DT
cord-002542-f7l4ty2j	387	14	range	range	NN
cord-002542-f7l4ty2j	387	15	of	of	IN
cord-002542-f7l4ty2j	387	16	deletions	deletion	NNS
cord-002542-f7l4ty2j	387	17	can	can	MD
cord-002542-f7l4ty2j	387	18	be	be	VB
cord-002542-f7l4ty2j	387	19	tolerated	tolerate	VBN
cord-002542-f7l4ty2j	387	20	.	.	.
cord-002542-f7l4ty2j	388	1	However	however	RB
cord-002542-f7l4ty2j	388	2	,	,	,
cord-002542-f7l4ty2j	388	3	it	-PRON-	PRP
cord-002542-f7l4ty2j	388	4	is	be	VBZ
cord-002542-f7l4ty2j	388	5	important	important	JJ
cord-002542-f7l4ty2j	388	6	to	to	TO
cord-002542-f7l4ty2j	388	7	note	note	VB
cord-002542-f7l4ty2j	388	8	that	that	IN
cord-002542-f7l4ty2j	388	9	while	while	IN
cord-002542-f7l4ty2j	388	10	each	each	DT
cord-002542-f7l4ty2j	388	11	replicate	replicate	VBP
cord-002542-f7l4ty2j	388	12	is	be	VBZ
cord-002542-f7l4ty2j	388	13	its	-PRON-	PRP$
cord-002542-f7l4ty2j	388	14	own	own	JJ
cord-002542-f7l4ty2j	388	15	distinct	distinct	JJ
cord-002542-f7l4ty2j	388	16	lineage	lineage	NN
cord-002542-f7l4ty2j	388	17	,	,	,
cord-002542-f7l4ty2j	388	18	each	each	DT
cord-002542-f7l4ty2j	388	19	replicate	replicate	VBP
cord-002542-f7l4ty2j	388	20	passaging	passaging	NN
cord-002542-f7l4ty2j	388	21	experiment	experiment	NN
cord-002542-f7l4ty2j	388	22	was	be	VBD
cord-002542-f7l4ty2j	388	23	derived	derive	VBN
cord-002542-f7l4ty2j	388	24	from	from	IN
cord-002542-f7l4ty2j	388	25	the	the	DT
cord-002542-f7l4ty2j	388	26	same	same	JJ
cord-002542-f7l4ty2j	388	27	initial	initial	JJ
cord-002542-f7l4ty2j	388	28	inoculum	inoculum	NN
cord-002542-f7l4ty2j	388	29	.	.	.
cord-002542-f7l4ty2j	389	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	389	2	chose	choose	VBD
cord-002542-f7l4ty2j	389	3	to	to	TO
cord-002542-f7l4ty2j	389	4	design	design	VB
cord-002542-f7l4ty2j	389	5	the	the	DT
cord-002542-f7l4ty2j	389	6	experiment	experiment	NN
cord-002542-f7l4ty2j	389	7	this	this	DT
cord-002542-f7l4ty2j	389	8	way	way	NN
cord-002542-f7l4ty2j	389	9	to	to	TO
cord-002542-f7l4ty2j	389	10	determine	determine	VB
cord-002542-f7l4ty2j	389	11	if	if	IN
cord-002542-f7l4ty2j	389	12	the	the	DT
cord-002542-f7l4ty2j	389	13	same	same	JJ
cord-002542-f7l4ty2j	389	14	DI	DI	NNP
cord-002542-f7l4ty2j	389	15	-	-	HYPH
cord-002542-f7l4ty2j	389	16	RNAs	rna	NNS
cord-002542-f7l4ty2j	389	17	would	would	MD
cord-002542-f7l4ty2j	389	18	be	be	VB
cord-002542-f7l4ty2j	389	19	generated	generate	VBN
cord-002542-f7l4ty2j	389	20	independently	independently	RB
cord-002542-f7l4ty2j	389	21	or	or	CC
cord-002542-f7l4ty2j	389	22	if	if	IN
cord-002542-f7l4ty2j	389	23	completely	completely	RB
cord-002542-f7l4ty2j	389	24	different	different	JJ
cord-002542-f7l4ty2j	389	25	deletions	deletion	NNS
cord-002542-f7l4ty2j	389	26	would	would	MD
cord-002542-f7l4ty2j	389	27	arise	arise	VB
cord-002542-f7l4ty2j	389	28	and	and	CC
cord-002542-f7l4ty2j	389	29	be	be	VB
cord-002542-f7l4ty2j	389	30	selected	select	VBN
cord-002542-f7l4ty2j	389	31	for	for	IN
cord-002542-f7l4ty2j	389	32	even	even	RB
cord-002542-f7l4ty2j	389	33	though	though	IN
cord-002542-f7l4ty2j	389	34	the	the	DT
cord-002542-f7l4ty2j	389	35	environmental	environmental	JJ
cord-002542-f7l4ty2j	389	36	conditions	condition	NNS
cord-002542-f7l4ty2j	389	37	are	be	VBP
cord-002542-f7l4ty2j	389	38	practically	practically	RB
cord-002542-f7l4ty2j	389	39	the	the	DT
cord-002542-f7l4ty2j	389	40	same	same	JJ
cord-002542-f7l4ty2j	389	41	.	.	.
cord-002542-f7l4ty2j	390	1	Here	here	RB
cord-002542-f7l4ty2j	390	2	,	,	,
cord-002542-f7l4ty2j	390	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	390	4	observe	observe	VBP
cord-002542-f7l4ty2j	390	5	the	the	DT
cord-002542-f7l4ty2j	390	6	latter	latter	JJ
cord-002542-f7l4ty2j	390	7	(	(	-LRB-
cord-002542-f7l4ty2j	390	8	Table	table	NN
cord-002542-f7l4ty2j	390	9	2	2	CD
cord-002542-f7l4ty2j	390	10	)	)	-RRB-
cord-002542-f7l4ty2j	390	11	.	.	.
cord-002542-f7l4ty2j	391	1	Few	few	JJ
cord-002542-f7l4ty2j	391	2	of	of	IN
cord-002542-f7l4ty2j	391	3	the	the	DT
cord-002542-f7l4ty2j	391	4	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	391	5	recombination	recombination	NN
cord-002542-f7l4ty2j	391	6	events	event	NNS
cord-002542-f7l4ty2j	391	7	observed	observe	VBN
cord-002542-f7l4ty2j	391	8	in	in	IN
cord-002542-f7l4ty2j	391	9	the	the	DT
cord-002542-f7l4ty2j	391	10	inoculum	inoculum	NN
cord-002542-f7l4ty2j	391	11	are	be	VBP
cord-002542-f7l4ty2j	391	12	observed	observe	VBN
cord-002542-f7l4ty2j	391	13	again	again	RB
cord-002542-f7l4ty2j	391	14	in	in	IN
cord-002542-f7l4ty2j	391	15	subsequent	subsequent	JJ
cord-002542-f7l4ty2j	391	16	passages	passage	NNS
cord-002542-f7l4ty2j	391	17	.	.	.
cord-002542-f7l4ty2j	392	1	Additionally	additionally	RB
cord-002542-f7l4ty2j	392	2	,	,	,
cord-002542-f7l4ty2j	392	3	even	even	RB
cord-002542-f7l4ty2j	392	4	though	though	IN
cord-002542-f7l4ty2j	392	5	we	-PRON-	PRP
cord-002542-f7l4ty2j	392	6	found	find	VBD
cord-002542-f7l4ty2j	392	7	the	the	DT
cord-002542-f7l4ty2j	392	8	event	event	NN
cord-002542-f7l4ty2j	392	9	'	'	''
cord-002542-f7l4ty2j	392	10	738	738	CD
cord-002542-f7l4ty2j	392	11	^	^	SYM
cord-002542-f7l4ty2j	392	12	1219	1219	CD
cord-002542-f7l4ty2j	392	13	'	'	''
cord-002542-f7l4ty2j	392	14	in	in	IN
cord-002542-f7l4ty2j	392	15	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	393	1	the	the	DT
cord-002542-f7l4ty2j	393	2	inoculum	inoculum	NN
cord-002542-f7l4ty2j	393	3	,	,	,
cord-002542-f7l4ty2j	393	4	this	this	DT
cord-002542-f7l4ty2j	393	5	was	be	VBD
cord-002542-f7l4ty2j	393	6	not	not	RB
cord-002542-f7l4ty2j	393	7	the	the	DT
cord-002542-f7l4ty2j	393	8	final	final	JJ
cord-002542-f7l4ty2j	393	9	predominant	predominant	JJ
cord-002542-f7l4ty2j	393	10	species	specie	NNS
cord-002542-f7l4ty2j	393	11	in	in	IN
cord-002542-f7l4ty2j	393	12	any	any	DT
cord-002542-f7l4ty2j	393	13	replicate	replicate	NN
cord-002542-f7l4ty2j	393	14	.	.	.
cord-002542-f7l4ty2j	394	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	394	2	,	,	,
cord-002542-f7l4ty2j	394	3	the	the	DT
cord-002542-f7l4ty2j	394	4	evolution	evolution	NN
cord-002542-f7l4ty2j	394	5	of	of	IN
cord-002542-f7l4ty2j	394	6	DI	DI	NNP
cord-002542-f7l4ty2j	394	7	-	-	HYPH
cord-002542-f7l4ty2j	394	8	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	394	9	was	be	VBD
cord-002542-f7l4ty2j	394	10	not	not	RB
cord-002542-f7l4ty2j	394	11	pre	pre	JJ
cord-002542-f7l4ty2j	394	12	-	-	JJ
cord-002542-f7l4ty2j	394	13	determined	determined	JJ
cord-002542-f7l4ty2j	395	1	by	by	IN
cord-002542-f7l4ty2j	395	2	the	the	DT
cord-002542-f7l4ty2j	395	3	presence	presence	NN
cord-002542-f7l4ty2j	395	4	of	of	IN
cord-002542-f7l4ty2j	395	5	rare	rare	JJ
cord-002542-f7l4ty2j	395	6	DI	DI	NNP
cord-002542-f7l4ty2j	395	7	-	-	HYPH
cord-002542-f7l4ty2j	395	8	RNA	RNA	NNP
cord-002542-f7l4ty2j	395	9	species	specie	NNS
cord-002542-f7l4ty2j	395	10	in	in	IN
cord-002542-f7l4ty2j	395	11	the	the	DT
cord-002542-f7l4ty2j	395	12	common	common	JJ
cord-002542-f7l4ty2j	395	13	inoculum	inoculum	NN
cord-002542-f7l4ty2j	395	14	(	(	-LRB-
cord-002542-f7l4ty2j	395	15	a	a	DT
cord-002542-f7l4ty2j	395	16	founder	founder	NN
cord-002542-f7l4ty2j	395	17	-	-	HYPH
cord-002542-f7l4ty2j	395	18	effect	effect	NN
cord-002542-f7l4ty2j	395	19	)	)	-RRB-
cord-002542-f7l4ty2j	395	20	,	,	,
cord-002542-f7l4ty2j	395	21	but	but	CC
cord-002542-f7l4ty2j	395	22	rather	rather	RB
cord-002542-f7l4ty2j	395	23	by	by	IN
cord-002542-f7l4ty2j	395	24	the	the	DT
cord-002542-f7l4ty2j	395	25	selection	selection	NN
cord-002542-f7l4ty2j	395	26	of	of	IN
cord-002542-f7l4ty2j	395	27	well	well	RB
cord-002542-f7l4ty2j	395	28	-	-	HYPH
cord-002542-f7l4ty2j	395	29	replicating	replicate	VBG
cord-002542-f7l4ty2j	395	30	DI	DI	NNP
cord-002542-f7l4ty2j	395	31	-	-	HYPH
cord-002542-f7l4ty2j	395	32	R	R	NNP
cord-002542-f7l4ty2j	395	33	-	-	HYPH
cord-002542-f7l4ty2j	395	34	NAs	NAs	NNPS
cord-002542-f7l4ty2j	395	35	that	that	WDT
cord-002542-f7l4ty2j	395	36	arose	arise	VBD
cord-002542-f7l4ty2j	395	37	later	later	RB
cord-002542-f7l4ty2j	395	38	during	during	IN
cord-002542-f7l4ty2j	395	39	serial	serial	JJ
cord-002542-f7l4ty2j	395	40	passaging	passaging	NN
cord-002542-f7l4ty2j	395	41	.	.	.
cord-002542-f7l4ty2j	396	1	Nonetheless	nonetheless	RB
cord-002542-f7l4ty2j	396	2	,	,	,
cord-002542-f7l4ty2j	396	3	the	the	DT
cord-002542-f7l4ty2j	396	4	final	final	JJ
cord-002542-f7l4ty2j	396	5	recombination	recombination	NN
cord-002542-f7l4ty2j	396	6	events	event	NNS
cord-002542-f7l4ty2j	396	7	are	be	VBP
cord-002542-f7l4ty2j	396	8	highly	highly	RB
cord-002542-f7l4ty2j	396	9	similar	similar	JJ
cord-002542-f7l4ty2j	396	10	between	between	IN
cord-002542-f7l4ty2j	396	11	replicates	replicate	NNS
cord-002542-f7l4ty2j	396	12	and	and	CC
cord-002542-f7l4ty2j	396	13	to	to	IN
cord-002542-f7l4ty2j	396	14	previous	previous	JJ
cord-002542-f7l4ty2j	396	15	reports	report	NNS
cord-002542-f7l4ty2j	396	16	from	from	IN
cord-002542-f7l4ty2j	396	17	different	different	JJ
cord-002542-f7l4ty2j	396	18	laboratories	laboratory	NNS
cord-002542-f7l4ty2j	396	19	.	.	.
cord-002542-f7l4ty2j	397	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	397	2	,	,	,
cord-002542-f7l4ty2j	397	3	this	this	DT
cord-002542-f7l4ty2j	397	4	indicates	indicate	VBZ
cord-002542-f7l4ty2j	397	5	that	that	IN
cord-002542-f7l4ty2j	397	6	either	either	CC
cord-002542-f7l4ty2j	397	7	the	the	DT
cord-002542-f7l4ty2j	397	8	DI	DI	NNP
cord-002542-f7l4ty2j	397	9	-	-	HYPH
cord-002542-f7l4ty2j	397	10	RNAs	rna	NNS
cord-002542-f7l4ty2j	397	11	have	have	VBP
cord-002542-f7l4ty2j	397	12	emerged	emerge	VBN
cord-002542-f7l4ty2j	397	13	due	due	IN
cord-002542-f7l4ty2j	397	14	to	to	IN
cord-002542-f7l4ty2j	397	15	a	a	DT
cord-002542-f7l4ty2j	397	16	common	common	JJ
cord-002542-f7l4ty2j	397	17	mechanism	mechanism	NN
cord-002542-f7l4ty2j	397	18	of	of	IN
cord-002542-f7l4ty2j	397	19	formation	formation	NN
cord-002542-f7l4ty2j	397	20	,	,	,
cord-002542-f7l4ty2j	397	21	the	the	DT
cord-002542-f7l4ty2j	397	22	presence	presence	NN
cord-002542-f7l4ty2j	397	23	of	of	IN
cord-002542-f7l4ty2j	397	24	a	a	DT
cord-002542-f7l4ty2j	397	25	common	common	JJ
cord-002542-f7l4ty2j	397	26	selectivity	selectivity	NN
cord-002542-f7l4ty2j	397	27	filter	filter	NN
cord-002542-f7l4ty2j	397	28	,	,	,
cord-002542-f7l4ty2j	397	29	or	or	CC
cord-002542-f7l4ty2j	397	30	both	both	DT
cord-002542-f7l4ty2j	397	31	.	.	.
cord-002542-f7l4ty2j	398	1	In	in	IN
cord-002542-f7l4ty2j	398	2	addition	addition	NN
cord-002542-f7l4ty2j	398	3	to	to	IN
cord-002542-f7l4ty2j	398	4	providing	provide	VBG
cord-002542-f7l4ty2j	398	5	a	a	DT
cord-002542-f7l4ty2j	398	6	thorough	thorough	JJ
cord-002542-f7l4ty2j	398	7	analysis	analysis	NN
cord-002542-f7l4ty2j	398	8	of	of	IN
cord-002542-f7l4ty2j	398	9	the	the	DT
cord-002542-f7l4ty2j	398	10	pathways	pathway	NNS
cord-002542-f7l4ty2j	398	11	of	of	IN
cord-002542-f7l4ty2j	398	12	defective	defective	JJ
cord-002542-f7l4ty2j	398	13	RNA	RNA	NNP
cord-002542-f7l4ty2j	398	14	formation	formation	NN
cord-002542-f7l4ty2j	398	15	and	and	CC
cord-002542-f7l4ty2j	398	16	evolution	evolution	NN
cord-002542-f7l4ty2j	398	17	,	,	,
cord-002542-f7l4ty2j	398	18	there	there	EX
cord-002542-f7l4ty2j	398	19	are	be	VBP
cord-002542-f7l4ty2j	398	20	two	two	CD
cord-002542-f7l4ty2j	398	21	unexpected	unexpected	JJ
cord-002542-f7l4ty2j	398	22	and	and	CC
cord-002542-f7l4ty2j	398	23	critical	critical	JJ
cord-002542-f7l4ty2j	398	24	observations	observation	NNS
cord-002542-f7l4ty2j	398	25	made	make	VBN
cord-002542-f7l4ty2j	398	26	through	through	IN
cord-002542-f7l4ty2j	398	27	this	this	DT
cord-002542-f7l4ty2j	398	28	study	study	NN
cord-002542-f7l4ty2j	398	29	.	.	.
cord-002542-f7l4ty2j	399	1	First	first	RB
cord-002542-f7l4ty2j	399	2	:	:	:
cord-002542-f7l4ty2j	399	3	while	while	IN
cord-002542-f7l4ty2j	399	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	399	5	observe	observe	VBP
cord-002542-f7l4ty2j	399	6	a	a	DT
cord-002542-f7l4ty2j	399	7	wide	wide	JJ
cord-002542-f7l4ty2j	399	8	range	range	NN
cord-002542-f7l4ty2j	399	9	of	of	IN
cord-002542-f7l4ty2j	399	10	recombination	recombination	NN
cord-002542-f7l4ty2j	399	11	events	event	NNS
cord-002542-f7l4ty2j	399	12	early	early	RB
cord-002542-f7l4ty2j	399	13	on	on	RB
cord-002542-f7l4ty2j	399	14	during	during	IN
cord-002542-f7l4ty2j	399	15	passaging	passaging	NN
cord-002542-f7l4ty2j	399	16	,	,	,
cord-002542-f7l4ty2j	399	17	only	only	RB
cord-002542-f7l4ty2j	399	18	a	a	DT
cord-002542-f7l4ty2j	399	19	limited	limited	JJ
cord-002542-f7l4ty2j	399	20	number	number	NN
cord-002542-f7l4ty2j	399	21	of	of	IN
cord-002542-f7l4ty2j	399	22	events	event	NNS
cord-002542-f7l4ty2j	399	23	are	be	VBP
cord-002542-f7l4ty2j	399	24	subsequently	subsequently	RB
cord-002542-f7l4ty2j	399	25	amplified	amplify	VBN
cord-002542-f7l4ty2j	399	26	and	and	CC
cord-002542-f7l4ty2j	399	27	later	later	RB
cord-002542-f7l4ty2j	399	28	define	define	VB
cord-002542-f7l4ty2j	399	29	DI	DI	NNP
cord-002542-f7l4ty2j	399	30	-	-	HYPH
cord-002542-f7l4ty2j	399	31	RNAs	rna	NNS
cord-002542-f7l4ty2j	399	32	.	.	.
cord-002542-f7l4ty2j	400	1	Moreover	moreover	RB
cord-002542-f7l4ty2j	400	2	,	,	,
cord-002542-f7l4ty2j	400	3	these	these	DT
cord-002542-f7l4ty2j	400	4	limited	limited	JJ
cord-002542-f7l4ty2j	400	5	sets	set	NNS
cord-002542-f7l4ty2j	400	6	of	of	IN
cord-002542-f7l4ty2j	400	7	events	event	NNS
cord-002542-f7l4ty2j	400	8	are	be	VBP
cord-002542-f7l4ty2j	400	9	similar	similar	JJ
cord-002542-f7l4ty2j	400	10	between	between	IN
cord-002542-f7l4ty2j	400	11	replicates	replicate	NNS
cord-002542-f7l4ty2j	400	12	,	,	,
cord-002542-f7l4ty2j	400	13	and	and	CC
cord-002542-f7l4ty2j	400	14	to	to	IN
cord-002542-f7l4ty2j	400	15	previous	previous	JJ
cord-002542-f7l4ty2j	400	16	studies	study	NNS
cord-002542-f7l4ty2j	400	17	.	.	.
cord-002542-f7l4ty2j	401	1	This	this	DT
cord-002542-f7l4ty2j	401	2	suggests	suggest	VBZ
cord-002542-f7l4ty2j	401	3	that	that	IN
cord-002542-f7l4ty2j	401	4	while	while	IN
cord-002542-f7l4ty2j	401	5	a	a	DT
cord-002542-f7l4ty2j	401	6	large	large	JJ
cord-002542-f7l4ty2j	401	7	pool	pool	NN
cord-002542-f7l4ty2j	401	8	of	of	IN
cord-002542-f7l4ty2j	401	9	potential	potential	JJ
cord-002542-f7l4ty2j	401	10	defective	defective	JJ
cord-002542-f7l4ty2j	401	11	RNAs	rna	NNS
cord-002542-f7l4ty2j	401	12	are	be	VBP
cord-002542-f7l4ty2j	401	13	generated	generate	VBN
cord-002542-f7l4ty2j	401	14	,	,	,
cord-002542-f7l4ty2j	401	15	only	only	RB
cord-002542-f7l4ty2j	401	16	a	a	DT
cord-002542-f7l4ty2j	401	17	small	small	JJ
cord-002542-f7l4ty2j	401	18	number	number	NN
cord-002542-f7l4ty2j	401	19	are	be	VBP
cord-002542-f7l4ty2j	401	20	capable	capable	JJ
cord-002542-f7l4ty2j	401	21	of	of	IN
cord-002542-f7l4ty2j	401	22	accumulating	accumulate	VBG
cord-002542-f7l4ty2j	401	23	.	.	.
cord-002542-f7l4ty2j	402	1	Secondly	secondly	RB
cord-002542-f7l4ty2j	402	2	:	:	:
cord-002542-f7l4ty2j	402	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	402	4	do	do	VBP
cord-002542-f7l4ty2j	402	5	not	not	RB
cord-002542-f7l4ty2j	402	6	observe	observe	VB
cord-002542-f7l4ty2j	402	7	the	the	DT
cord-002542-f7l4ty2j	402	8	amplification	amplification	NN
cord-002542-f7l4ty2j	402	9	of	of	IN
cord-002542-f7l4ty2j	402	10	DI	DI	NNP
cord-002542-f7l4ty2j	402	11	-	-	HYPH
cord-002542-f7l4ty2j	402	12	RNAs	rna	NNS
cord-002542-f7l4ty2j	402	13	with	with	IN
cord-002542-f7l4ty2j	402	14	only	only	RB
cord-002542-f7l4ty2j	402	15	one	one	CD
cord-002542-f7l4ty2j	402	16	deletion	deletion	NN
cord-002542-f7l4ty2j	402	17	.	.	.
cord-002542-f7l4ty2j	403	1	In	in	IN
cord-002542-f7l4ty2j	403	2	contrast	contrast	NN
cord-002542-f7l4ty2j	403	3	,	,	,
cord-002542-f7l4ty2j	403	4	'	'	``
cord-002542-f7l4ty2j	403	5	mature	mature	VB
cord-002542-f7l4ty2j	403	6	'	'	''
cord-002542-f7l4ty2j	403	7	DI	di	NN
cord-002542-f7l4ty2j	403	8	-	-	HYPH
cord-002542-f7l4ty2j	403	9	RNAs	rna	NNS
cord-002542-f7l4ty2j	403	10	accumulate	accumulate	VBP
cord-002542-f7l4ty2j	403	11	rapidly	rapidly	RB
cord-002542-f7l4ty2j	403	12	.	.	.
cord-002542-f7l4ty2j	404	1	Nonetheless	nonetheless	RB
cord-002542-f7l4ty2j	404	2	,	,	,
cord-002542-f7l4ty2j	404	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	404	4	do	do	VBP
cord-002542-f7l4ty2j	404	5	find	find	VB
cord-002542-f7l4ty2j	404	6	evidence	evidence	NN
cord-002542-f7l4ty2j	404	7	for	for	IN
cord-002542-f7l4ty2j	404	8	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	404	9	DI	DI	NNP
cord-002542-f7l4ty2j	404	10	-	-	HYPH
cord-002542-f7l4ty2j	404	11	RNAs	rna	NNS
cord-002542-f7l4ty2j	404	12	as	as	RB
cord-002542-f7l4ty2j	404	13	early	early	RB
cord-002542-f7l4ty2j	404	14	as	as	IN
cord-002542-f7l4ty2j	404	15	the	the	DT
cord-002542-f7l4ty2j	404	16	inoculum	inoculum	NN
cord-002542-f7l4ty2j	404	17	sample	sample	NN
cord-002542-f7l4ty2j	404	18	.	.	.
cord-002542-f7l4ty2j	405	1	This	this	DT
cord-002542-f7l4ty2j	405	2	indicates	indicate	VBZ
cord-002542-f7l4ty2j	405	3	that	that	IN
cord-002542-f7l4ty2j	405	4	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	405	5	defective	defective	JJ
cord-002542-f7l4ty2j	405	6	-	-	HYPH
cord-002542-f7l4ty2j	405	7	species	specie	NNS
cord-002542-f7l4ty2j	405	8	are	be	VBP
cord-002542-f7l4ty2j	405	9	either	either	CC
cord-002542-f7l4ty2j	405	10	non	non	JJ
cord-002542-f7l4ty2j	405	11	-	-	JJ
cord-002542-f7l4ty2j	405	12	competitive	competitive	JJ
cord-002542-f7l4ty2j	405	13	and	and	CC
cord-002542-f7l4ty2j	405	14	do	do	VBP
cord-002542-f7l4ty2j	405	15	not	not	RB
cord-002542-f7l4ty2j	405	16	accumulate	accumulate	VB
cord-002542-f7l4ty2j	405	17	or	or	CC
cord-002542-f7l4ty2j	405	18	are	be	VBP
cord-002542-f7l4ty2j	405	19	not	not	RB
cord-002542-f7l4ty2j	405	20	formed	form	VBN
cord-002542-f7l4ty2j	405	21	as	as	IN
cord-002542-f7l4ty2j	405	22	a	a	DT
cord-002542-f7l4ty2j	405	23	pre	pre	NN
cord-002542-f7l4ty2j	405	24	-	-	NN
cord-002542-f7l4ty2j	405	25	cursor	cursor	NN
cord-002542-f7l4ty2j	405	26	to	to	IN
cord-002542-f7l4ty2j	405	27	mature	mature	VB
cord-002542-f7l4ty2j	405	28	DI	DI	NNP
cord-002542-f7l4ty2j	405	29	-	-	HYPH
cord-002542-f7l4ty2j	405	30	RNAs	rna	NNS
cord-002542-f7l4ty2j	405	31	.	.	.
cord-002542-f7l4ty2j	406	1	These	these	DT
cord-002542-f7l4ty2j	406	2	two	two	CD
cord-002542-f7l4ty2j	406	3	observations	observation	NNS
cord-002542-f7l4ty2j	406	4	provide	provide	VBP
cord-002542-f7l4ty2j	406	5	important	important	JJ
cord-002542-f7l4ty2j	406	6	insights	insight	NNS
cord-002542-f7l4ty2j	406	7	into	into	IN
cord-002542-f7l4ty2j	406	8	the	the	DT
cord-002542-f7l4ty2j	406	9	potential	potential	JJ
cord-002542-f7l4ty2j	406	10	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	406	11	of	of	IN
cord-002542-f7l4ty2j	406	12	DI	DI	NNP
cord-002542-f7l4ty2j	406	13	-	-	HYPH
cord-002542-f7l4ty2j	406	14	RNA	RNA	NNP
cord-002542-f7l4ty2j	406	15	emergence	emergence	NN
cord-002542-f7l4ty2j	406	16	and	and	CC
cord-002542-f7l4ty2j	406	17	evolution	evolution	NN
cord-002542-f7l4ty2j	406	18	.	.	.
cord-002542-f7l4ty2j	407	1	While	while	IN
cord-002542-f7l4ty2j	407	2	there	there	EX
cord-002542-f7l4ty2j	407	3	is	be	VBZ
cord-002542-f7l4ty2j	407	4	a	a	DT
cord-002542-f7l4ty2j	407	5	strong	strong	JJ
cord-002542-f7l4ty2j	407	6	selection	selection	NN
cord-002542-f7l4ty2j	407	7	pressure	pressure	NN
cord-002542-f7l4ty2j	407	8	for	for	IN
cord-002542-f7l4ty2j	407	9	DI	DI	NNP
cord-002542-f7l4ty2j	407	10	-	-	HYPH
cord-002542-f7l4ty2j	407	11	RNAs	rna	NNS
cord-002542-f7l4ty2j	407	12	to	to	TO
cord-002542-f7l4ty2j	407	13	retain	retain	VB
cord-002542-f7l4ty2j	407	14	essential	essential	JJ
cord-002542-f7l4ty2j	407	15	functional	functional	JJ
cord-002542-f7l4ty2j	407	16	genomic	genomic	JJ
cord-002542-f7l4ty2j	407	17	elements	element	NNS
cord-002542-f7l4ty2j	407	18	,	,	,
cord-002542-f7l4ty2j	407	19	it	-PRON-	PRP
cord-002542-f7l4ty2j	407	20	is	be	VBZ
cord-002542-f7l4ty2j	407	21	also	also	RB
cord-002542-f7l4ty2j	407	22	postulated	postulate	VBN
cord-002542-f7l4ty2j	407	23	that	that	IN
cord-002542-f7l4ty2j	407	24	a	a	DT
cord-002542-f7l4ty2j	407	25	shorter	short	JJR
cord-002542-f7l4ty2j	407	26	defective	defective	JJ
cord-002542-f7l4ty2j	407	27	RNA	RNA	NNP
cord-002542-f7l4ty2j	407	28	would	would	MD
cord-002542-f7l4ty2j	407	29	be	be	VB
cord-002542-f7l4ty2j	407	30	replicated	replicate	VBN
cord-002542-f7l4ty2j	407	31	more	more	RBR
cord-002542-f7l4ty2j	407	32	quickly	quickly	RB
cord-002542-f7l4ty2j	407	33	and	and	CC
cord-002542-f7l4ty2j	407	34	thus	thus	RB
cord-002542-f7l4ty2j	407	35	more	more	RBR
cord-002542-f7l4ty2j	407	36	competitively	competitively	RB
cord-002542-f7l4ty2j	407	37	[	[	-LRB-
cord-002542-f7l4ty2j	407	38	10	10	CD
cord-002542-f7l4ty2j	407	39	]	]	-RRB-
cord-002542-f7l4ty2j	407	40	.	.	.
cord-002542-f7l4ty2j	408	1	In	in	IN
cord-002542-f7l4ty2j	408	2	our	-PRON-	PRP$
cord-002542-f7l4ty2j	408	3	analysis	analysis	NN
cord-002542-f7l4ty2j	408	4	,	,	,
cord-002542-f7l4ty2j	408	5	while	while	IN
cord-002542-f7l4ty2j	408	6	the~250	the~250	NNP
cord-002542-f7l4ty2j	408	7	-	-	HYPH
cord-002542-f7l4ty2j	408	8	550	550	CD
cord-002542-f7l4ty2j	408	9	deletion	deletion	NN
cord-002542-f7l4ty2j	408	10	in	in	IN
cord-002542-f7l4ty2j	408	11	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	408	12	(	(	-LRB-
cord-002542-f7l4ty2j	408	13	for	for	IN
cord-002542-f7l4ty2j	408	14	example	example	NN
cord-002542-f7l4ty2j	408	15	)	)	-RRB-
cord-002542-f7l4ty2j	408	16	is	be	VBZ
cord-002542-f7l4ty2j	408	17	very	very	RB
cord-002542-f7l4ty2j	408	18	common	common	JJ
cord-002542-f7l4ty2j	408	19	we	-PRON-	PRP
cord-002542-f7l4ty2j	408	20	do	do	VBP
cord-002542-f7l4ty2j	408	21	not	not	RB
cord-002542-f7l4ty2j	408	22	observe	observe	VB
cord-002542-f7l4ty2j	408	23	the	the	DT
cord-002542-f7l4ty2j	408	24	accumulation	accumulation	NN
cord-002542-f7l4ty2j	408	25	of	of	IN
cord-002542-f7l4ty2j	408	26	deletion	deletion	NN
cord-002542-f7l4ty2j	408	27	events	event	NNS
cord-002542-f7l4ty2j	408	28	that	that	WDT
cord-002542-f7l4ty2j	408	29	are	be	VBP
cord-002542-f7l4ty2j	408	30	smaller	small	JJR
cord-002542-f7l4ty2j	408	31	than	than	IN
cord-002542-f7l4ty2j	408	32	this	this	DT
cord-002542-f7l4ty2j	408	33	(	(	-LRB-
cord-002542-f7l4ty2j	408	34	e.g.	e.g.	RB
cord-002542-f7l4ty2j	408	35	300	300	CD
cord-002542-f7l4ty2j	408	36	-	-	SYM
cord-002542-f7l4ty2j	408	37	450	450	CD
cord-002542-f7l4ty2j	408	38	)	)	-RRB-
cord-002542-f7l4ty2j	408	39	.	.	.
cord-002542-f7l4ty2j	409	1	This	this	DT
cord-002542-f7l4ty2j	409	2	is	be	VBZ
cord-002542-f7l4ty2j	409	3	despite	despite	IN
cord-002542-f7l4ty2j	409	4	the	the	DT
cord-002542-f7l4ty2j	409	5	fact	fact	NN
cord-002542-f7l4ty2j	409	6	that	that	IN
cord-002542-f7l4ty2j	409	7	we	-PRON-	PRP
cord-002542-f7l4ty2j	409	8	can	can	MD
cord-002542-f7l4ty2j	409	9	detect	detect	VB
cord-002542-f7l4ty2j	409	10	and	and	CC
cord-002542-f7l4ty2j	409	11	observe	observe	VB
cord-002542-f7l4ty2j	409	12	such	such	JJ
cord-002542-f7l4ty2j	409	13	species	specie	NNS
cord-002542-f7l4ty2j	409	14	in	in	IN
cord-002542-f7l4ty2j	409	15	low	low	JJ
cord-002542-f7l4ty2j	409	16	frequencies	frequency	NNS
cord-002542-f7l4ty2j	409	17	both	both	DT
cord-002542-f7l4ty2j	409	18	in	in	IN
cord-002542-f7l4ty2j	409	19	early	early	JJ
cord-002542-f7l4ty2j	409	20	and	and	CC
cord-002542-f7l4ty2j	409	21	late	late	JJ
cord-002542-f7l4ty2j	409	22	passages	passage	NNS
cord-002542-f7l4ty2j	409	23	,	,	,
cord-002542-f7l4ty2j	409	24	suggesting	suggest	VBG
cord-002542-f7l4ty2j	409	25	that	that	IN
cord-002542-f7l4ty2j	409	26	they	-PRON-	PRP
cord-002542-f7l4ty2j	409	27	are	be	VBP
cord-002542-f7l4ty2j	409	28	indeed	indeed	RB
cord-002542-f7l4ty2j	409	29	generated	generate	VBN
cord-002542-f7l4ty2j	409	30	but	but	CC
cord-002542-f7l4ty2j	409	31	are	be	VBP
cord-002542-f7l4ty2j	409	32	not	not	RB
cord-002542-f7l4ty2j	409	33	selectively	selectively	RB
cord-002542-f7l4ty2j	409	34	amplified	amplify	VBN
cord-002542-f7l4ty2j	409	35	.	.	.
cord-002542-f7l4ty2j	410	1	This	this	DT
cord-002542-f7l4ty2j	410	2	may	may	MD
cord-002542-f7l4ty2j	410	3	in	in	IN
cord-002542-f7l4ty2j	410	4	part	part	NN
cord-002542-f7l4ty2j	410	5	be	be	VB
cord-002542-f7l4ty2j	410	6	due	due	JJ
cord-002542-f7l4ty2j	410	7	to	to	IN
cord-002542-f7l4ty2j	410	8	selecting	select	VBG
cord-002542-f7l4ty2j	410	9	for	for	IN
cord-002542-f7l4ty2j	410	10	DI	DI	NNP
cord-002542-f7l4ty2j	410	11	-	-	HYPH
cord-002542-f7l4ty2j	410	12	RNA	RNA	NNP
cord-002542-f7l4ty2j	410	13	genomes	genome	NNS
cord-002542-f7l4ty2j	410	14	that	that	WDT
cord-002542-f7l4ty2j	410	15	are	be	VBP
cord-002542-f7l4ty2j	410	16	as	as	RB
cord-002542-f7l4ty2j	410	17	small	small	JJ
cord-002542-f7l4ty2j	410	18	as	as	IN
cord-002542-f7l4ty2j	410	19	possible	possible	JJ
cord-002542-f7l4ty2j	410	20	,	,	,
cord-002542-f7l4ty2j	410	21	while	while	IN
cord-002542-f7l4ty2j	410	22	retaining	retain	VBG
cord-002542-f7l4ty2j	410	23	the	the	DT
cord-002542-f7l4ty2j	410	24	minimal	minimal	JJ
cord-002542-f7l4ty2j	410	25	amount	amount	NN
cord-002542-f7l4ty2j	410	26	of	of	IN
cord-002542-f7l4ty2j	410	27	genetic	genetic	JJ
cord-002542-f7l4ty2j	410	28	material	material	NN
cord-002542-f7l4ty2j	410	29	to	to	TO
cord-002542-f7l4ty2j	410	30	form	form	VB
cord-002542-f7l4ty2j	410	31	functional	functional	JJ
cord-002542-f7l4ty2j	410	32	genetic	genetic	JJ
cord-002542-f7l4ty2j	410	33	elements	element	NNS
cord-002542-f7l4ty2j	410	34	.	.	.
cord-002542-f7l4ty2j	411	1	However	however	RB
cord-002542-f7l4ty2j	411	2	,	,	,
cord-002542-f7l4ty2j	411	3	it	-PRON-	PRP
cord-002542-f7l4ty2j	411	4	may	may	MD
cord-002542-f7l4ty2j	411	5	also	also	RB
cord-002542-f7l4ty2j	411	6	be	be	VB
cord-002542-f7l4ty2j	411	7	the	the	DT
cord-002542-f7l4ty2j	411	8	result	result	NN
cord-002542-f7l4ty2j	411	9	of	of	IN
cord-002542-f7l4ty2j	411	10	a	a	DT
cord-002542-f7l4ty2j	411	11	negative	negative	JJ
cord-002542-f7l4ty2j	411	12	selection	selection	NN
cord-002542-f7l4ty2j	411	13	pressure	pressure	NN
cord-002542-f7l4ty2j	411	14	or	or	CC
cord-002542-f7l4ty2j	411	15	restrictive	restrictive	JJ
cord-002542-f7l4ty2j	411	16	barrier	barrier	NN
cord-002542-f7l4ty2j	411	17	that	that	WDT
cord-002542-f7l4ty2j	411	18	is	be	VBZ
cord-002542-f7l4ty2j	411	19	released	release	VBN
cord-002542-f7l4ty2j	411	20	only	only	RB
cord-002542-f7l4ty2j	411	21	after	after	IN
cord-002542-f7l4ty2j	411	22	excising	excise	VBG
cord-002542-f7l4ty2j	411	23	specific	specific	JJ
cord-002542-f7l4ty2j	411	24	portions	portion	NNS
cord-002542-f7l4ty2j	411	25	of	of	IN
cord-002542-f7l4ty2j	411	26	the	the	DT
cord-002542-f7l4ty2j	411	27	viral	viral	JJ
cord-002542-f7l4ty2j	411	28	genome	genome	NN
cord-002542-f7l4ty2j	411	29	.	.	.
cord-002542-f7l4ty2j	412	1	An	an	DT
cord-002542-f7l4ty2j	412	2	example	example	NN
cord-002542-f7l4ty2j	412	3	of	of	IN
cord-002542-f7l4ty2j	412	4	this	this	DT
cord-002542-f7l4ty2j	412	5	scenario	scenario	NN
cord-002542-f7l4ty2j	412	6	has	have	VBZ
cord-002542-f7l4ty2j	412	7	been	be	VBN
cord-002542-f7l4ty2j	412	8	demonstrated	demonstrate	VBN
cord-002542-f7l4ty2j	412	9	for	for	IN
cord-002542-f7l4ty2j	412	10	tomato	tomato	NN
cord-002542-f7l4ty2j	412	11	bushy	bushy	JJ
cord-002542-f7l4ty2j	412	12	stunt	stunt	NN
cord-002542-f7l4ty2j	412	13	virus	virus	NN
cord-002542-f7l4ty2j	412	14	(	(	-LRB-
cord-002542-f7l4ty2j	412	15	TBSV	TBSV	NNP
cord-002542-f7l4ty2j	412	16	)	)	-RRB-
cord-002542-f7l4ty2j	412	17	associated	associate	VBD
cord-002542-f7l4ty2j	412	18	DI	DI	NNP
cord-002542-f7l4ty2j	412	19	-	-	HYPH
cord-002542-f7l4ty2j	412	20	RNAs	rna	NNS
cord-002542-f7l4ty2j	412	21	whereby	whereby	VBZ
cord-002542-f7l4ty2j	412	22	deletion	deletion	NN
cord-002542-f7l4ty2j	412	23	of	of	IN
cord-002542-f7l4ty2j	412	24	a	a	DT
cord-002542-f7l4ty2j	412	25	translation	translation	NN
cord-002542-f7l4ty2j	412	26	enhancer	enhancer	NN
cord-002542-f7l4ty2j	412	27	functional	functional	JJ
cord-002542-f7l4ty2j	412	28	element	element	NN
cord-002542-f7l4ty2j	412	29	removes	remove	VBZ
cord-002542-f7l4ty2j	412	30	the	the	DT
cord-002542-f7l4ty2j	412	31	competition	competition	NN
cord-002542-f7l4ty2j	412	32	between	between	IN
cord-002542-f7l4ty2j	412	33	translation	translation	NN
cord-002542-f7l4ty2j	412	34	and	and	CC
cord-002542-f7l4ty2j	412	35	replication	replication	NN
cord-002542-f7l4ty2j	412	36	,	,	,
cord-002542-f7l4ty2j	412	37	thus	thus	RB
cord-002542-f7l4ty2j	412	38	favoring	favor	VBG
cord-002542-f7l4ty2j	412	39	replication	replication	NN
cord-002542-f7l4ty2j	412	40	of	of	IN
cord-002542-f7l4ty2j	412	41	the	the	DT
cord-002542-f7l4ty2j	412	42	smaller	small	JJR
cord-002542-f7l4ty2j	412	43	DI	DI	NNP
cord-002542-f7l4ty2j	412	44	-	-	HYPH
cord-002542-f7l4ty2j	412	45	RNA	RNA	NNP
cord-002542-f7l4ty2j	412	46	[	[	-LRB-
cord-002542-f7l4ty2j	412	47	68	68	CD
cord-002542-f7l4ty2j	412	48	]	]	-RRB-
cord-002542-f7l4ty2j	412	49	.	.	.
cord-002542-f7l4ty2j	413	1	Therefore	therefore	RB
cord-002542-f7l4ty2j	413	2	,	,	,
cord-002542-f7l4ty2j	413	3	the	the	DT
cord-002542-f7l4ty2j	413	4	final	final	JJ
cord-002542-f7l4ty2j	413	5	structure	structure	NN
cord-002542-f7l4ty2j	413	6	of	of	IN
cord-002542-f7l4ty2j	413	7	DI	DI	NNP
cord-002542-f7l4ty2j	413	8	-	-	HYPH
cord-002542-f7l4ty2j	413	9	RNAs	rna	NNS
cord-002542-f7l4ty2j	413	10	may	may	MD
cord-002542-f7l4ty2j	413	11	depend	depend	VB
cord-002542-f7l4ty2j	413	12	both	both	DT
cord-002542-f7l4ty2j	413	13	on	on	IN
cord-002542-f7l4ty2j	413	14	the	the	DT
cord-002542-f7l4ty2j	413	15	retention	retention	NN
cord-002542-f7l4ty2j	413	16	of	of	IN
cord-002542-f7l4ty2j	413	17	essential	essential	JJ
cord-002542-f7l4ty2j	413	18	functional	functional	JJ
cord-002542-f7l4ty2j	413	19	RNA	RNA	NNP
cord-002542-f7l4ty2j	413	20	elements	element	NNS
cord-002542-f7l4ty2j	413	21	,	,	,
cord-002542-f7l4ty2j	413	22	as	as	RB
cord-002542-f7l4ty2j	413	23	well	well	RB
cord-002542-f7l4ty2j	413	24	as	as	IN
cord-002542-f7l4ty2j	413	25	the	the	DT
cord-002542-f7l4ty2j	413	26	removal	removal	NN
cord-002542-f7l4ty2j	413	27	of	of	IN
cord-002542-f7l4ty2j	413	28	restrictive	restrictive	JJ
cord-002542-f7l4ty2j	413	29	barriers	barrier	NNS
cord-002542-f7l4ty2j	413	30	that	that	WDT
cord-002542-f7l4ty2j	413	31	attenuate	attenuate	VBP
cord-002542-f7l4ty2j	413	32	RNA	RNA	NNP
cord-002542-f7l4ty2j	413	33	replication	replication	NN
cord-002542-f7l4ty2j	413	34	.	.	.
cord-002542-f7l4ty2j	414	1	One	one	CD
cord-002542-f7l4ty2j	414	2	model	model	NN
cord-002542-f7l4ty2j	414	3	for	for	IN
cord-002542-f7l4ty2j	414	4	the	the	DT
cord-002542-f7l4ty2j	414	5	evolution	evolution	NN
cord-002542-f7l4ty2j	414	6	of	of	IN
cord-002542-f7l4ty2j	414	7	DI	DI	NNP
cord-002542-f7l4ty2j	414	8	-	-	HYPH
cord-002542-f7l4ty2j	414	9	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	414	10	is	be	VBZ
cord-002542-f7l4ty2j	414	11	through	through	IN
cord-002542-f7l4ty2j	414	12	the	the	DT
cord-002542-f7l4ty2j	414	13	step	step	NN
cord-002542-f7l4ty2j	414	14	-	-	HYPH
cord-002542-f7l4ty2j	414	15	wise	wise	JJ
cord-002542-f7l4ty2j	414	16	accumulation	accumulation	NN
cord-002542-f7l4ty2j	414	17	of	of	IN
cord-002542-f7l4ty2j	414	18	deletion	deletion	NN
cord-002542-f7l4ty2j	414	19	events	event	NNS
cord-002542-f7l4ty2j	414	20	through	through	IN
cord-002542-f7l4ty2j	414	21	a	a	DT
cord-002542-f7l4ty2j	414	22	series	series	NN
cord-002542-f7l4ty2j	414	23	of	of	IN
cord-002542-f7l4ty2j	414	24	individual	individual	JJ
cord-002542-f7l4ty2j	414	25	recombination	recombination	NN
cord-002542-f7l4ty2j	414	26	events	event	NNS
cord-002542-f7l4ty2j	414	27	[	[	-LRB-
cord-002542-f7l4ty2j	414	28	68	68	CD
cord-002542-f7l4ty2j	414	29	]	]	-RRB-
cord-002542-f7l4ty2j	414	30	.	.	.
cord-002542-f7l4ty2j	415	1	The	the	DT
cord-002542-f7l4ty2j	415	2	MinION	minion	NN
cord-002542-f7l4ty2j	415	3	data	datum	NNS
cord-002542-f7l4ty2j	415	4	reveals	reveal	VBZ
cord-002542-f7l4ty2j	415	5	that	that	IN
cord-002542-f7l4ty2j	415	6	the	the	DT
cord-002542-f7l4ty2j	415	7	defective	defective	JJ
cord-002542-f7l4ty2j	415	8	RNAs	rna	NNS
cord-002542-f7l4ty2j	415	9	that	that	WDT
cord-002542-f7l4ty2j	415	10	accumulate	accumulate	VBP
cord-002542-f7l4ty2j	415	11	(	(	-LRB-
cord-002542-f7l4ty2j	415	12	rapidly	rapidly	RB
cord-002542-f7l4ty2j	415	13	over	over	IN
cord-002542-f7l4ty2j	415	14	the	the	DT
cord-002542-f7l4ty2j	415	15	course	course	NN
cord-002542-f7l4ty2j	415	16	2	2	CD
cord-002542-f7l4ty2j	415	17	-	-	SYM
cord-002542-f7l4ty2j	415	18	3	3	CD
cord-002542-f7l4ty2j	415	19	passages	passage	NNS
cord-002542-f7l4ty2j	415	20	)	)	-RRB-
cord-002542-f7l4ty2j	415	21	contain	contain	VBP
cord-002542-f7l4ty2j	415	22	multiple	multiple	JJ
cord-002542-f7l4ty2j	415	23	deletion	deletion	NN
cord-002542-f7l4ty2j	415	24	events	event	NNS
cord-002542-f7l4ty2j	415	25	.	.	.
cord-002542-f7l4ty2j	416	1	However	however	RB
cord-002542-f7l4ty2j	416	2	,	,	,
cord-002542-f7l4ty2j	416	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	416	4	do	do	VBP
cord-002542-f7l4ty2j	416	5	not	not	RB
cord-002542-f7l4ty2j	416	6	see	see	VB
cord-002542-f7l4ty2j	416	7	the	the	DT
cord-002542-f7l4ty2j	416	8	rapid	rapid	JJ
cord-002542-f7l4ty2j	416	9	accumulation	accumulation	NN
cord-002542-f7l4ty2j	416	10	of	of	IN
cord-002542-f7l4ty2j	416	11	the	the	DT
cord-002542-f7l4ty2j	416	12	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	416	13	DI	DI	NNP
cord-002542-f7l4ty2j	416	14	-	-	HYPH
cord-002542-f7l4ty2j	416	15	RNAs	rna	NNS
cord-002542-f7l4ty2j	416	16	,	,	,
cord-002542-f7l4ty2j	416	17	despite	despite	IN
cord-002542-f7l4ty2j	416	18	evidence	evidence	NN
cord-002542-f7l4ty2j	416	19	for	for	IN
cord-002542-f7l4ty2j	416	20	their	-PRON-	PRP$
cord-002542-f7l4ty2j	416	21	presence	presence	NN
cord-002542-f7l4ty2j	416	22	early	early	RB
cord-002542-f7l4ty2j	416	23	in	in	IN
cord-002542-f7l4ty2j	416	24	viral	viral	JJ
cord-002542-f7l4ty2j	416	25	passaging	passaging	NN
cord-002542-f7l4ty2j	416	26	.	.	.
cord-002542-f7l4ty2j	417	1	This	this	DT
cord-002542-f7l4ty2j	417	2	suggests	suggest	VBZ
cord-002542-f7l4ty2j	417	3	that	that	IN
cord-002542-f7l4ty2j	417	4	the	the	DT
cord-002542-f7l4ty2j	417	5	mature	mature	JJ
cord-002542-f7l4ty2j	417	6	DI	DI	NNP
cord-002542-f7l4ty2j	417	7	-	-	HYPH
cord-002542-f7l4ty2j	417	8	R	R	NNP
cord-002542-f7l4ty2j	417	9	-	-	HYPH
cord-002542-f7l4ty2j	417	10	NAs	NAs	NNPS
cord-002542-f7l4ty2j	417	11	have	have	VBP
cord-002542-f7l4ty2j	417	12	a	a	DT
cord-002542-f7l4ty2j	417	13	competitive	competitive	JJ
cord-002542-f7l4ty2j	417	14	advantage	advantage	NN
cord-002542-f7l4ty2j	417	15	over	over	IN
cord-002542-f7l4ty2j	417	16	their	-PRON-	PRP$
cord-002542-f7l4ty2j	417	17	presumed	presume	VBN
cord-002542-f7l4ty2j	417	18	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	417	19	precursors	precursor	NNS
cord-002542-f7l4ty2j	417	20	.	.	.
cord-002542-f7l4ty2j	418	1	If	if	IN
cord-002542-f7l4ty2j	418	2	this	this	DT
cord-002542-f7l4ty2j	418	3	is	be	VBZ
cord-002542-f7l4ty2j	418	4	the	the	DT
cord-002542-f7l4ty2j	418	5	case	case	NN
cord-002542-f7l4ty2j	418	6	,	,	,
cord-002542-f7l4ty2j	418	7	the	the	DT
cord-002542-f7l4ty2j	418	8	multiple	multiple	JJ
cord-002542-f7l4ty2j	418	9	deletions	deletion	NNS
cord-002542-f7l4ty2j	418	10	may	may	MD
cord-002542-f7l4ty2j	418	11	function	function	VB
cord-002542-f7l4ty2j	418	12	epistatically	epistatically	RB
cord-002542-f7l4ty2j	418	13	either	either	CC
cord-002542-f7l4ty2j	418	14	through	through	IN
cord-002542-f7l4ty2j	418	15	an	an	DT
cord-002542-f7l4ty2j	418	16	undefined	undefined	JJ
cord-002542-f7l4ty2j	418	17	cooperative	cooperative	JJ
cord-002542-f7l4ty2j	418	18	/	/	SYM
cord-002542-f7l4ty2j	418	19	additive	additive	NN
cord-002542-f7l4ty2j	418	20	mechanism	mechanism	NN
cord-002542-f7l4ty2j	418	21	or	or	CC
cord-002542-f7l4ty2j	418	22	through	through	IN
cord-002542-f7l4ty2j	418	23	the	the	DT
cord-002542-f7l4ty2j	418	24	release	release	NN
cord-002542-f7l4ty2j	418	25	of	of	IN
cord-002542-f7l4ty2j	418	26	multiple	multiple	JJ
cord-002542-f7l4ty2j	418	27	restriction	restriction	NN
cord-002542-f7l4ty2j	418	28	barriers	barrier	NNS
cord-002542-f7l4ty2j	418	29	,	,	,
cord-002542-f7l4ty2j	418	30	as	as	IN
cord-002542-f7l4ty2j	418	31	proposed	propose	VBN
cord-002542-f7l4ty2j	418	32	above	above	RB
cord-002542-f7l4ty2j	418	33	.	.	.
cord-002542-f7l4ty2j	419	1	If	if	IN
cord-002542-f7l4ty2j	419	2	multiple	multiple	JJ
cord-002542-f7l4ty2j	419	3	restriction	restriction	NN
cord-002542-f7l4ty2j	419	4	barriers	barrier	NNS
cord-002542-f7l4ty2j	419	5	are	be	VBP
cord-002542-f7l4ty2j	419	6	required	require	VBN
cord-002542-f7l4ty2j	419	7	to	to	TO
cord-002542-f7l4ty2j	419	8	be	be	VB
cord-002542-f7l4ty2j	419	9	excised	excise	VBN
cord-002542-f7l4ty2j	419	10	for	for	IN
cord-002542-f7l4ty2j	419	11	the	the	DT
cord-002542-f7l4ty2j	419	12	formation	formation	NN
cord-002542-f7l4ty2j	419	13	of	of	IN
cord-002542-f7l4ty2j	419	14	DI	DI	NNP
cord-002542-f7l4ty2j	419	15	-	-	HYPH
cord-002542-f7l4ty2j	419	16	RNAs	rna	NNS
cord-002542-f7l4ty2j	419	17	,	,	,
cord-002542-f7l4ty2j	419	18	small	small	JJ
cord-002542-f7l4ty2j	419	19	or	or	CC
cord-002542-f7l4ty2j	419	20	multipartite	multipartite	NNP
cord-002542-f7l4ty2j	419	21	RNA	RNA	NNP
cord-002542-f7l4ty2j	419	22	viruses	virus	NNS
cord-002542-f7l4ty2j	419	23	,	,	,
cord-002542-f7l4ty2j	419	24	such	such	JJ
cord-002542-f7l4ty2j	419	25	as	as	IN
cord-002542-f7l4ty2j	419	26	FHV	FHV	NNP
cord-002542-f7l4ty2j	419	27	or	or	CC
cord-002542-f7l4ty2j	419	28	influenza	influenza	NN
cord-002542-f7l4ty2j	419	29	[	[	-LRB-
cord-002542-f7l4ty2j	419	30	17	17	CD
cord-002542-f7l4ty2j	419	31	]	]	-RRB-
cord-002542-f7l4ty2j	419	32	,	,	,
cord-002542-f7l4ty2j	419	33	may	may	MD
cord-002542-f7l4ty2j	419	34	therefore	therefore	RB
cord-002542-f7l4ty2j	419	35	generate	generate	VB
cord-002542-f7l4ty2j	419	36	DI	DI	NNP
cord-002542-f7l4ty2j	419	37	-	-	HYPH
cord-002542-f7l4ty2j	419	38	RNAs	rna	NNS
cord-002542-f7l4ty2j	419	39	more	more	RBR
cord-002542-f7l4ty2j	419	40	readily	readily	RB
cord-002542-f7l4ty2j	419	41	by	by	IN
cord-002542-f7l4ty2j	419	42	requiring	require	VBG
cord-002542-f7l4ty2j	419	43	fewer	few	JJR
cord-002542-f7l4ty2j	419	44	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	419	45	steps	step	NNS
cord-002542-f7l4ty2j	419	46	than	than	IN
cord-002542-f7l4ty2j	419	47	long	long	RB
cord-002542-f7l4ty2j	419	48	,	,	,
cord-002542-f7l4ty2j	419	49	monopartite	monopartite	NNP
cord-002542-f7l4ty2j	419	50	RNA	RNA	NNP
cord-002542-f7l4ty2j	419	51	viruses	virus	NNS
cord-002542-f7l4ty2j	419	52	.	.	.
cord-002542-f7l4ty2j	420	1	Moreover	moreover	RB
cord-002542-f7l4ty2j	420	2	,	,	,
cord-002542-f7l4ty2j	420	3	if	if	IN
cord-002542-f7l4ty2j	420	4	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	420	5	defective	defective	JJ
cord-002542-f7l4ty2j	420	6	RNAs	rna	NNS
cord-002542-f7l4ty2j	420	7	fail	fail	VBP
cord-002542-f7l4ty2j	420	8	to	to	TO
cord-002542-f7l4ty2j	420	9	accumulate	accumulate	VB
cord-002542-f7l4ty2j	420	10	,	,	,
cord-002542-f7l4ty2j	420	11	this	this	DT
cord-002542-f7l4ty2j	420	12	reduces	reduce	VBZ
cord-002542-f7l4ty2j	420	13	the	the	DT
cord-002542-f7l4ty2j	420	14	likelihood	likelihood	NN
cord-002542-f7l4ty2j	420	15	that	that	IN
cord-002542-f7l4ty2j	420	16	mature	mature	JJ
cord-002542-f7l4ty2j	420	17	DI	DI	NNP
cord-002542-f7l4ty2j	420	18	-	-	HYPH
cord-002542-f7l4ty2j	420	19	RNAs	rna	NNS
cord-002542-f7l4ty2j	420	20	can	can	MD
cord-002542-f7l4ty2j	420	21	subsequently	subsequently	RB
cord-002542-f7l4ty2j	420	22	be	be	VB
cord-002542-f7l4ty2j	420	23	generated	generate	VBN
cord-002542-f7l4ty2j	420	24	and	and	CC
cord-002542-f7l4ty2j	420	25	may	may	MD
cord-002542-f7l4ty2j	420	26	place	place	VB
cord-002542-f7l4ty2j	420	27	substantial	substantial	JJ
cord-002542-f7l4ty2j	420	28	limitations	limitation	NNS
cord-002542-f7l4ty2j	420	29	on	on	IN
cord-002542-f7l4ty2j	420	30	the	the	DT
cord-002542-f7l4ty2j	420	31	ability	ability	NN
cord-002542-f7l4ty2j	420	32	of	of	IN
cord-002542-f7l4ty2j	420	33	some	some	DT
cord-002542-f7l4ty2j	420	34	viruses	virus	NNS
cord-002542-f7l4ty2j	420	35	to	to	TO
cord-002542-f7l4ty2j	420	36	generate	generate	VB
cord-002542-f7l4ty2j	420	37	DI	DI	NNP
cord-002542-f7l4ty2j	420	38	-	-	HYPH
cord-002542-f7l4ty2j	420	39	RNAs	rna	NNS
cord-002542-f7l4ty2j	420	40	altogether	altogether	RB
cord-002542-f7l4ty2j	420	41	.	.	.
cord-002542-f7l4ty2j	421	1	An	an	DT
cord-002542-f7l4ty2j	421	2	alternative	alternative	JJ
cord-002542-f7l4ty2j	421	3	reason	reason	NN
cord-002542-f7l4ty2j	421	4	for	for	IN
cord-002542-f7l4ty2j	421	5	the	the	DT
cord-002542-f7l4ty2j	421	6	rarity	rarity	NN
cord-002542-f7l4ty2j	421	7	of	of	IN
cord-002542-f7l4ty2j	421	8	precursor	precursor	NN
cord-002542-f7l4ty2j	421	9	/	/	SYM
cord-002542-f7l4ty2j	421	10	intermediate	intermediate	JJ
cord-002542-f7l4ty2j	421	11	defective	defective	JJ
cord-002542-f7l4ty2j	421	12	RNAs	rna	NNS
cord-002542-f7l4ty2j	421	13	is	be	VBZ
cord-002542-f7l4ty2j	421	14	that	that	IN
cord-002542-f7l4ty2j	421	15	the	the	DT
cord-002542-f7l4ty2j	421	16	mature	mature	JJ
cord-002542-f7l4ty2j	421	17	DI	DI	NNP
cord-002542-f7l4ty2j	421	18	-	-	HYPH
cord-002542-f7l4ty2j	421	19	RNAs	rna	NNS
cord-002542-f7l4ty2j	421	20	are	be	VBP
cord-002542-f7l4ty2j	421	21	generated	generate	VBN
cord-002542-f7l4ty2j	421	22	in	in	IN
cord-002542-f7l4ty2j	421	23	one	one	CD
cord-002542-f7l4ty2j	421	24	single	single	JJ
cord-002542-f7l4ty2j	421	25	event	event	NN
cord-002542-f7l4ty2j	421	26	.	.	.
cord-002542-f7l4ty2j	422	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	422	2	are	be	VBP
cord-002542-f7l4ty2j	422	3	yet	yet	RB
cord-002542-f7l4ty2j	422	4	to	to	TO
cord-002542-f7l4ty2j	422	5	determine	determine	VB
cord-002542-f7l4ty2j	422	6	the	the	DT
cord-002542-f7l4ty2j	422	7	molecular	molecular	JJ
cord-002542-f7l4ty2j	422	8	mechanism	mechanism	NN
cord-002542-f7l4ty2j	422	9	of	of	IN
cord-002542-f7l4ty2j	422	10	recombination	recombination	NN
cord-002542-f7l4ty2j	422	11	that	that	WDT
cord-002542-f7l4ty2j	422	12	leads	lead	VBZ
cord-002542-f7l4ty2j	422	13	to	to	IN
cord-002542-f7l4ty2j	422	14	DI	DI	NNP
cord-002542-f7l4ty2j	422	15	-	-	HYPH
cord-002542-f7l4ty2j	422	16	RNA	RNA	NNP
cord-002542-f7l4ty2j	422	17	formation	formation	NN
cord-002542-f7l4ty2j	422	18	.	.	.
cord-002542-f7l4ty2j	423	1	Both	both	DT
cord-002542-f7l4ty2j	423	2	template	template	NN
cord-002542-f7l4ty2j	423	3	-	-	HYPH
cord-002542-f7l4ty2j	423	4	switching	switch	VBG
cord-002542-f7l4ty2j	423	5	,	,	,
cord-002542-f7l4ty2j	423	6	secondary	secondary	JJ
cord-002542-f7l4ty2j	423	7	-	-	HYPH
cord-002542-f7l4ty2j	423	8	structure	structure	NN
cord-002542-f7l4ty2j	423	9	jumping	jumping	NN
cord-002542-f7l4ty2j	423	10	,	,	,
cord-002542-f7l4ty2j	423	11	and	and	CC
cord-002542-f7l4ty2j	423	12	non	non	JJ
cord-002542-f7l4ty2j	423	13	-	-	JJ
cord-002542-f7l4ty2j	423	14	replicative	replicative	JJ
cord-002542-f7l4ty2j	423	15	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	423	16	have	have	VBP
cord-002542-f7l4ty2j	423	17	been	be	VBN
cord-002542-f7l4ty2j	423	18	proposed	propose	VBN
cord-002542-f7l4ty2j	423	19	,	,	,
cord-002542-f7l4ty2j	423	20	and	and	CC
cord-002542-f7l4ty2j	423	21	indeed	indeed	RB
cord-002542-f7l4ty2j	423	22	these	these	DT
cord-002542-f7l4ty2j	423	23	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	423	24	need	nee	MD
cord-002542-f7l4ty2j	423	25	not	not	RB
cord-002542-f7l4ty2j	423	26	be	be	VB
cord-002542-f7l4ty2j	423	27	mutually	mutually	RB
cord-002542-f7l4ty2j	423	28	exclusive	exclusive	JJ
cord-002542-f7l4ty2j	423	29	.	.	.
cord-002542-f7l4ty2j	424	1	Our	-PRON-	PRP$
cord-002542-f7l4ty2j	424	2	observation	observation	NN
cord-002542-f7l4ty2j	424	3	of	of	IN
cord-002542-f7l4ty2j	424	4	nucleotide	nucleotide	JJ
cord-002542-f7l4ty2j	424	5	preferences	preference	NNS
cord-002542-f7l4ty2j	424	6	at	at	IN
cord-002542-f7l4ty2j	424	7	recombination	recombination	NN
cord-002542-f7l4ty2j	424	8	junctions	junction	NNS
cord-002542-f7l4ty2j	424	9	(	(	-LRB-
cord-002542-f7l4ty2j	424	10	Fig	Fig	NNP
cord-002542-f7l4ty2j	424	11	2C	2c	NN
cord-002542-f7l4ty2j	424	12	)	)	-RRB-
cord-002542-f7l4ty2j	424	13	may	may	MD
cord-002542-f7l4ty2j	424	14	arise	arise	VB
cord-002542-f7l4ty2j	424	15	through	through	IN
cord-002542-f7l4ty2j	424	16	any	any	DT
cord-002542-f7l4ty2j	424	17	of	of	IN
cord-002542-f7l4ty2j	424	18	these	these	DT
cord-002542-f7l4ty2j	424	19	potential	potential	JJ
cord-002542-f7l4ty2j	424	20	mechanisms	mechanism	NNS
cord-002542-f7l4ty2j	424	21	.	.	.
cord-002542-f7l4ty2j	425	1	Alternatively	alternatively	RB
cord-002542-f7l4ty2j	425	2	,	,	,
cord-002542-f7l4ty2j	425	3	it	-PRON-	PRP
cord-002542-f7l4ty2j	425	4	is	be	VBZ
cord-002542-f7l4ty2j	425	5	possible	possible	JJ
cord-002542-f7l4ty2j	425	6	that	that	IN
cord-002542-f7l4ty2j	425	7	multiple	multiple	JJ
cord-002542-f7l4ty2j	425	8	reassembly	reassembly	NN
cord-002542-f7l4ty2j	425	9	/	/	SYM
cord-002542-f7l4ty2j	425	10	deletion	deletion	NN
cord-002542-f7l4ty2j	425	11	events	event	NNS
cord-002542-f7l4ty2j	425	12	occur	occur	VBP
cord-002542-f7l4ty2j	425	13	in	in	IN
cord-002542-f7l4ty2j	425	14	a	a	DT
cord-002542-f7l4ty2j	425	15	single	single	JJ
cord-002542-f7l4ty2j	425	16	step	step	NN
cord-002542-f7l4ty2j	425	17	,	,	,
cord-002542-f7l4ty2j	425	18	in	in	IN
cord-002542-f7l4ty2j	425	19	a	a	DT
cord-002542-f7l4ty2j	425	20	manner	manner	NN
cord-002542-f7l4ty2j	425	21	reminiscent	reminiscent	JJ
cord-002542-f7l4ty2j	425	22	of	of	IN
cord-002542-f7l4ty2j	425	23	chromosome	chromosome	NN
cord-002542-f7l4ty2j	425	24	shattering	shattering	NN
cord-002542-f7l4ty2j	425	25	(	(	-LRB-
cord-002542-f7l4ty2j	425	26	chromothripsis	chromothripsis	NNP
cord-002542-f7l4ty2j	425	27	)	)	-RRB-
cord-002542-f7l4ty2j	425	28	[	[	-LRB-
cord-002542-f7l4ty2j	425	29	69	69	CD
cord-002542-f7l4ty2j	425	30	]	]	-RRB-
cord-002542-f7l4ty2j	425	31	;	;	:
cord-002542-f7l4ty2j	425	32	or	or	CC
cord-002542-f7l4ty2j	425	33	'	'	``
cord-002542-f7l4ty2j	425	34	virothripsis	virothripsis	NN
cord-002542-f7l4ty2j	425	35	'	'	''
cord-002542-f7l4ty2j	425	36	.	.	.
cord-002542-f7l4ty2j	426	1	Within	within	IN
cord-002542-f7l4ty2j	426	2	the	the	DT
cord-002542-f7l4ty2j	426	3	confined	confined	JJ
cord-002542-f7l4ty2j	426	4	invaginations	invagination	NNS
cord-002542-f7l4ty2j	426	5	of	of	IN
cord-002542-f7l4ty2j	426	6	the	the	DT
cord-002542-f7l4ty2j	426	7	mitochondrial	mitochondrial	JJ
cord-002542-f7l4ty2j	426	8	membranes	membrane	NNS
cord-002542-f7l4ty2j	426	9	that	that	WDT
cord-002542-f7l4ty2j	426	10	form	form	VBP
cord-002542-f7l4ty2j	426	11	the	the	DT
cord-002542-f7l4ty2j	426	12	replication	replication	NN
cord-002542-f7l4ty2j	426	13	factories	factory	NNS
cord-002542-f7l4ty2j	426	14	of	of	IN
cord-002542-f7l4ty2j	426	15	RNA	RNA	NNP
cord-002542-f7l4ty2j	426	16	viruses	virus	NNS
cord-002542-f7l4ty2j	426	17	such	such	JJ
cord-002542-f7l4ty2j	426	18	as	as	IN
cord-002542-f7l4ty2j	426	19	FHV	FHV	NNP
cord-002542-f7l4ty2j	426	20	[	[	-LRB-
cord-002542-f7l4ty2j	426	21	70	70	CD
cord-002542-f7l4ty2j	426	22	]	]	-RRB-
cord-002542-f7l4ty2j	426	23	,	,	,
cord-002542-f7l4ty2j	426	24	the	the	DT
cord-002542-f7l4ty2j	426	25	fragmentation	fragmentation	NN
cord-002542-f7l4ty2j	426	26	the	the	DT
cord-002542-f7l4ty2j	426	27	RNA	RNA	NNP
cord-002542-f7l4ty2j	426	28	virus	virus	NN
cord-002542-f7l4ty2j	426	29	genome	genome	NN
cord-002542-f7l4ty2j	426	30	followed	follow	VBN
cord-002542-f7l4ty2j	426	31	by	by	IN
cord-002542-f7l4ty2j	426	32	incorrect	incorrect	JJ
cord-002542-f7l4ty2j	426	33	re	re	NN
cord-002542-f7l4ty2j	426	34	-	-	NN
cord-002542-f7l4ty2j	426	35	stitching	stitching	NN
cord-002542-f7l4ty2j	426	36	of	of	IN
cord-002542-f7l4ty2j	426	37	these	these	DT
cord-002542-f7l4ty2j	426	38	genome	genome	NN
cord-002542-f7l4ty2j	426	39	pieces	piece	NNS
cord-002542-f7l4ty2j	426	40	,	,	,
cord-002542-f7l4ty2j	426	41	either	either	CC
cord-002542-f7l4ty2j	426	42	through	through	IN
cord-002542-f7l4ty2j	426	43	forced	force	VBN
cord-002542-f7l4ty2j	426	44	-	-	HYPH
cord-002542-f7l4ty2j	426	45	copy	copy	NN
cord-002542-f7l4ty2j	426	46	choice	choice	NN
cord-002542-f7l4ty2j	426	47	template	template	NN
cord-002542-f7l4ty2j	426	48	switching	switch	VBG
cord-002542-f7l4ty2j	426	49	or	or	CC
cord-002542-f7l4ty2j	426	50	a	a	DT
cord-002542-f7l4ty2j	426	51	non	non	JJ
cord-002542-f7l4ty2j	426	52	-	-	JJ
cord-002542-f7l4ty2j	426	53	replicative	replicative	JJ
cord-002542-f7l4ty2j	426	54	mechanism	mechanism	NN
cord-002542-f7l4ty2j	426	55	,	,	,
cord-002542-f7l4ty2j	426	56	could	could	MD
cord-002542-f7l4ty2j	426	57	create	create	VB
cord-002542-f7l4ty2j	426	58	the	the	DT
cord-002542-f7l4ty2j	426	59	DI	DI	NNP
cord-002542-f7l4ty2j	426	60	-	-	HYPH
cord-002542-f7l4ty2j	426	61	RNAs	rna	NNS
cord-002542-f7l4ty2j	426	62	observed	observe	VBD
cord-002542-f7l4ty2j	426	63	here	here	RB
cord-002542-f7l4ty2j	426	64	including	include	VBG
cord-002542-f7l4ty2j	426	65	the	the	DT
cord-002542-f7l4ty2j	426	66	complex	complex	JJ
cord-002542-f7l4ty2j	426	67	rearrangements	rearrangement	NNS
cord-002542-f7l4ty2j	426	68	observed	observe	VBN
cord-002542-f7l4ty2j	426	69	for	for	IN
cord-002542-f7l4ty2j	426	70	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	426	71	.	.	.
cord-002542-f7l4ty2j	427	1	A	a	DT
cord-002542-f7l4ty2j	427	2	defective	defective	JJ
cord-002542-f7l4ty2j	427	3	-	-	HYPH
cord-002542-f7l4ty2j	427	4	interfering	interfere	VBG
cord-002542-f7l4ty2j	427	5	RNA	RNA	NNP
cord-002542-f7l4ty2j	427	6	is	be	VBZ
cord-002542-f7l4ty2j	427	7	a	a	DT
cord-002542-f7l4ty2j	427	8	defective	defective	JJ
cord-002542-f7l4ty2j	427	9	RNA	RNA	NNP
cord-002542-f7l4ty2j	427	10	that	that	WDT
cord-002542-f7l4ty2j	427	11	has	have	VBZ
cord-002542-f7l4ty2j	427	12	the	the	DT
cord-002542-f7l4ty2j	427	13	ability	ability	NN
cord-002542-f7l4ty2j	427	14	to	to	TO
cord-002542-f7l4ty2j	427	15	compete	compete	VB
cord-002542-f7l4ty2j	427	16	with	with	IN
cord-002542-f7l4ty2j	427	17	or	or	CC
cord-002542-f7l4ty2j	427	18	otherwise	otherwise	RB
cord-002542-f7l4ty2j	427	19	attenuate	attenuate	VB
cord-002542-f7l4ty2j	427	20	the	the	DT
cord-002542-f7l4ty2j	427	21	replication	replication	NN
cord-002542-f7l4ty2j	427	22	and	and	CC
cord-002542-f7l4ty2j	427	23	proliferation	proliferation	NN
cord-002542-f7l4ty2j	427	24	of	of	IN
cord-002542-f7l4ty2j	427	25	the	the	DT
cord-002542-f7l4ty2j	427	26	wild	wild	JJ
cord-002542-f7l4ty2j	427	27	-	-	HYPH
cord-002542-f7l4ty2j	427	28	type	type	NN
cord-002542-f7l4ty2j	427	29	helper	helper	NN
cord-002542-f7l4ty2j	427	30	virus	virus	NN
cord-002542-f7l4ty2j	427	31	.	.	.
cord-002542-f7l4ty2j	428	1	In	in	IN
cord-002542-f7l4ty2j	428	2	our	-PRON-	PRP$
cord-002542-f7l4ty2j	428	3	study	study	NN
cord-002542-f7l4ty2j	428	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	428	5	demonstrate	demonstrate	VBP
cord-002542-f7l4ty2j	428	6	that	that	IN
cord-002542-f7l4ty2j	428	7	the	the	DT
cord-002542-f7l4ty2j	428	8	viral	viral	JJ
cord-002542-f7l4ty2j	428	9	swarm	swarm	NNS
cord-002542-f7l4ty2j	428	10	,	,	,
cord-002542-f7l4ty2j	428	11	even	even	RB
cord-002542-f7l4ty2j	428	12	after	after	IN
cord-002542-f7l4ty2j	428	13	only	only	RB
cord-002542-f7l4ty2j	428	14	a	a	DT
cord-002542-f7l4ty2j	428	15	few	few	JJ
cord-002542-f7l4ty2j	428	16	passages	passage	NNS
cord-002542-f7l4ty2j	428	17	,	,	,
cord-002542-f7l4ty2j	428	18	is	be	VBZ
cord-002542-f7l4ty2j	428	19	replete	replete	JJ
cord-002542-f7l4ty2j	428	20	with	with	IN
cord-002542-f7l4ty2j	428	21	many	many	JJ
cord-002542-f7l4ty2j	428	22	varieties	variety	NNS
cord-002542-f7l4ty2j	428	23	of	of	IN
cord-002542-f7l4ty2j	428	24	defective	defective	JJ
cord-002542-f7l4ty2j	428	25	RNAs	rna	NNS
cord-002542-f7l4ty2j	428	26	.	.	.
cord-002542-f7l4ty2j	429	1	With	with	IN
cord-002542-f7l4ty2j	429	2	a	a	DT
cord-002542-f7l4ty2j	429	3	single	single	JJ
cord-002542-f7l4ty2j	429	4	sequencing	sequencing	NN
cord-002542-f7l4ty2j	429	5	experiment	experiment	NN
cord-002542-f7l4ty2j	429	6	,	,	,
cord-002542-f7l4ty2j	429	7	we	-PRON-	PRP
cord-002542-f7l4ty2j	429	8	would	would	MD
cord-002542-f7l4ty2j	429	9	not	not	RB
cord-002542-f7l4ty2j	429	10	be	be	VB
cord-002542-f7l4ty2j	429	11	able	able	JJ
cord-002542-f7l4ty2j	429	12	to	to	TO
cord-002542-f7l4ty2j	429	13	determine	determine	VB
cord-002542-f7l4ty2j	429	14	whether	whether	IN
cord-002542-f7l4ty2j	429	15	these	these	DT
cord-002542-f7l4ty2j	429	16	defective	defective	JJ
cord-002542-f7l4ty2j	429	17	RNAs	rna	NNS
cord-002542-f7l4ty2j	429	18	are	be	VBP
cord-002542-f7l4ty2j	429	19	accumulating	accumulate	VBG
cord-002542-f7l4ty2j	429	20	,	,	,
cord-002542-f7l4ty2j	429	21	diminishing	diminish	VBG
cord-002542-f7l4ty2j	429	22	or	or	CC
cord-002542-f7l4ty2j	429	23	make	make	VB
cord-002542-f7l4ty2j	429	24	-	-	HYPH
cord-002542-f7l4ty2j	429	25	up	up	RP
cord-002542-f7l4ty2j	429	26	a	a	DT
cord-002542-f7l4ty2j	429	27	static	static	JJ
cord-002542-f7l4ty2j	429	28	component	component	NN
cord-002542-f7l4ty2j	429	29	of	of	IN
cord-002542-f7l4ty2j	429	30	the	the	DT
cord-002542-f7l4ty2j	429	31	viral	viral	JJ
cord-002542-f7l4ty2j	429	32	quasi	quasi	JJ
cord-002542-f7l4ty2j	429	33	-	-	NNS
cord-002542-f7l4ty2j	429	34	species	specie	NNS
cord-002542-f7l4ty2j	429	35	.	.	.
cord-002542-f7l4ty2j	430	1	However	however	RB
cord-002542-f7l4ty2j	430	2	,	,	,
cord-002542-f7l4ty2j	430	3	as	as	IN
cord-002542-f7l4ty2j	430	4	we	-PRON-	PRP
cord-002542-f7l4ty2j	430	5	perform	perform	VBP
cord-002542-f7l4ty2j	430	6	serial	serial	JJ
cord-002542-f7l4ty2j	430	7	passaging	passaging	NN
cord-002542-f7l4ty2j	430	8	with	with	IN
cord-002542-f7l4ty2j	430	9	sequential	sequential	JJ
cord-002542-f7l4ty2j	430	10	sequencing	sequencing	NN
cord-002542-f7l4ty2j	430	11	experiments	experiment	NNS
cord-002542-f7l4ty2j	430	12	,	,	,
cord-002542-f7l4ty2j	430	13	we	-PRON-	PRP
cord-002542-f7l4ty2j	430	14	can	can	MD
cord-002542-f7l4ty2j	430	15	determine	determine	VB
cord-002542-f7l4ty2j	430	16	which	which	WDT
cord-002542-f7l4ty2j	430	17	defective	defective	JJ
cord-002542-f7l4ty2j	430	18	RNAs	rna	NNS
cord-002542-f7l4ty2j	430	19	are	be	VBP
cord-002542-f7l4ty2j	430	20	accumulating	accumulate	VBG
cord-002542-f7l4ty2j	430	21	(	(	-LRB-
cord-002542-f7l4ty2j	430	22	for	for	IN
cord-002542-f7l4ty2j	430	23	example	example	NN
cord-002542-f7l4ty2j	430	24	the	the	DT
cord-002542-f7l4ty2j	430	25	'	'	``
cord-002542-f7l4ty2j	430	26	mature	mature	JJ
cord-002542-f7l4ty2j	430	27	'	'	''
cord-002542-f7l4ty2j	430	28	DI	di	NN
cord-002542-f7l4ty2j	430	29	-	-	HYPH
cord-002542-f7l4ty2j	430	30	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	430	31	)	)	-RRB-
cord-002542-f7l4ty2j	430	32	and	and	CC
cord-002542-f7l4ty2j	430	33	which	which	WDT
cord-002542-f7l4ty2j	430	34	are	be	VBP
cord-002542-f7l4ty2j	430	35	not	not	RB
cord-002542-f7l4ty2j	430	36	(	(	-LRB-
cord-002542-f7l4ty2j	430	37	e.g.	e.g.	RB
cord-002542-f7l4ty2j	430	38	the	the	DT
cord-002542-f7l4ty2j	430	39	putative	putative	JJ
cord-002542-f7l4ty2j	430	40	intermediate	intermediate	NN
cord-002542-f7l4ty2j	430	41	,	,	,
cord-002542-f7l4ty2j	430	42	or	or	CC
cord-002542-f7l4ty2j	430	43	'	'	``
cord-002542-f7l4ty2j	430	44	immature	immature	JJ
cord-002542-f7l4ty2j	430	45	'	'	''
cord-002542-f7l4ty2j	430	46	defective	defective	JJ
cord-002542-f7l4ty2j	430	47	RNAs	rna	NNS
cord-002542-f7l4ty2j	430	48	)	)	-RRB-
cord-002542-f7l4ty2j	430	49	.	.	.
cord-002542-f7l4ty2j	431	1	It	-PRON-	PRP
cord-002542-f7l4ty2j	431	2	would	would	MD
cord-002542-f7l4ty2j	431	3	be	be	VB
cord-002542-f7l4ty2j	431	4	impractical	impractical	JJ
cord-002542-f7l4ty2j	431	5	to	to	TO
cord-002542-f7l4ty2j	431	6	validate	validate	VB
cord-002542-f7l4ty2j	431	7	each	each	DT
cord-002542-f7l4ty2j	431	8	of	of	IN
cord-002542-f7l4ty2j	431	9	the	the	DT
cord-002542-f7l4ty2j	431	10	many	many	JJ
cord-002542-f7l4ty2j	431	11	hundreds	hundred	NNS
cord-002542-f7l4ty2j	431	12	of	of	IN
cord-002542-f7l4ty2j	431	13	detected	detect	VBN
cord-002542-f7l4ty2j	431	14	defective	defective	JJ
cord-002542-f7l4ty2j	431	15	RNA	RNA	NNP
cord-002542-f7l4ty2j	431	16	species	specie	NNS
cord-002542-f7l4ty2j	431	17	with	with	IN
cord-002542-f7l4ty2j	431	18	molecular	molecular	JJ
cord-002542-f7l4ty2j	431	19	virological	virological	JJ
cord-002542-f7l4ty2j	431	20	experiments	experiment	NNS
cord-002542-f7l4ty2j	431	21	to	to	TO
cord-002542-f7l4ty2j	431	22	determine	determine	VB
cord-002542-f7l4ty2j	431	23	whether	whether	IN
cord-002542-f7l4ty2j	431	24	they	-PRON-	PRP
cord-002542-f7l4ty2j	431	25	truly	truly	RB
cord-002542-f7l4ty2j	431	26	can	can	MD
cord-002542-f7l4ty2j	431	27	attenuate	attenuate	VB
cord-002542-f7l4ty2j	431	28	or	or	CC
cord-002542-f7l4ty2j	431	29	interfere	interfere	VB
cord-002542-f7l4ty2j	431	30	with	with	IN
cord-002542-f7l4ty2j	431	31	wild	wild	JJ
cord-002542-f7l4ty2j	431	32	-	-	HYPH
cord-002542-f7l4ty2j	431	33	type	type	NN
cord-002542-f7l4ty2j	431	34	virus	virus	NN
cord-002542-f7l4ty2j	431	35	replication	replication	NN
cord-002542-f7l4ty2j	431	36	and	and	CC
cord-002542-f7l4ty2j	431	37	to	to	TO
cord-002542-f7l4ty2j	431	38	therefore	therefore	RB
cord-002542-f7l4ty2j	431	39	categorize	categorize	VB
cord-002542-f7l4ty2j	431	40	that	that	DT
cord-002542-f7l4ty2j	431	41	species	specie	NNS
cord-002542-f7l4ty2j	431	42	as	as	IN
cord-002542-f7l4ty2j	431	43	a	a	DT
cord-002542-f7l4ty2j	431	44	defective	defective	JJ
cord-002542-f7l4ty2j	431	45	-	-	HYPH
cord-002542-f7l4ty2j	431	46	interfering	interfere	VBG
cord-002542-f7l4ty2j	431	47	RNA	RNA	NNP
cord-002542-f7l4ty2j	431	48	.	.	.
cord-002542-f7l4ty2j	432	1	Indeed	indeed	RB
cord-002542-f7l4ty2j	432	2	,	,	,
cord-002542-f7l4ty2j	432	3	we	-PRON-	PRP
cord-002542-f7l4ty2j	432	4	can	can	MD
cord-002542-f7l4ty2j	432	5	not	not	RB
cord-002542-f7l4ty2j	432	6	exclude	exclude	VB
cord-002542-f7l4ty2j	432	7	the	the	DT
cord-002542-f7l4ty2j	432	8	possibility	possibility	NN
cord-002542-f7l4ty2j	432	9	that	that	IN
cord-002542-f7l4ty2j	432	10	multiple	multiple	JJ
cord-002542-f7l4ty2j	432	11	DI	DI	NNP
cord-002542-f7l4ty2j	432	12	-	-	HYPH
cord-002542-f7l4ty2j	432	13	R	R	NNP
cord-002542-f7l4ty2j	432	14	-	-	HYPH
cord-002542-f7l4ty2j	432	15	NAs	NAs	NNP
cord-002542-f7l4ty2j	432	16	act	act	NNP
cord-002542-f7l4ty2j	432	17	co	co	NNP
cord-002542-f7l4ty2j	432	18	-	-	NN
cord-002542-f7l4ty2j	432	19	operatively	operatively	RB
cord-002542-f7l4ty2j	432	20	within	within	IN
cord-002542-f7l4ty2j	432	21	the	the	DT
cord-002542-f7l4ty2j	432	22	viral	viral	JJ
cord-002542-f7l4ty2j	432	23	quasi	quasi	JJ
cord-002542-f7l4ty2j	432	24	-	-	HYPH
cord-002542-f7l4ty2j	432	25	species	specie	NNS
cord-002542-f7l4ty2j	432	26	and	and	CC
cord-002542-f7l4ty2j	432	27	are	be	VBP
cord-002542-f7l4ty2j	432	28	mutually	mutually	RB
cord-002542-f7l4ty2j	432	29	dependent	dependent	JJ
cord-002542-f7l4ty2j	432	30	upon	upon	IN
cord-002542-f7l4ty2j	432	31	one	one	CD
cord-002542-f7l4ty2j	432	32	another	another	DT
cord-002542-f7l4ty2j	432	33	.	.	.
cord-002542-f7l4ty2j	433	1	However	however	RB
cord-002542-f7l4ty2j	433	2	,	,	,
cord-002542-f7l4ty2j	433	3	the	the	DT
cord-002542-f7l4ty2j	433	4	demonstration	demonstration	NN
cord-002542-f7l4ty2j	433	5	here	here	RB
cord-002542-f7l4ty2j	433	6	of	of	IN
cord-002542-f7l4ty2j	433	7	an	an	DT
cord-002542-f7l4ty2j	433	8	accumulation	accumulation	NN
cord-002542-f7l4ty2j	433	9	during	during	IN
cord-002542-f7l4ty2j	433	10	serial	serial	JJ
cord-002542-f7l4ty2j	433	11	passaging	passaging	NN
cord-002542-f7l4ty2j	433	12	is	be	VBZ
cord-002542-f7l4ty2j	433	13	strong	strong	JJ
cord-002542-f7l4ty2j	433	14	evidence	evidence	NN
cord-002542-f7l4ty2j	433	15	that	that	IN
cord-002542-f7l4ty2j	433	16	these	these	DT
cord-002542-f7l4ty2j	433	17	species	specie	NNS
cord-002542-f7l4ty2j	433	18	are	be	VBP
cord-002542-f7l4ty2j	433	19	interfering	interfere	VBG
cord-002542-f7l4ty2j	433	20	,	,	,
cord-002542-f7l4ty2j	433	21	as	as	IN
cord-002542-f7l4ty2j	433	22	their	-PRON-	PRP$
cord-002542-f7l4ty2j	433	23	accumulation	accumulation	NN
cord-002542-f7l4ty2j	433	24	essentially	essentially	RB
cord-002542-f7l4ty2j	433	25	dilutes	dilute	VBZ
cord-002542-f7l4ty2j	433	26	the	the	DT
cord-002542-f7l4ty2j	433	27	pool	pool	NN
cord-002542-f7l4ty2j	433	28	of	of	IN
cord-002542-f7l4ty2j	433	29	wild	wild	JJ
cord-002542-f7l4ty2j	433	30	-	-	HYPH
cord-002542-f7l4ty2j	433	31	type	type	NN
cord-002542-f7l4ty2j	433	32	functional	functional	JJ
cord-002542-f7l4ty2j	433	33	virus	virus	NN
cord-002542-f7l4ty2j	433	34	.	.	.
cord-002542-f7l4ty2j	434	1	With	with	IN
cord-002542-f7l4ty2j	434	2	this	this	DT
cord-002542-f7l4ty2j	434	3	in	in	IN
cord-002542-f7l4ty2j	434	4	mind	mind	NN
cord-002542-f7l4ty2j	434	5	,	,	,
cord-002542-f7l4ty2j	434	6	we	-PRON-	PRP
cord-002542-f7l4ty2j	434	7	believe	believe	VBP
cord-002542-f7l4ty2j	434	8	it	-PRON-	PRP
cord-002542-f7l4ty2j	434	9	would	would	MD
cord-002542-f7l4ty2j	434	10	be	be	VB
cord-002542-f7l4ty2j	434	11	suitable	suitable	JJ
cord-002542-f7l4ty2j	434	12	to	to	TO
cord-002542-f7l4ty2j	434	13	describe	describe	VB
cord-002542-f7l4ty2j	434	14	the	the	DT
cord-002542-f7l4ty2j	434	15	mature	mature	JJ
cord-002542-f7l4ty2j	434	16	defective	defective	JJ
cord-002542-f7l4ty2j	434	17	RNAs	rna	NNS
cord-002542-f7l4ty2j	434	18	as	as	IN
cord-002542-f7l4ty2j	434	19	defective	defective	JJ
cord-002542-f7l4ty2j	434	20	-	-	HYPH
cord-002542-f7l4ty2j	434	21	interfering	interfere	VBG
cord-002542-f7l4ty2j	434	22	RNAs	rna	NNS
cord-002542-f7l4ty2j	434	23	(	(	-LRB-
cord-002542-f7l4ty2j	434	24	DI	DI	NNP
cord-002542-f7l4ty2j	434	25	-	-	HYPH
cord-002542-f7l4ty2j	434	26	RNAs	RNAs	NNPS
cord-002542-f7l4ty2j	434	27	)	)	-RRB-
cord-002542-f7l4ty2j	434	28	,	,	,
cord-002542-f7l4ty2j	434	29	and	and	CC
cord-002542-f7l4ty2j	434	30	the	the	DT
cord-002542-f7l4ty2j	434	31	'	'	``
cord-002542-f7l4ty2j	434	32	immature	immature	JJ
cord-002542-f7l4ty2j	434	33	'	'	''
cord-002542-f7l4ty2j	434	34	only	only	RB
cord-002542-f7l4ty2j	434	35	as	as	IN
cord-002542-f7l4ty2j	434	36	defective	defective	JJ
cord-002542-f7l4ty2j	434	37	RNAs	rna	NNS
cord-002542-f7l4ty2j	434	38	.	.	.
cord-002542-f7l4ty2j	435	1	It	-PRON-	PRP
cord-002542-f7l4ty2j	435	2	is	be	VBZ
cord-002542-f7l4ty2j	435	3	remarkable	remarkable	JJ
cord-002542-f7l4ty2j	435	4	that	that	IN
cord-002542-f7l4ty2j	435	5	FHV	FHV	NNP
cord-002542-f7l4ty2j	435	6	is	be	VBZ
cord-002542-f7l4ty2j	435	7	able	able	JJ
cord-002542-f7l4ty2j	435	8	to	to	TO
cord-002542-f7l4ty2j	435	9	maintain	maintain	VB
cord-002542-f7l4ty2j	435	10	a	a	DT
cord-002542-f7l4ty2j	435	11	viable	viable	JJ
cord-002542-f7l4ty2j	435	12	infection	infection	NN
cord-002542-f7l4ty2j	435	13	despite	despite	IN
cord-002542-f7l4ty2j	435	14	being	be	VBG
cord-002542-f7l4ty2j	435	15	burdened	burden	VBN
cord-002542-f7l4ty2j	435	16	with	with	IN
cord-002542-f7l4ty2j	435	17	such	such	PDT
cord-002542-f7l4ty2j	435	18	a	a	DT
cord-002542-f7l4ty2j	435	19	gross	gross	JJ
cord-002542-f7l4ty2j	435	20	excess	excess	NN
cord-002542-f7l4ty2j	435	21	of	of	IN
cord-002542-f7l4ty2j	435	22	DI	DI	NNP
cord-002542-f7l4ty2j	435	23	-	-	HYPH
cord-002542-f7l4ty2j	435	24	RNAs	rna	NNS
cord-002542-f7l4ty2j	435	25	in	in	IN
cord-002542-f7l4ty2j	435	26	the	the	DT
cord-002542-f7l4ty2j	435	27	final	final	JJ
cord-002542-f7l4ty2j	435	28	passages	passage	NNS
cord-002542-f7l4ty2j	435	29	presented	present	VBN
cord-002542-f7l4ty2j	435	30	here	here	RB
cord-002542-f7l4ty2j	435	31	.	.	.
cord-002542-f7l4ty2j	436	1	By	by	IN
cord-002542-f7l4ty2j	436	2	performing	perform	VBG
cord-002542-f7l4ty2j	436	3	TCID50	TCID50	NNP
cord-002542-f7l4ty2j	436	4	assays	assay	NNS
cord-002542-f7l4ty2j	436	5	of	of	IN
cord-002542-f7l4ty2j	436	6	the	the	DT
cord-002542-f7l4ty2j	436	7	original	original	JJ
cord-002542-f7l4ty2j	436	8	inocula	inocula	NN
cord-002542-f7l4ty2j	436	9	used	use	VBN
cord-002542-f7l4ty2j	436	10	between	between	IN
cord-002542-f7l4ty2j	436	11	each	each	DT
cord-002542-f7l4ty2j	436	12	of	of	IN
cord-002542-f7l4ty2j	436	13	the	the	DT
cord-002542-f7l4ty2j	436	14	passages	passage	NNS
cord-002542-f7l4ty2j	436	15	and	and	CC
cord-002542-f7l4ty2j	436	16	of	of	IN
cord-002542-f7l4ty2j	436	17	the	the	DT
cord-002542-f7l4ty2j	436	18	particles	particle	NNS
cord-002542-f7l4ty2j	436	19	purified	purify	VBN
cord-002542-f7l4ty2j	436	20	from	from	IN
cord-002542-f7l4ty2j	436	21	each	each	DT
cord-002542-f7l4ty2j	436	22	passage	passage	NN
cord-002542-f7l4ty2j	436	23	,	,	,
cord-002542-f7l4ty2j	436	24	we	-PRON-	PRP
cord-002542-f7l4ty2j	436	25	show	show	VBP
cord-002542-f7l4ty2j	436	26	that	that	IN
cord-002542-f7l4ty2j	436	27	there	there	EX
cord-002542-f7l4ty2j	436	28	is	be	VBZ
cord-002542-f7l4ty2j	436	29	a	a	DT
cord-002542-f7l4ty2j	436	30	dramatic	dramatic	JJ
cord-002542-f7l4ty2j	436	31	reduction	reduction	NN
cord-002542-f7l4ty2j	436	32	in	in	IN
cord-002542-f7l4ty2j	436	33	specific	specific	JJ
cord-002542-f7l4ty2j	436	34	infectivity	infectivity	NN
cord-002542-f7l4ty2j	436	35	during	during	IN
cord-002542-f7l4ty2j	436	36	passaging	passaging	NN
cord-002542-f7l4ty2j	436	37	corresponding	correspond	VBG
cord-002542-f7l4ty2j	436	38	with	with	IN
cord-002542-f7l4ty2j	436	39	the	the	DT
cord-002542-f7l4ty2j	436	40	increase	increase	NN
cord-002542-f7l4ty2j	436	41	in	in	IN
cord-002542-f7l4ty2j	436	42	the	the	DT
cord-002542-f7l4ty2j	436	43	DI	DI	NNP
cord-002542-f7l4ty2j	436	44	-	-	HYPH
cord-002542-f7l4ty2j	436	45	RNA	RNA	NNP
cord-002542-f7l4ty2j	436	46	content	content	NN
cord-002542-f7l4ty2j	436	47	.	.	.
cord-002542-f7l4ty2j	437	1	DI	DI	NNP
cord-002542-f7l4ty2j	437	2	-	-	HYPH
cord-002542-f7l4ty2j	437	3	RNAs	rna	NNS
cord-002542-f7l4ty2j	437	4	have	have	VBP
cord-002542-f7l4ty2j	437	5	generally	generally	RB
cord-002542-f7l4ty2j	437	6	been	be	VBN
cord-002542-f7l4ty2j	437	7	demonstrated	demonstrate	VBN
cord-002542-f7l4ty2j	437	8	to	to	TO
cord-002542-f7l4ty2j	437	9	arise	arise	VB
cord-002542-f7l4ty2j	437	10	at	at	IN
cord-002542-f7l4ty2j	437	11	high	high	JJ
cord-002542-f7l4ty2j	437	12	MOIs	mois	NN
cord-002542-f7l4ty2j	437	13	,	,	,
cord-002542-f7l4ty2j	437	14	as	as	IN
cord-002542-f7l4ty2j	437	15	was	be	VBD
cord-002542-f7l4ty2j	437	16	the	the	DT
cord-002542-f7l4ty2j	437	17	scenario	scenario	NN
cord-002542-f7l4ty2j	437	18	with	with	IN
cord-002542-f7l4ty2j	437	19	our	-PRON-	PRP$
cord-002542-f7l4ty2j	437	20	first	first	JJ
cord-002542-f7l4ty2j	437	21	passages	passage	NNS
cord-002542-f7l4ty2j	437	22	.	.	.
cord-002542-f7l4ty2j	438	1	However	however	RB
cord-002542-f7l4ty2j	438	2	,	,	,
cord-002542-f7l4ty2j	438	3	our	-PRON-	PRP$
cord-002542-f7l4ty2j	438	4	calculated	calculate	VBN
cord-002542-f7l4ty2j	438	5	MOI	MOI	NNP
cord-002542-f7l4ty2j	438	6	drops	drop	VBZ
cord-002542-f7l4ty2j	438	7	rapidly	rapidly	RB
cord-002542-f7l4ty2j	438	8	after	after	IN
cord-002542-f7l4ty2j	438	9	DI	DI	NNP
cord-002542-f7l4ty2j	438	10	-	-	HYPH
cord-002542-f7l4ty2j	438	11	RNAs	rna	NNS
cord-002542-f7l4ty2j	438	12	have	have	VBP
cord-002542-f7l4ty2j	438	13	formed	form	VBN
cord-002542-f7l4ty2j	438	14	to	to	IN
cord-002542-f7l4ty2j	438	15	levels	level	NNS
cord-002542-f7l4ty2j	438	16	that	that	WDT
cord-002542-f7l4ty2j	438	17	might	may	MD
cord-002542-f7l4ty2j	438	18	be	be	VB
cord-002542-f7l4ty2j	438	19	expected	expect	VBN
cord-002542-f7l4ty2j	438	20	during	during	IN
cord-002542-f7l4ty2j	438	21	typical	typical	JJ
cord-002542-f7l4ty2j	438	22	in	in	IN
cord-002542-f7l4ty2j	438	23	vivo	vivo	FW
cord-002542-f7l4ty2j	438	24	viral	viral	JJ
cord-002542-f7l4ty2j	438	25	passaging	passaging	NN
cord-002542-f7l4ty2j	438	26	scenarios	scenario	NNS
cord-002542-f7l4ty2j	438	27	.	.	.
cord-002542-f7l4ty2j	439	1	However	however	RB
cord-002542-f7l4ty2j	439	2	,	,	,
cord-002542-f7l4ty2j	439	3	in	in	IN
cord-002542-f7l4ty2j	439	4	this	this	DT
cord-002542-f7l4ty2j	439	5	experiment	experiment	NN
cord-002542-f7l4ty2j	439	6	we	-PRON-	PRP
cord-002542-f7l4ty2j	439	7	were	be	VBD
cord-002542-f7l4ty2j	439	8	actually	actually	RB
cord-002542-f7l4ty2j	439	9	passaging	passage	VBG
cord-002542-f7l4ty2j	439	10	a	a	DT
cord-002542-f7l4ty2j	439	11	large	large	JJ
cord-002542-f7l4ty2j	439	12	number	number	NN
cord-002542-f7l4ty2j	439	13	of	of	IN
cord-002542-f7l4ty2j	439	14	virus	virus	NN
cord-002542-f7l4ty2j	439	15	particles	particle	NNS
cord-002542-f7l4ty2j	439	16	between	between	IN
cord-002542-f7l4ty2j	439	17	cells	cell	NNS
cord-002542-f7l4ty2j	439	18	,	,	,
cord-002542-f7l4ty2j	439	19	but	but	CC
cord-002542-f7l4ty2j	439	20	with	with	IN
cord-002542-f7l4ty2j	439	21	a	a	DT
cord-002542-f7l4ty2j	439	22	low	low	JJ
cord-002542-f7l4ty2j	439	23	specific	specific	JJ
cord-002542-f7l4ty2j	439	24	infectivity	infectivity	NN
cord-002542-f7l4ty2j	439	25	.	.	.
cord-002542-f7l4ty2j	440	1	It	-PRON-	PRP
cord-002542-f7l4ty2j	440	2	is	be	VBZ
cord-002542-f7l4ty2j	440	3	also	also	RB
cord-002542-f7l4ty2j	440	4	interesting	interesting	JJ
cord-002542-f7l4ty2j	440	5	to	to	TO
cord-002542-f7l4ty2j	440	6	observe	observe	VB
cord-002542-f7l4ty2j	440	7	that	that	DT
cord-002542-f7l4ty2j	440	8	for	for	IN
cord-002542-f7l4ty2j	440	9	the	the	DT
cord-002542-f7l4ty2j	440	10	final	final	JJ
cord-002542-f7l4ty2j	440	11	passages	passage	NNS
cord-002542-f7l4ty2j	440	12	there	there	EX
cord-002542-f7l4ty2j	440	13	appears	appear	VBZ
cord-002542-f7l4ty2j	440	14	to	to	TO
cord-002542-f7l4ty2j	440	15	be	be	VB
cord-002542-f7l4ty2j	440	16	a	a	DT
cord-002542-f7l4ty2j	440	17	protective	protective	JJ
cord-002542-f7l4ty2j	440	18	property	property	NN
cord-002542-f7l4ty2j	440	19	of	of	IN
cord-002542-f7l4ty2j	440	20	the	the	DT
cord-002542-f7l4ty2j	440	21	DI	DI	NNP
cord-002542-f7l4ty2j	440	22	-	-	HYPH
cord-002542-f7l4ty2j	440	23	RNAs	rna	NNS
cord-002542-f7l4ty2j	440	24	as	as	IN
cord-002542-f7l4ty2j	440	25	determined	determine	VBN
cord-002542-f7l4ty2j	440	26	by	by	IN
cord-002542-f7l4ty2j	440	27	flow	flow	NN
cord-002542-f7l4ty2j	440	28	-	-	HYPH
cord-002542-f7l4ty2j	440	29	cytometry	cytometry	NN
cord-002542-f7l4ty2j	440	30	,	,	,
cord-002542-f7l4ty2j	440	31	but	but	CC
cord-002542-f7l4ty2j	440	32	only	only	RB
cord-002542-f7l4ty2j	440	33	when	when	WRB
cord-002542-f7l4ty2j	440	34	administered	administer	VBN
cord-002542-f7l4ty2j	440	35	at	at	IN
cord-002542-f7l4ty2j	440	36	the	the	DT
cord-002542-f7l4ty2j	440	37	highest	high	JJS
cord-002542-f7l4ty2j	440	38	doses	dose	NNS
cord-002542-f7l4ty2j	440	39	corresponding	correspond	VBG
cord-002542-f7l4ty2j	440	40	to	to	IN
cord-002542-f7l4ty2j	440	41	over~30,000	over~30,000	NNP
cord-002542-f7l4ty2j	440	42	particles	particle	NNS
cord-002542-f7l4ty2j	440	43	per	per	IN
cord-002542-f7l4ty2j	440	44	cell	cell	NN
cord-002542-f7l4ty2j	440	45	.	.	.
cord-002542-f7l4ty2j	441	1	However	however	RB
cord-002542-f7l4ty2j	441	2	,	,	,
cord-002542-f7l4ty2j	441	3	the	the	DT
cord-002542-f7l4ty2j	441	4	role	role	NN
cord-002542-f7l4ty2j	441	5	that	that	WDT
cord-002542-f7l4ty2j	441	6	DI	DI	NNP
cord-002542-f7l4ty2j	441	7	-	-	HYPH
cord-002542-f7l4ty2j	441	8	RNAs	rna	NNS
cord-002542-f7l4ty2j	441	9	might	may	MD
cord-002542-f7l4ty2j	441	10	play	play	VB
cord-002542-f7l4ty2j	441	11	in	in	IN
cord-002542-f7l4ty2j	441	12	vivo	vivo	NN
cord-002542-f7l4ty2j	441	13	is	be	VBZ
cord-002542-f7l4ty2j	441	14	not	not	RB
cord-002542-f7l4ty2j	441	15	clear	clear	JJ
cord-002542-f7l4ty2j	441	16	,	,	,
cord-002542-f7l4ty2j	441	17	as	as	IN
cord-002542-f7l4ty2j	441	18	these	these	DT
cord-002542-f7l4ty2j	441	19	very	very	RB
cord-002542-f7l4ty2j	441	20	high	high	JJ
cord-002542-f7l4ty2j	441	21	doses	dose	NNS
cord-002542-f7l4ty2j	441	22	may	may	MD
cord-002542-f7l4ty2j	441	23	not	not	RB
cord-002542-f7l4ty2j	441	24	be	be	VB
cord-002542-f7l4ty2j	441	25	physiologically	physiologically	RB
cord-002542-f7l4ty2j	441	26	relevant	relevant	JJ
cord-002542-f7l4ty2j	441	27	.	.	.
cord-002542-f7l4ty2j	442	1	DI	DI	NNP
cord-002542-f7l4ty2j	442	2	-	-	HYPH
cord-002542-f7l4ty2j	442	3	RNAs	rna	NNS
cord-002542-f7l4ty2j	442	4	for	for	IN
cord-002542-f7l4ty2j	442	5	FHV	FHV	NNP
cord-002542-f7l4ty2j	442	6	similar	similar	JJ
cord-002542-f7l4ty2j	442	7	to	to	IN
cord-002542-f7l4ty2j	442	8	the	the	DT
cord-002542-f7l4ty2j	442	9	ones	one	NNS
cord-002542-f7l4ty2j	442	10	described	describe	VBN
cord-002542-f7l4ty2j	442	11	here	here	RB
cord-002542-f7l4ty2j	442	12	have	have	VBP
cord-002542-f7l4ty2j	442	13	been	be	VBN
cord-002542-f7l4ty2j	442	14	observed	observe	VBN
cord-002542-f7l4ty2j	442	15	to	to	TO
cord-002542-f7l4ty2j	442	16	arise	arise	VB
cord-002542-f7l4ty2j	442	17	in	in	IN
cord-002542-f7l4ty2j	442	18	experimental	experimental	JJ
cord-002542-f7l4ty2j	442	19	fruit	fruit	NN
cord-002542-f7l4ty2j	442	20	fly	fly	VBP
cord-002542-f7l4ty2j	442	21	infections	infection	NNS
cord-002542-f7l4ty2j	442	22	[	[	-LRB-
cord-002542-f7l4ty2j	442	23	33	33	CD
cord-002542-f7l4ty2j	442	24	]	]	-RRB-
cord-002542-f7l4ty2j	442	25	and	and	CC
cord-002542-f7l4ty2j	442	26	so	so	RB
cord-002542-f7l4ty2j	442	27	the	the	DT
cord-002542-f7l4ty2j	442	28	mechanism	mechanism	NN
cord-002542-f7l4ty2j	442	29	of	of	IN
cord-002542-f7l4ty2j	442	30	formation	formation	NN
cord-002542-f7l4ty2j	442	31	and/or	and/or	CC
cord-002542-f7l4ty2j	442	32	selection	selection	NN
cord-002542-f7l4ty2j	442	33	is	be	VBZ
cord-002542-f7l4ty2j	442	34	likely	likely	JJ
cord-002542-f7l4ty2j	442	35	to	to	TO
cord-002542-f7l4ty2j	442	36	be	be	VB
cord-002542-f7l4ty2j	442	37	similar	similar	JJ
cord-002542-f7l4ty2j	442	38	in	in	IN
cord-002542-f7l4ty2j	442	39	cell	cell	NN
cord-002542-f7l4ty2j	442	40	culture	culture	NN
cord-002542-f7l4ty2j	442	41	and	and	CC
cord-002542-f7l4ty2j	442	42	in	in	IN
cord-002542-f7l4ty2j	442	43	vivo	vivo	NNP
cord-002542-f7l4ty2j	442	44	.	.	.
cord-002542-f7l4ty2j	443	1	However	however	RB
cord-002542-f7l4ty2j	443	2	,	,	,
cord-002542-f7l4ty2j	443	3	whether	whether	IN
cord-002542-f7l4ty2j	443	4	RNA	RNA	NNP
cord-002542-f7l4ty2j	443	5	viruses	virus	NNS
cord-002542-f7l4ty2j	443	6	such	such	JJ
cord-002542-f7l4ty2j	443	7	as	as	IN
cord-002542-f7l4ty2j	443	8	FHV	FHV	NNP
cord-002542-f7l4ty2j	443	9	have	have	VBP
cord-002542-f7l4ty2j	443	10	evolved	evolve	VBN
cord-002542-f7l4ty2j	443	11	to	to	TO
cord-002542-f7l4ty2j	443	12	favor	favor	VB
cord-002542-f7l4ty2j	443	13	the	the	DT
cord-002542-f7l4ty2j	443	14	spontaneous	spontaneous	JJ
cord-002542-f7l4ty2j	443	15	formation	formation	NN
cord-002542-f7l4ty2j	443	16	of	of	IN
cord-002542-f7l4ty2j	443	17	DI	DI	NNP
cord-002542-f7l4ty2j	443	18	-	-	HYPH
cord-002542-f7l4ty2j	443	19	RNAs	rna	NNS
cord-002542-f7l4ty2j	443	20	and	and	CC
cord-002542-f7l4ty2j	443	21	if	if	IN
cord-002542-f7l4ty2j	443	22	so	so	RB
cord-002542-f7l4ty2j	443	23	whether	whether	IN
cord-002542-f7l4ty2j	443	24	these	these	DT
cord-002542-f7l4ty2j	443	25	DI	DI	NNP
cord-002542-f7l4ty2j	443	26	-	-	HYPH
cord-002542-f7l4ty2j	443	27	RNAs	rna	NNS
cord-002542-f7l4ty2j	443	28	play	play	VBP
cord-002542-f7l4ty2j	443	29	an	an	DT
cord-002542-f7l4ty2j	443	30	important	important	JJ
cord-002542-f7l4ty2j	443	31	role	role	NN
cord-002542-f7l4ty2j	443	32	in	in	IN
cord-002542-f7l4ty2j	443	33	modifying	modify	VBG
cord-002542-f7l4ty2j	443	34	the	the	DT
cord-002542-f7l4ty2j	443	35	life	life	NN
cord-002542-f7l4ty2j	443	36	-	-	HYPH
cord-002542-f7l4ty2j	443	37	cycle	cycle	NN
cord-002542-f7l4ty2j	443	38	of	of	IN
cord-002542-f7l4ty2j	443	39	the	the	DT
cord-002542-f7l4ty2j	443	40	virus	virus	NN
cord-002542-f7l4ty2j	443	41	,	,	,
cord-002542-f7l4ty2j	443	42	is	be	VBZ
cord-002542-f7l4ty2j	443	43	yet	yet	RB
cord-002542-f7l4ty2j	443	44	to	to	TO
cord-002542-f7l4ty2j	443	45	be	be	VB
cord-002542-f7l4ty2j	443	46	determined	determine	VBN
cord-002542-f7l4ty2j	443	47	.	.	.
cord-002542-f7l4ty2j	444	1	and	and	CC
cord-002542-f7l4ty2j	444	2	the	the	DT
cord-002542-f7l4ty2j	444	3	stacked	stacked	JJ
cord-002542-f7l4ty2j	444	4	frequencies	frequency	NNS
cord-002542-f7l4ty2j	444	5	of	of	IN
cord-002542-f7l4ty2j	444	6	each	each	DT
cord-002542-f7l4ty2j	444	7	detected	detect	VBN
cord-002542-f7l4ty2j	444	8	defective	defective	JJ
cord-002542-f7l4ty2j	444	9	RNA	RNA	NNP
cord-002542-f7l4ty2j	444	10	is	be	VBZ
cord-002542-f7l4ty2j	444	11	shown	show	VBN
cord-002542-f7l4ty2j	444	12	in	in	IN
cord-002542-f7l4ty2j	444	13	the	the	DT
cord-002542-f7l4ty2j	444	14	y	y	NN
cord-002542-f7l4ty2j	444	15	-	-	HYPH
cord-002542-f7l4ty2j	444	16	axis	axis	NN
cord-002542-f7l4ty2j	444	17	.	.	.
cord-002542-f7l4ty2j	445	1	Each	each	DT
cord-002542-f7l4ty2j	445	2	noncontiguous	noncontiguous	JJ
cord-002542-f7l4ty2j	445	3	color	color	NN
cord-002542-f7l4ty2j	445	4	represents	represent	VBZ
cord-002542-f7l4ty2j	445	5	a	a	DT
cord-002542-f7l4ty2j	445	6	specific	specific	JJ
cord-002542-f7l4ty2j	445	7	genome	genome	NN
cord-002542-f7l4ty2j	445	8	characterized	characterize	VBN
cord-002542-f7l4ty2j	445	9	by	by	IN
cord-002542-f7l4ty2j	445	10	MinION	MinION	VBG
cord-002542-f7l4ty2j	445	11	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	445	12	sequencing	sequencing	NN
cord-002542-f7l4ty2j	445	13	.	.	.
cord-002542-f7l4ty2j	446	1	Wild	wild	JJ
cord-002542-f7l4ty2j	446	2	-	-	HYPH
cord-002542-f7l4ty2j	446	3	type	type	NN
cord-002542-f7l4ty2j	446	4	genomes	genome	NNS
cord-002542-f7l4ty2j	446	5	are	be	VBP
cord-002542-f7l4ty2j	446	6	colored	color	VBN
cord-002542-f7l4ty2j	446	7	green	green	JJ
cord-002542-f7l4ty2j	446	8	,	,	,
cord-002542-f7l4ty2j	446	9	genomes	genome	NNS
cord-002542-f7l4ty2j	446	10	with	with	IN
cord-002542-f7l4ty2j	446	11	one	one	CD
cord-002542-f7l4ty2j	446	12	deletion	deletion	NN
cord-002542-f7l4ty2j	446	13	are	be	VBP
cord-002542-f7l4ty2j	446	14	colored	color	VBN
cord-002542-f7l4ty2j	446	15	in	in	IN
cord-002542-f7l4ty2j	446	16	shades	shade	NNS
cord-002542-f7l4ty2j	446	17	of	of	IN
cord-002542-f7l4ty2j	446	18	blue	blue	JJ
cord-002542-f7l4ty2j	446	19	,	,	,
cord-002542-f7l4ty2j	446	20	and	and	CC
cord-002542-f7l4ty2j	446	21	genomes	genome	NNS
cord-002542-f7l4ty2j	446	22	with	with	IN
cord-002542-f7l4ty2j	446	23	two	two	CD
cord-002542-f7l4ty2j	446	24	or	or	CC
cord-002542-f7l4ty2j	446	25	more	more	JJR
cord-002542-f7l4ty2j	446	26	deletions	deletion	NNS
cord-002542-f7l4ty2j	446	27	are	be	VBP
cord-002542-f7l4ty2j	446	28	colored	color	VBN
cord-002542-f7l4ty2j	446	29	in	in	IN
cord-002542-f7l4ty2j	446	30	shades	shade	NNS
cord-002542-f7l4ty2j	446	31	of	of	IN
cord-002542-f7l4ty2j	446	32	oranges	orange	NNS
cord-002542-f7l4ty2j	446	33	(	(	-LRB-
cord-002542-f7l4ty2j	446	34	using	use	VBG
cord-002542-f7l4ty2j	446	35	the	the	DT
cord-002542-f7l4ty2j	446	36	same	same	JJ
cord-002542-f7l4ty2j	446	37	color	color	NN
cord-002542-f7l4ty2j	446	38	scheme	scheme	NN
cord-002542-f7l4ty2j	446	39	as	as	IN
cord-002542-f7l4ty2j	446	40	in	in	IN
cord-002542-f7l4ty2j	446	41	Fig	Fig	NNP
cord-002542-f7l4ty2j	446	42	5C	5c	CD
cord-002542-f7l4ty2j	446	43	)	)	-RRB-
cord-002542-f7l4ty2j	446	44	.	.	.
cord-002542-f7l4ty2j	446	45	 	 	_SP
cord-002542-f7l4ty2j	447	1	Each	each	DT
cord-002542-f7l4ty2j	447	2	passage	passage	NN
cord-002542-f7l4ty2j	447	3	in	in	IN
cord-002542-f7l4ty2j	447	4	each	each	DT
cord-002542-f7l4ty2j	447	5	replicate	replicate	VBP
cord-002542-f7l4ty2j	447	6	as	as	RB
cord-002542-f7l4ty2j	447	7	well	well	RB
cord-002542-f7l4ty2j	447	8	as	as	IN
cord-002542-f7l4ty2j	447	9	the	the	DT
cord-002542-f7l4ty2j	447	10	inoculum	inoculum	NN
cord-002542-f7l4ty2j	447	11	is	be	VBZ
cord-002542-f7l4ty2j	447	12	shown	show	VBN
cord-002542-f7l4ty2j	447	13	.	.	.
cord-002542-f7l4ty2j	448	1	Output	output	NN
cord-002542-f7l4ty2j	448	2	format	format	NN
cord-002542-f7l4ty2j	448	3	,	,	,
cord-002542-f7l4ty2j	448	4	as	as	IN
cord-002542-f7l4ty2j	448	5	described	describe	VBN
cord-002542-f7l4ty2j	448	6	in	in	IN
cord-002542-f7l4ty2j	448	7	Routh	Routh	NNP
cord-002542-f7l4ty2j	448	8	et	et	NNP
cord-002542-f7l4ty2j	448	9	al	al	NNP
cord-002542-f7l4ty2j	448	10	.	.	.
cord-002542-f7l4ty2j	449	1	[	[	-LRB-
cord-002542-f7l4ty2j	449	2	32	32	CD
cord-002542-f7l4ty2j	449	3	]	]	-RRB-
cord-002542-f7l4ty2j	449	4	,	,	,
cord-002542-f7l4ty2j	449	5	is	be	VBZ
cord-002542-f7l4ty2j	449	6	given	give	VBN
cord-002542-f7l4ty2j	449	7	as	as	IN
cord-002542-f7l4ty2j	449	8	"	"	``
cord-002542-f7l4ty2j	449	9	DonorCoord_to_AcceptorCoord_#_Counts	donorcoord_to_acceptorcoord_#_count	NNS
cord-002542-f7l4ty2j	449	10	"	"	''
cord-002542-f7l4ty2j	449	11	.	.	.
cord-002542-f7l4ty2j	450	1	This	this	DT
cord-002542-f7l4ty2j	450	2	is	be	VBZ
cord-002542-f7l4ty2j	450	3	the	the	DT
cord-002542-f7l4ty2j	450	4	raw	raw	JJ
cord-002542-f7l4ty2j	450	5	data	datum	NNS
cord-002542-f7l4ty2j	450	6	used	use	VBN
cord-002542-f7l4ty2j	450	7	to	to	TO
cord-002542-f7l4ty2j	450	8	populate	populate	VB
cord-002542-f7l4ty2j	450	9	Table	Table	NNP
cord-002542-f7l4ty2j	450	10	1	1	CD
cord-002542-f7l4ty2j	450	11	and	and	CC
cord-002542-f7l4ty2j	450	12	S1	S1	NNP
cord-002542-f7l4ty2j	450	13	Table	Table	NNP
cord-002542-f7l4ty2j	450	14	.	.	.
cord-002542-f7l4ty2j	451	1	(	(	-LRB-
cord-002542-f7l4ty2j	451	2	ZIP	zip	NN
cord-002542-f7l4ty2j	451	3	)	)	-RRB-
cord-002542-f7l4ty2j	451	4	S2	S2	NNP
cord-002542-f7l4ty2j	451	5	Datafile	Datafile	NNP
cord-002542-f7l4ty2j	451	6	.	.	.
cord-002542-f7l4ty2j	452	1	Genomes	genome	NNS
cord-002542-f7l4ty2j	452	2	characterized	characterize	VBN
cord-002542-f7l4ty2j	452	3	by	by	IN
cord-002542-f7l4ty2j	452	4	MinION	MinION	VBG
cord-002542-f7l4ty2j	452	5	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	452	6	sequencing	sequencing	NN
cord-002542-f7l4ty2j	452	7	.	.	.
cord-002542-f7l4ty2j	453	1	Table	table	NN
cord-002542-f7l4ty2j	453	2	reports	report	VBZ
cord-002542-f7l4ty2j	453	3	the	the	DT
cord-002542-f7l4ty2j	453	4	annotated	annotate	VBN
cord-002542-f7l4ty2j	453	5	genomes	genome	NNS
cord-002542-f7l4ty2j	453	6	(	(	-LRB-
cord-002542-f7l4ty2j	453	7	wild	wild	JJ
cord-002542-f7l4ty2j	453	8	-	-	HYPH
cord-002542-f7l4ty2j	453	9	type	type	NN
cord-002542-f7l4ty2j	453	10	or	or	CC
cord-002542-f7l4ty2j	453	11	defective	defective	JJ
cord-002542-f7l4ty2j	453	12	)	)	-RRB-
cord-002542-f7l4ty2j	453	13	and	and	CC
cord-002542-f7l4ty2j	453	14	the	the	DT
cord-002542-f7l4ty2j	453	15	number	number	NN
cord-002542-f7l4ty2j	453	16	of	of	IN
cord-002542-f7l4ty2j	453	17	mapped	map	VBN
cord-002542-f7l4ty2j	453	18	reads	read	VBZ
cord-002542-f7l4ty2j	453	19	in	in	IN
cord-002542-f7l4ty2j	453	20	each	each	DT
cord-002542-f7l4ty2j	453	21	passage	passage	NN
cord-002542-f7l4ty2j	453	22	.	.	.
cord-002542-f7l4ty2j	454	1	This	this	DT
cord-002542-f7l4ty2j	454	2	the	the	DT
cord-002542-f7l4ty2j	454	3	raw	raw	JJ
cord-002542-f7l4ty2j	454	4	data	datum	NNS
cord-002542-f7l4ty2j	454	5	used	use	VBN
cord-002542-f7l4ty2j	454	6	to	to	TO
cord-002542-f7l4ty2j	454	7	populate	populate	VB
cord-002542-f7l4ty2j	454	8	the	the	DT
cord-002542-f7l4ty2j	454	9	stacked	stack	VBN
cord-002542-f7l4ty2j	454	10	-	-	HYPH
cord-002542-f7l4ty2j	454	11	area	area	NN
cord-002542-f7l4ty2j	454	12	plots	plot	NNS
cord-002542-f7l4ty2j	454	13	in	in	IN
cord-002542-f7l4ty2j	454	14	Fig	Fig	NNP
cord-002542-f7l4ty2j	454	15	6	6	CD
cord-002542-f7l4ty2j	454	16	and	and	CC
cord-002542-f7l4ty2j	454	17	S6	S6	NNP
cord-002542-f7l4ty2j	454	18	Fig	Fig	NNP
cord-002542-f7l4ty2j	454	19	.	.	.
cord-002542-f7l4ty2j	454	20	 	 	_SP
cord-002542-f7l4ty2j	455	1	(	(	-LRB-
cord-002542-f7l4ty2j	455	2	XLSX	XLSX	NNP
cord-002542-f7l4ty2j	455	3	)	)	-RRB-
cord-002542-f7l4ty2j	455	4	 	 	_SP
cord-002542-f7l4ty2j	456	1	Chimeric	chimeric	JJ
cord-002542-f7l4ty2j	456	2	16S	16S	NNP
cord-002542-f7l4ty2j	456	3	rRNA	rrna	NN
cord-002542-f7l4ty2j	456	4	sequence	sequence	NN
cord-002542-f7l4ty2j	456	5	formation	formation	NN
cord-002542-f7l4ty2j	456	6	and	and	CC
cord-002542-f7l4ty2j	456	7	detection	detection	NN
cord-002542-f7l4ty2j	456	8	in	in	IN
cord-002542-f7l4ty2j	456	9	Sanger	Sanger	NNP
cord-002542-f7l4ty2j	456	10	and	and	CC
cord-002542-f7l4ty2j	456	11	454-pyrosequenced	454-pyrosequenced	CD
cord-002542-f7l4ty2j	456	12	PCR	PCR	NNP
cord-002542-f7l4ty2j	456	13	amplicons	amplicon	NNS
cord-002542-f7l4ty2j	457	1	Why	why	WRB
cord-002542-f7l4ty2j	457	2	do	do	VBP
cord-002542-f7l4ty2j	457	3	RNA	RNA	NNP
cord-002542-f7l4ty2j	457	4	viruses	virus	NNS
cord-002542-f7l4ty2j	457	5	recombine	recombine	VB
cord-002542-f7l4ty2j	457	6	?	?	.
cord-002542-f7l4ty2j	458	1	The	the	DT
cord-002542-f7l4ty2j	458	2	mechanism	mechanism	NN
cord-002542-f7l4ty2j	458	3	of	of	IN
cord-002542-f7l4ty2j	458	4	RNA	RNA	NNP
cord-002542-f7l4ty2j	458	5	recombination	recombination	NN
cord-002542-f7l4ty2j	458	6	in	in	IN
cord-002542-f7l4ty2j	458	7	poliovirus	poliovirus	NN
cord-002542-f7l4ty2j	458	8	RNA	RNA	NNP
cord-002542-f7l4ty2j	458	9	recombination	recombination	NN
cord-002542-f7l4ty2j	458	10	in	in	IN
cord-002542-f7l4ty2j	458	11	vivo	vivo	NN
cord-002542-f7l4ty2j	458	12	in	in	IN
cord-002542-f7l4ty2j	458	13	the	the	DT
cord-002542-f7l4ty2j	458	14	absence	absence	NN
cord-002542-f7l4ty2j	458	15	of	of	IN
cord-002542-f7l4ty2j	458	16	viral	viral	JJ
cord-002542-f7l4ty2j	458	17	replication	replication	NN
cord-002542-f7l4ty2j	458	18	Sequencing	sequencing	NN
cord-002542-f7l4ty2j	458	19	and	and	CC
cord-002542-f7l4ty2j	458	20	analyses	analysis	NNS
cord-002542-f7l4ty2j	458	21	of	of	IN
cord-002542-f7l4ty2j	458	22	all	all	DT
cord-002542-f7l4ty2j	458	23	known	know	VBN
cord-002542-f7l4ty2j	458	24	human	human	JJ
cord-002542-f7l4ty2j	458	25	rhinovirus	rhinovirus	NN
cord-002542-f7l4ty2j	458	26	genomes	genome	NNS
cord-002542-f7l4ty2j	458	27	reveal	reveal	VBP
cord-002542-f7l4ty2j	458	28	structure	structure	NN
cord-002542-f7l4ty2j	458	29	and	and	CC
cord-002542-f7l4ty2j	458	30	evolution	evolution	NN
cord-002542-f7l4ty2j	458	31	Widespread	widespread	JJ
cord-002542-f7l4ty2j	458	32	intra	intra	JJ
cord-002542-f7l4ty2j	458	33	-	-	JJ
cord-002542-f7l4ty2j	458	34	serotype	serotype	JJ
cord-002542-f7l4ty2j	458	35	recombination	recombination	NN
cord-002542-f7l4ty2j	458	36	in	in	IN
cord-002542-f7l4ty2j	458	37	natural	natural	JJ
cord-002542-f7l4ty2j	458	38	populations	population	NNS
cord-002542-f7l4ty2j	458	39	of	of	IN
cord-002542-f7l4ty2j	458	40	dengue	dengue	NN
cord-002542-f7l4ty2j	458	41	virus	virus	NN
cord-002542-f7l4ty2j	458	42	Long	long	JJ
cord-002542-f7l4ty2j	458	43	-	-	HYPH
cord-002542-f7l4ty2j	458	44	term	term	NN
cord-002542-f7l4ty2j	458	45	circulation	circulation	NN
cord-002542-f7l4ty2j	458	46	of	of	IN
cord-002542-f7l4ty2j	458	47	vaccine	vaccine	NN
cord-002542-f7l4ty2j	458	48	-	-	HYPH
cord-002542-f7l4ty2j	458	49	derived	derive	VBN
cord-002542-f7l4ty2j	458	50	poliovirus	poliovirus	NN
cord-002542-f7l4ty2j	458	51	that	that	WDT
cord-002542-f7l4ty2j	458	52	causes	cause	VBZ
cord-002542-f7l4ty2j	458	53	paralytic	paralytic	JJ
cord-002542-f7l4ty2j	458	54	disease	disease	NN
cord-002542-f7l4ty2j	458	55	Nucleotide	nucleotide	JJ
cord-002542-f7l4ty2j	458	56	-	-	HYPH
cord-002542-f7l4ty2j	458	57	resolution	resolution	NN
cord-002542-f7l4ty2j	458	58	profiling	profiling	NN
cord-002542-f7l4ty2j	458	59	of	of	IN
cord-002542-f7l4ty2j	458	60	RNA	RNA	NNP
cord-002542-f7l4ty2j	458	61	recombination	recombination	NN
cord-002542-f7l4ty2j	458	62	in	in	IN
cord-002542-f7l4ty2j	458	63	the	the	DT
cord-002542-f7l4ty2j	458	64	encapsidated	encapsidated	JJ
cord-002542-f7l4ty2j	458	65	genome	genome	NN
cord-002542-f7l4ty2j	458	66	of	of	IN
cord-002542-f7l4ty2j	458	67	a	a	DT
cord-002542-f7l4ty2j	458	68	eukaryotic	eukaryotic	JJ
cord-002542-f7l4ty2j	458	69	RNA	RNA	NNP
cord-002542-f7l4ty2j	458	70	virus	virus	NN
cord-002542-f7l4ty2j	458	71	by	by	IN
cord-002542-f7l4ty2j	458	72	next	next	JJ
cord-002542-f7l4ty2j	458	73	-	-	HYPH
cord-002542-f7l4ty2j	458	74	generation	generation	NN
cord-002542-f7l4ty2j	458	75	sequencing	sequencing	NN
cord-002542-f7l4ty2j	458	76	Defective	defective	JJ
cord-002542-f7l4ty2j	458	77	Interfering	Interfering	NNP
cord-002542-f7l4ty2j	458	78	RNAs	rna	NNS
cord-002542-f7l4ty2j	458	79	:	:	:
cord-002542-f7l4ty2j	458	80	Foes	foe	NNS
cord-002542-f7l4ty2j	458	81	of	of	IN
cord-002542-f7l4ty2j	458	82	Viruses	virus	NNS
cord-002542-f7l4ty2j	458	83	and	and	CC
cord-002542-f7l4ty2j	458	84	Friends	friend	NNS
cord-002542-f7l4ty2j	458	85	of	of	IN
cord-002542-f7l4ty2j	458	86	Virologists	Virologists	NNP
cord-002542-f7l4ty2j	458	87	Defective	defective	JJ
cord-002542-f7l4ty2j	458	88	viral	viral	JJ
cord-002542-f7l4ty2j	458	89	particles	particle	NNS
cord-002542-f7l4ty2j	458	90	and	and	CC
cord-002542-f7l4ty2j	458	91	viral	viral	JJ
cord-002542-f7l4ty2j	458	92	disease	disease	NN
cord-002542-f7l4ty2j	458	93	processes	process	NNS
cord-002542-f7l4ty2j	459	1	A	a	DT
cord-002542-f7l4ty2j	459	2	Defective	defective	JJ
cord-002542-f7l4ty2j	460	1	Interfering	interfere	VBG
cord-002542-f7l4ty2j	460	2	Influenza	Influenza	NNP
cord-002542-f7l4ty2j	460	3	RNA	RNA	NNP
cord-002542-f7l4ty2j	460	4	Inhibits	inhibit	VBZ
cord-002542-f7l4ty2j	460	5	Infectious	Infectious	NNP
cord-002542-f7l4ty2j	460	6	Influenza	Influenza	NNP
cord-002542-f7l4ty2j	460	7	Virus	Virus	NNP
cord-002542-f7l4ty2j	460	8	Replication	Replication	NNP
cord-002542-f7l4ty2j	460	9	in	in	IN
cord-002542-f7l4ty2j	460	10	Human	Human	NNP
cord-002542-f7l4ty2j	460	11	Respiratory	respiratory	JJ
cord-002542-f7l4ty2j	460	12	Tract	Tract	NNP
cord-002542-f7l4ty2j	460	13	Cells	cell	NNS
cord-002542-f7l4ty2j	460	14	:	:	:
cord-002542-f7l4ty2j	461	1	A	a	DT
cord-002542-f7l4ty2j	461	2	Potential	potential	JJ
cord-002542-f7l4ty2j	461	3	New	New	NNP
cord-002542-f7l4ty2j	461	4	Human	Human	NNP
cord-002542-f7l4ty2j	461	5	Antiviral	Antiviral	NNP
cord-002542-f7l4ty2j	461	6	Immunostimulatory	Immunostimulatory	NNP
cord-002542-f7l4ty2j	461	7	Defective	defective	JJ
cord-002542-f7l4ty2j	461	8	Viral	Viral	NNP
cord-002542-f7l4ty2j	461	9	Genomes	Genomes	NNPS
cord-002542-f7l4ty2j	461	10	from	from	IN
cord-002542-f7l4ty2j	461	11	Respiratory	respiratory	JJ
cord-002542-f7l4ty2j	461	12	Syncytial	Syncytial	NNP
cord-002542-f7l4ty2j	461	13	Virus	virus	NN
cord-002542-f7l4ty2j	461	14	Promote	promote	VB
cord-002542-f7l4ty2j	461	15	a	a	DT
cord-002542-f7l4ty2j	461	16	Strong	strong	JJ
cord-002542-f7l4ty2j	461	17	Innate	Innate	NNP
cord-002542-f7l4ty2j	461	18	Antiviral	Antiviral	NNP
cord-002542-f7l4ty2j	461	19	Response	response	NN
cord-002542-f7l4ty2j	461	20	during	during	IN
cord-002542-f7l4ty2j	461	21	Infection	Infection	NNP
cord-002542-f7l4ty2j	461	22	in	in	IN
cord-002542-f7l4ty2j	461	23	Mice	Mice	NNP
cord-002542-f7l4ty2j	461	24	and	and	CC
cord-002542-f7l4ty2j	461	25	Humans	Humans	NNPS
cord-002542-f7l4ty2j	461	26	Effects	effect	NNS
cord-002542-f7l4ty2j	461	27	of	of	IN
cord-002542-f7l4ty2j	461	28	defective	defective	JJ
cord-002542-f7l4ty2j	461	29	interfering	interfere	VBG
cord-002542-f7l4ty2j	461	30	viruses	virus	NNS
cord-002542-f7l4ty2j	461	31	on	on	IN
cord-002542-f7l4ty2j	461	32	virus	virus	NN
cord-002542-f7l4ty2j	461	33	replication	replication	NN
cord-002542-f7l4ty2j	461	34	and	and	CC
cord-002542-f7l4ty2j	461	35	pathogenesis	pathogenesis	NN
cord-002542-f7l4ty2j	461	36	in	in	IN
cord-002542-f7l4ty2j	461	37	vitro	vitro	FW
cord-002542-f7l4ty2j	461	38	and	and	CC
cord-002542-f7l4ty2j	461	39	in	in	IN
cord-002542-f7l4ty2j	461	40	vivo	vivo	NN
cord-002542-f7l4ty2j	461	41	Defective	defective	JJ
cord-002542-f7l4ty2j	461	42	viral	viral	JJ
cord-002542-f7l4ty2j	461	43	genomes	genome	NNS
cord-002542-f7l4ty2j	461	44	arising	arise	VBG
cord-002542-f7l4ty2j	461	45	in	in	IN
cord-002542-f7l4ty2j	461	46	vivo	vivo	NN
cord-002542-f7l4ty2j	461	47	provide	provide	VBP
cord-002542-f7l4ty2j	461	48	critical	critical	JJ
cord-002542-f7l4ty2j	461	49	danger	danger	NN
cord-002542-f7l4ty2j	461	50	signals	signal	NNS
cord-002542-f7l4ty2j	461	51	for	for	IN
cord-002542-f7l4ty2j	461	52	the	the	DT
cord-002542-f7l4ty2j	461	53	triggering	triggering	NN
cord-002542-f7l4ty2j	461	54	of	of	IN
cord-002542-f7l4ty2j	461	55	lung	lung	NN
cord-002542-f7l4ty2j	461	56	antiviral	antiviral	JJ
cord-002542-f7l4ty2j	461	57	immunity	immunity	NN
cord-002542-f7l4ty2j	461	58	Engineering	Engineering	NNP
cord-002542-f7l4ty2j	461	59	of	of	IN
cord-002542-f7l4ty2j	461	60	homologous	homologous	JJ
cord-002542-f7l4ty2j	461	61	recombination	recombination	NN
cord-002542-f7l4ty2j	461	62	hotspots	hotspot	NNS
cord-002542-f7l4ty2j	461	63	with	with	IN
cord-002542-f7l4ty2j	461	64	AU	AU	NNP
cord-002542-f7l4ty2j	461	65	-	-	HYPH
cord-002542-f7l4ty2j	461	66	rich	rich	JJ
cord-002542-f7l4ty2j	461	67	sequences	sequence	NNS
cord-002542-f7l4ty2j	461	68	in	in	IN
cord-002542-f7l4ty2j	461	69	brome	brome	NNP
cord-002542-f7l4ty2j	461	70	mosaic	mosaic	NNP
cord-002542-f7l4ty2j	461	71	virus	virus	NN
cord-002542-f7l4ty2j	461	72	Identification	identification	NN
cord-002542-f7l4ty2j	461	73	and	and	CC
cord-002542-f7l4ty2j	461	74	manipulation	manipulation	NN
cord-002542-f7l4ty2j	461	75	of	of	IN
cord-002542-f7l4ty2j	461	76	the	the	DT
cord-002542-f7l4ty2j	461	77	molecular	molecular	JJ
cord-002542-f7l4ty2j	461	78	determinants	determinant	NNS
cord-002542-f7l4ty2j	461	79	influencing	influence	VBG
cord-002542-f7l4ty2j	461	80	poliovirus	poliovirus	NN
cord-002542-f7l4ty2j	461	81	recombination	recombination	NN
cord-002542-f7l4ty2j	461	82	Defective	defective	JJ
cord-002542-f7l4ty2j	461	83	interfering	interfere	VBG
cord-002542-f7l4ty2j	461	84	influenza	influenza	NN
cord-002542-f7l4ty2j	461	85	virus	virus	NN
cord-002542-f7l4ty2j	461	86	RNAs	rna	NNS
cord-002542-f7l4ty2j	461	87	:	:	:
cord-002542-f7l4ty2j	461	88	time	time	NN
cord-002542-f7l4ty2j	461	89	to	to	TO
cord-002542-f7l4ty2j	461	90	reevaluate	reevaluate	VB
cord-002542-f7l4ty2j	461	91	their	-PRON-	PRP$
cord-002542-f7l4ty2j	461	92	clinical	clinical	JJ
cord-002542-f7l4ty2j	461	93	potential	potential	NN
cord-002542-f7l4ty2j	461	94	as	as	IN
cord-002542-f7l4ty2j	461	95	broad	broad	JJ
cord-002542-f7l4ty2j	461	96	-	-	HYPH
cord-002542-f7l4ty2j	461	97	spectrum	spectrum	NN
cord-002542-f7l4ty2j	461	98	antivirals	antiviral	NNS
cord-002542-f7l4ty2j	461	99	?	?	.
cord-002542-f7l4ty2j	462	1	Analysis	analysis	NN
cord-002542-f7l4ty2j	462	2	of	of	IN
cord-002542-f7l4ty2j	462	3	efficiently	efficiently	RB
cord-002542-f7l4ty2j	462	4	packaged	package	VBN
cord-002542-f7l4ty2j	462	5	defective	defective	JJ
cord-002542-f7l4ty2j	462	6	interfering	interfere	VBG
cord-002542-f7l4ty2j	462	7	RNAs	rna	NNS
cord-002542-f7l4ty2j	462	8	of	of	IN
cord-002542-f7l4ty2j	462	9	murine	murine	JJ
cord-002542-f7l4ty2j	462	10	coronavirus	coronavirus	NN
cord-002542-f7l4ty2j	462	11	:	:	:
cord-002542-f7l4ty2j	462	12	localization	localization	NN
cord-002542-f7l4ty2j	462	13	of	of	IN
cord-002542-f7l4ty2j	462	14	a	a	DT
cord-002542-f7l4ty2j	462	15	possible	possible	JJ
cord-002542-f7l4ty2j	462	16	RNA	rna	NN
cord-002542-f7l4ty2j	462	17	-	-	HYPH
cord-002542-f7l4ty2j	462	18	packaging	packaging	NN
cord-002542-f7l4ty2j	462	19	signal	signal	NN
cord-002542-f7l4ty2j	462	20	Defective	defective	JJ
cord-002542-f7l4ty2j	462	21	virus	virus	NN
cord-002542-f7l4ty2j	462	22	drives	drive	VBZ
cord-002542-f7l4ty2j	462	23	human	human	JJ
cord-002542-f7l4ty2j	462	24	immunodeficiency	immunodeficiency	NN
cord-002542-f7l4ty2j	462	25	virus	virus	NN
cord-002542-f7l4ty2j	462	26	infection	infection	NN
cord-002542-f7l4ty2j	462	27	,	,	,
cord-002542-f7l4ty2j	462	28	persistence	persistence	NN
cord-002542-f7l4ty2j	462	29	,	,	,
cord-002542-f7l4ty2j	462	30	and	and	CC
cord-002542-f7l4ty2j	462	31	pathogenesis	pathogenesis	NN
cord-002542-f7l4ty2j	462	32	Biased	bias	VBN
cord-002542-f7l4ty2j	462	33	hypermutation	hypermutation	NN
cord-002542-f7l4ty2j	462	34	and	and	CC
cord-002542-f7l4ty2j	462	35	other	other	JJ
cord-002542-f7l4ty2j	462	36	genetic	genetic	JJ
cord-002542-f7l4ty2j	462	37	changes	change	NNS
cord-002542-f7l4ty2j	462	38	in	in	IN
cord-002542-f7l4ty2j	462	39	defective	defective	JJ
cord-002542-f7l4ty2j	462	40	measles	measle	NNS
cord-002542-f7l4ty2j	462	41	viruses	virus	NNS
cord-002542-f7l4ty2j	462	42	in	in	IN
cord-002542-f7l4ty2j	462	43	human	human	JJ
cord-002542-f7l4ty2j	462	44	brain	brain	NN
cord-002542-f7l4ty2j	462	45	infections	infection	NNS
cord-002542-f7l4ty2j	462	46	Defective	defective	JJ
cord-002542-f7l4ty2j	462	47	interfering	interfere	VBG
cord-002542-f7l4ty2j	462	48	viral	viral	JJ
cord-002542-f7l4ty2j	462	49	particles	particle	NNS
cord-002542-f7l4ty2j	462	50	in	in	IN
cord-002542-f7l4ty2j	462	51	acute	acute	JJ
cord-002542-f7l4ty2j	462	52	dengue	dengue	NN
cord-002542-f7l4ty2j	462	53	infections	infection	NNS
cord-002542-f7l4ty2j	462	54	Genetic	genetic	JJ
cord-002542-f7l4ty2j	462	55	analysis	analysis	NN
cord-002542-f7l4ty2j	462	56	of	of	IN
cord-002542-f7l4ty2j	462	57	hepatitis	hepatitis	NN
cord-002542-f7l4ty2j	462	58	C	C	NNP
cord-002542-f7l4ty2j	462	59	virus	virus	NN
cord-002542-f7l4ty2j	462	60	with	with	IN
cord-002542-f7l4ty2j	462	61	defective	defective	JJ
cord-002542-f7l4ty2j	462	62	genome	genome	NN
cord-002542-f7l4ty2j	462	63	and	and	CC
cord-002542-f7l4ty2j	462	64	its	-PRON-	PRP$
cord-002542-f7l4ty2j	462	65	infectivity	infectivity	NN
cord-002542-f7l4ty2j	462	66	in	in	IN
cord-002542-f7l4ty2j	462	67	vitro	vitro	FW
cord-002542-f7l4ty2j	462	68	Internally	internally	RB
cord-002542-f7l4ty2j	462	69	deleted	delete	VBN
cord-002542-f7l4ty2j	462	70	WNV	WNV	NNP
cord-002542-f7l4ty2j	462	71	genomes	genome	NNS
cord-002542-f7l4ty2j	462	72	isolated	isolate	VBN
cord-002542-f7l4ty2j	462	73	from	from	IN
cord-002542-f7l4ty2j	462	74	exotic	exotic	JJ
cord-002542-f7l4ty2j	462	75	birds	bird	NNS
cord-002542-f7l4ty2j	462	76	in	in	IN
cord-002542-f7l4ty2j	462	77	New	New	NNP
cord-002542-f7l4ty2j	462	78	Mexico	Mexico	NNP
cord-002542-f7l4ty2j	462	79	:	:	:
cord-002542-f7l4ty2j	462	80	function	function	NN
cord-002542-f7l4ty2j	462	81	in	in	IN
cord-002542-f7l4ty2j	462	82	cells	cell	NNS
cord-002542-f7l4ty2j	462	83	,	,	,
cord-002542-f7l4ty2j	462	84	mosquitoes	mosquito	NNS
cord-002542-f7l4ty2j	462	85	,	,	,
cord-002542-f7l4ty2j	462	86	and	and	CC
cord-002542-f7l4ty2j	462	87	mice	mouse	NNS
cord-002542-f7l4ty2j	462	88	Sequence	sequence	NN
cord-002542-f7l4ty2j	462	89	analysis	analysis	NN
cord-002542-f7l4ty2j	462	90	of	of	IN
cord-002542-f7l4ty2j	462	91	in	in	IN
cord-002542-f7l4ty2j	462	92	vivo	vivo	NN
cord-002542-f7l4ty2j	462	93	defective	defective	JJ
cord-002542-f7l4ty2j	462	94	interfering	interfere	VBG
cord-002542-f7l4ty2j	462	95	-	-	HYPH
cord-002542-f7l4ty2j	462	96	like	like	JJ
cord-002542-f7l4ty2j	462	97	RNA	RNA	NNP
cord-002542-f7l4ty2j	462	98	of	of	IN
cord-002542-f7l4ty2j	462	99	influenza	influenza	NN
cord-002542-f7l4ty2j	462	100	A	a	DT
cord-002542-f7l4ty2j	462	101	H1N1	H1N1	NNP
cord-002542-f7l4ty2j	462	102	pandemic	pandemic	NN
cord-002542-f7l4ty2j	462	103	virus	virus	NN
cord-002542-f7l4ty2j	462	104	Flock	Flock	NNP
cord-002542-f7l4ty2j	462	105	House	House	NNP
cord-002542-f7l4ty2j	462	106	virus	virus	NN
cord-002542-f7l4ty2j	462	107	:	:	:
cord-002542-f7l4ty2j	462	108	a	a	DT
cord-002542-f7l4ty2j	462	109	nodavirus	nodavirus	NN
cord-002542-f7l4ty2j	462	110	isolated	isolate	VBN
cord-002542-f7l4ty2j	462	111	from	from	IN
cord-002542-f7l4ty2j	462	112	Costelytra	Costelytra	NNP
cord-002542-f7l4ty2j	462	113	zealandica	zealandica	NNP
cord-002542-f7l4ty2j	463	1	(	(	-LRB-
cord-002542-f7l4ty2j	463	2	White	White	NNP
cord-002542-f7l4ty2j	463	3	)	)	-RRB-
cord-002542-f7l4ty2j	464	1	(	(	-LRB-
cord-002542-f7l4ty2j	464	2	Coleoptera	Coleoptera	NNP
cord-002542-f7l4ty2j	464	3	:	:	:
cord-002542-f7l4ty2j	464	4	Scarabaeidae	scarabaeidae	NN
cord-002542-f7l4ty2j	464	5	)	)	-RRB-
cord-002542-f7l4ty2j	464	6	Replication	replication	NN
cord-002542-f7l4ty2j	464	7	of	of	IN
cord-002542-f7l4ty2j	464	8	flock	flock	NN
cord-002542-f7l4ty2j	464	9	house	house	NN
cord-002542-f7l4ty2j	464	10	virus	virus	NN
cord-002542-f7l4ty2j	464	11	in	in	IN
cord-002542-f7l4ty2j	464	12	three	three	CD
cord-002542-f7l4ty2j	464	13	genera	genus	NNS
cord-002542-f7l4ty2j	464	14	of	of	IN
cord-002542-f7l4ty2j	464	15	medically	medically	RB
cord-002542-f7l4ty2j	464	16	important	important	JJ
cord-002542-f7l4ty2j	464	17	insects	insect	NNS
cord-002542-f7l4ty2j	464	18	Flock	Flock	NNP
cord-002542-f7l4ty2j	464	19	house	house	NN
cord-002542-f7l4ty2j	464	20	virus	virus	NN
cord-002542-f7l4ty2j	464	21	:	:	:
cord-002542-f7l4ty2j	464	22	a	a	DT
cord-002542-f7l4ty2j	464	23	model	model	NN
cord-002542-f7l4ty2j	464	24	system	system	NN
cord-002542-f7l4ty2j	464	25	for	for	IN
cord-002542-f7l4ty2j	464	26	understanding	understand	VBG
cord-002542-f7l4ty2j	464	27	non	non	JJ
cord-002542-f7l4ty2j	464	28	-	-	JJ
cord-002542-f7l4ty2j	464	29	enveloped	enveloped	JJ
cord-002542-f7l4ty2j	464	30	virus	virus	NN
cord-002542-f7l4ty2j	464	31	entry	entry	NN
cord-002542-f7l4ty2j	464	32	and	and	CC
cord-002542-f7l4ty2j	464	33	membrane	membrane	NN
cord-002542-f7l4ty2j	464	34	penetration	penetration	NN
cord-002542-f7l4ty2j	465	1	Induction	induction	NN
cord-002542-f7l4ty2j	465	2	and	and	CC
cord-002542-f7l4ty2j	465	3	suppression	suppression	NN
cord-002542-f7l4ty2j	465	4	of	of	IN
cord-002542-f7l4ty2j	465	5	RNA	RNA	NNP
cord-002542-f7l4ty2j	465	6	silencing	silencing	NN
cord-002542-f7l4ty2j	465	7	by	by	IN
cord-002542-f7l4ty2j	465	8	an	an	DT
cord-002542-f7l4ty2j	465	9	animal	animal	NN
cord-002542-f7l4ty2j	465	10	virus	virus	NN
cord-002542-f7l4ty2j	465	11	Evidence	evidence	NN
cord-002542-f7l4ty2j	465	12	that	that	IN
cord-002542-f7l4ty2j	465	13	the	the	DT
cord-002542-f7l4ty2j	465	14	packaging	packaging	NN
cord-002542-f7l4ty2j	465	15	signal	signal	NN
cord-002542-f7l4ty2j	465	16	for	for	IN
cord-002542-f7l4ty2j	465	17	nodaviral	nodaviral	NNP
cord-002542-f7l4ty2j	465	18	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	465	19	is	be	VBZ
cord-002542-f7l4ty2j	465	20	a	a	DT
cord-002542-f7l4ty2j	465	21	bulged	bulge	VBN
cord-002542-f7l4ty2j	465	22	stem	stem	NN
cord-002542-f7l4ty2j	465	23	-	-	HYPH
cord-002542-f7l4ty2j	465	24	loop	loop	NN
cord-002542-f7l4ty2j	465	25	cis	cis	NNP
cord-002542-f7l4ty2j	465	26	-	-	HYPH
cord-002542-f7l4ty2j	465	27	acting	act	VBG
cord-002542-f7l4ty2j	465	28	requirements	requirement	NNS
cord-002542-f7l4ty2j	465	29	for	for	IN
cord-002542-f7l4ty2j	465	30	the	the	DT
cord-002542-f7l4ty2j	465	31	replication	replication	NN
cord-002542-f7l4ty2j	465	32	of	of	IN
cord-002542-f7l4ty2j	465	33	flock	flock	NN
cord-002542-f7l4ty2j	465	34	house	house	NN
cord-002542-f7l4ty2j	465	35	virus	virus	NN
cord-002542-f7l4ty2j	465	36	RNA	RNA	NNP
cord-002542-f7l4ty2j	465	37	2	2	CD
cord-002542-f7l4ty2j	465	38	Molecular	molecular	JJ
cord-002542-f7l4ty2j	465	39	characterization	characterization	NN
cord-002542-f7l4ty2j	465	40	of	of	IN
cord-002542-f7l4ty2j	465	41	Drosophila	drosophila	JJ
cord-002542-f7l4ty2j	465	42	cells	cell	NNS
cord-002542-f7l4ty2j	465	43	persistently	persistently	RB
cord-002542-f7l4ty2j	465	44	infected	infect	VBN
cord-002542-f7l4ty2j	465	45	with	with	IN
cord-002542-f7l4ty2j	465	46	Flock	Flock	NNP
cord-002542-f7l4ty2j	465	47	House	House	NNP
cord-002542-f7l4ty2j	465	48	virus	virus	NN
cord-002542-f7l4ty2j	465	49	Discovery	Discovery	NNP
cord-002542-f7l4ty2j	465	50	of	of	IN
cord-002542-f7l4ty2j	465	51	functional	functional	JJ
cord-002542-f7l4ty2j	465	52	genomic	genomic	JJ
cord-002542-f7l4ty2j	465	53	motifs	motif	NNS
cord-002542-f7l4ty2j	465	54	in	in	IN
cord-002542-f7l4ty2j	465	55	viruses	virus	NNS
cord-002542-f7l4ty2j	465	56	with	with	IN
cord-002542-f7l4ty2j	465	57	ViReMa	virema	FW
cord-002542-f7l4ty2j	465	58	-	-	HYPH
cord-002542-f7l4ty2j	465	59	a	a	DT
cord-002542-f7l4ty2j	465	60	Virus	Virus	NNP
cord-002542-f7l4ty2j	465	61	Recombination	Recombination	NNP
cord-002542-f7l4ty2j	465	62	Mapper	mapper	NN
cord-002542-f7l4ty2j	465	63	-	-	HYPH
cord-002542-f7l4ty2j	465	64	for	for	IN
cord-002542-f7l4ty2j	465	65	analysis	analysis	NN
cord-002542-f7l4ty2j	465	66	of	of	IN
cord-002542-f7l4ty2j	465	67	next	next	JJ
cord-002542-f7l4ty2j	465	68	-	-	HYPH
cord-002542-f7l4ty2j	465	69	generation	generation	NN
cord-002542-f7l4ty2j	465	70	sequencing	sequencing	NN
cord-002542-f7l4ty2j	465	71	data	datum	NNS
cord-002542-f7l4ty2j	465	72	RNA	RNA	NNP
cord-002542-f7l4ty2j	465	73	-	-	HYPH
cord-002542-f7l4ty2j	465	74	mediated	mediate	VBN
cord-002542-f7l4ty2j	465	75	interference	interference	NN
cord-002542-f7l4ty2j	465	76	and	and	CC
cord-002542-f7l4ty2j	465	77	reverse	reverse	VB
cord-002542-f7l4ty2j	465	78	transcription	transcription	NN
cord-002542-f7l4ty2j	465	79	control	control	NN
cord-002542-f7l4ty2j	465	80	the	the	DT
cord-002542-f7l4ty2j	465	81	persistence	persistence	NN
cord-002542-f7l4ty2j	465	82	of	of	IN
cord-002542-f7l4ty2j	465	83	RNA	RNA	NNP
cord-002542-f7l4ty2j	465	84	viruses	virus	NNS
cord-002542-f7l4ty2j	465	85	in	in	IN
cord-002542-f7l4ty2j	465	86	the	the	DT
cord-002542-f7l4ty2j	465	87	insect	insect	NN
cord-002542-f7l4ty2j	465	88	model	model	NN
cord-002542-f7l4ty2j	465	89	Drosophila	Drosophila	NNP
cord-002542-f7l4ty2j	465	90	Host	Host	NNP
cord-002542-f7l4ty2j	465	91	RNAs	rna	NNS
cord-002542-f7l4ty2j	465	92	,	,	,
cord-002542-f7l4ty2j	465	93	including	include	VBG
cord-002542-f7l4ty2j	465	94	transposons	transposon	NNS
cord-002542-f7l4ty2j	465	95	,	,	,
cord-002542-f7l4ty2j	466	1	are	be	VBP
cord-002542-f7l4ty2j	466	2	encapsidated	encapsidate	VBN
cord-002542-f7l4ty2j	466	3	by	by	IN
cord-002542-f7l4ty2j	466	4	a	a	DT
cord-002542-f7l4ty2j	466	5	eukaryotic	eukaryotic	JJ
cord-002542-f7l4ty2j	466	6	single	single	RB
cord-002542-f7l4ty2j	466	7	-	-	HYPH
cord-002542-f7l4ty2j	466	8	stranded	strand	VBN
cord-002542-f7l4ty2j	466	9	RNA	RNA	NNP
cord-002542-f7l4ty2j	466	10	virus	virus	NN
cord-002542-f7l4ty2j	466	11	ClickSeq	ClickSeq	NNP
cord-002542-f7l4ty2j	466	12	:	:	:
cord-002542-f7l4ty2j	467	1	Fragmentation	fragmentation	NN
cord-002542-f7l4ty2j	467	2	-	-	HYPH
cord-002542-f7l4ty2j	467	3	Free	Free	NNP
cord-002542-f7l4ty2j	467	4	Next	Next	NNP
cord-002542-f7l4ty2j	467	5	-	-	HYPH
cord-002542-f7l4ty2j	467	6	Generation	Generation	NNP
cord-002542-f7l4ty2j	467	7	Sequencing	Sequencing	NNP
cord-002542-f7l4ty2j	467	8	via	via	IN
cord-002542-f7l4ty2j	467	9	Click	Click	NNP
cord-002542-f7l4ty2j	467	10	Ligation	Ligation	NNP
cord-002542-f7l4ty2j	467	11	of	of	IN
cord-002542-f7l4ty2j	467	12	Adaptors	adaptor	NNS
cord-002542-f7l4ty2j	468	1	to	to	IN
cord-002542-f7l4ty2j	468	2	Stochastically	Stochastically	NNP
cord-002542-f7l4ty2j	468	3	Terminated	terminate	VBN
cord-002542-f7l4ty2j	468	4	3'-Azido	3'-Azido	NNP
cord-002542-f7l4ty2j	469	1	cDNAs	cDNAs	.
cord-002542-f7l4ty2j	470	1	Solid	solid	JJ
cord-002542-f7l4ty2j	470	2	phase	phase	NN
cord-002542-f7l4ty2j	470	3	click	click	VBP
cord-002542-f7l4ty2j	470	4	ligation	ligation	NN
cord-002542-f7l4ty2j	470	5	for	for	IN
cord-002542-f7l4ty2j	470	6	the	the	DT
cord-002542-f7l4ty2j	470	7	synthesis	synthesis	NN
cord-002542-f7l4ty2j	470	8	of	of	IN
cord-002542-f7l4ty2j	470	9	very	very	RB
cord-002542-f7l4ty2j	470	10	long	long	JJ
cord-002542-f7l4ty2j	470	11	oligonucleotides	oligonucleotide	NNS
cord-002542-f7l4ty2j	471	1	A	a	DT
cord-002542-f7l4ty2j	471	2	first	first	JJ
cord-002542-f7l4ty2j	471	3	look	look	NN
cord-002542-f7l4ty2j	471	4	at	at	IN
cord-002542-f7l4ty2j	471	5	the	the	DT
cord-002542-f7l4ty2j	471	6	Oxford	Oxford	NNP
cord-002542-f7l4ty2j	471	7	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	471	8	MinION	minion	NN
cord-002542-f7l4ty2j	471	9	sequencer	sequencer	NN
cord-002542-f7l4ty2j	471	10	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	471	11	sequencing	sequencing	NN
cord-002542-f7l4ty2j	471	12	and	and	CC
cord-002542-f7l4ty2j	471	13	assembly	assembly	NN
cord-002542-f7l4ty2j	471	14	of	of	IN
cord-002542-f7l4ty2j	471	15	a	a	DT
cord-002542-f7l4ty2j	471	16	human	human	JJ
cord-002542-f7l4ty2j	471	17	genome	genome	NN
cord-002542-f7l4ty2j	471	18	with	with	IN
cord-002542-f7l4ty2j	471	19	ultra	ultra	JJ
cord-002542-f7l4ty2j	471	20	-	-	JJ
cord-002542-f7l4ty2j	471	21	long	long	JJ
cord-002542-f7l4ty2j	471	22	reads	read	VBZ
cord-002542-f7l4ty2j	471	23	Rapid	Rapid	NNP
cord-002542-f7l4ty2j	471	24	metagenomic	metagenomic	JJ
cord-002542-f7l4ty2j	471	25	identification	identification	NN
cord-002542-f7l4ty2j	471	26	of	of	IN
cord-002542-f7l4ty2j	471	27	viral	viral	JJ
cord-002542-f7l4ty2j	471	28	pathogens	pathogen	NNS
cord-002542-f7l4ty2j	471	29	in	in	IN
cord-002542-f7l4ty2j	471	30	clinical	clinical	JJ
cord-002542-f7l4ty2j	471	31	samples	sample	NNS
cord-002542-f7l4ty2j	471	32	by	by	IN
cord-002542-f7l4ty2j	471	33	real	real	JJ
cord-002542-f7l4ty2j	471	34	-	-	HYPH
cord-002542-f7l4ty2j	471	35	time	time	NN
cord-002542-f7l4ty2j	471	36	nanopore	nanopore	JJ
cord-002542-f7l4ty2j	471	37	sequencing	sequencing	NN
cord-002542-f7l4ty2j	471	38	analysis	analysis	NN
cord-002542-f7l4ty2j	471	39	Real	real	JJ
cord-002542-f7l4ty2j	471	40	-	-	HYPH
cord-002542-f7l4ty2j	471	41	time	time	NN
cord-002542-f7l4ty2j	471	42	,	,	,
cord-002542-f7l4ty2j	471	43	portable	portable	JJ
cord-002542-f7l4ty2j	471	44	genome	genome	NN
cord-002542-f7l4ty2j	471	45	sequencing	sequencing	NN
cord-002542-f7l4ty2j	471	46	for	for	IN
cord-002542-f7l4ty2j	471	47	Ebola	Ebola	NNP
cord-002542-f7l4ty2j	471	48	surveillance	surveillance	NN
cord-002542-f7l4ty2j	471	49	MinION	minion	XX
cord-002542-f7l4ty2j	471	50	nanopore	nanopore	JJ
cord-002542-f7l4ty2j	471	51	sequencing	sequencing	NN
cord-002542-f7l4ty2j	471	52	of	of	IN
cord-002542-f7l4ty2j	471	53	an	an	DT
cord-002542-f7l4ty2j	471	54	influenza	influenza	NN
cord-002542-f7l4ty2j	471	55	genome	genome	NN
cord-002542-f7l4ty2j	471	56	Highly	highly	RB
cord-002542-f7l4ty2j	471	57	parallel	parallel	JJ
cord-002542-f7l4ty2j	471	58	direct	direct	JJ
cord-002542-f7l4ty2j	471	59	RNA	rna	NN
cord-002542-f7l4ty2j	471	60	sequencing	sequencing	NN
cord-002542-f7l4ty2j	471	61	on	on	IN
cord-002542-f7l4ty2j	471	62	an	an	DT
cord-002542-f7l4ty2j	471	63	array	array	NN
cord-002542-f7l4ty2j	471	64	of	of	IN
cord-002542-f7l4ty2j	471	65	nanopores	nanopore	NNS
cord-002542-f7l4ty2j	471	66	.	.	.
cord-002542-f7l4ty2j	472	1	bioRxiv	biorxiv	RB
cord-002542-f7l4ty2j	473	1	Improved	improved	JJ
cord-002542-f7l4ty2j	473	2	data	data	NN
cord-002542-f7l4ty2j	473	3	analysis	analysis	NN
cord-002542-f7l4ty2j	473	4	for	for	IN
cord-002542-f7l4ty2j	473	5	the	the	DT
cord-002542-f7l4ty2j	473	6	MinION	MinION	NNP
cord-002542-f7l4ty2j	473	7	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	473	8	sequencer	sequencer	NN
cord-002542-f7l4ty2j	474	1	CoVaMa	covama	NN
cord-002542-f7l4ty2j	474	2	:	:	:
cord-002542-f7l4ty2j	474	3	Co	co	NN
cord-002542-f7l4ty2j	474	4	-	-	NN
cord-002542-f7l4ty2j	474	5	Variation	Variation	NNP
cord-002542-f7l4ty2j	474	6	Mapper	mapper	NN
cord-002542-f7l4ty2j	474	7	for	for	IN
cord-002542-f7l4ty2j	474	8	disequilibrium	disequilibrium	NN
cord-002542-f7l4ty2j	474	9	analysis	analysis	NN
cord-002542-f7l4ty2j	474	10	of	of	IN
cord-002542-f7l4ty2j	474	11	mutant	mutant	JJ
cord-002542-f7l4ty2j	474	12	loci	locus	NNS
cord-002542-f7l4ty2j	474	13	in	in	IN
cord-002542-f7l4ty2j	474	14	viral	viral	JJ
cord-002542-f7l4ty2j	474	15	populations	population	NNS
cord-002542-f7l4ty2j	474	16	using	use	VBG
cord-002542-f7l4ty2j	474	17	next	next	JJ
cord-002542-f7l4ty2j	474	18	-	-	HYPH
cord-002542-f7l4ty2j	474	19	generation	generation	NN
cord-002542-f7l4ty2j	474	20	sequence	sequence	NN
cord-002542-f7l4ty2j	474	21	data	data	NN
cord-002542-f7l4ty2j	474	22	Poly(A)-ClickSeq	Poly(A)-ClickSeq	NNP
cord-002542-f7l4ty2j	474	23	:	:	:
cord-002542-f7l4ty2j	474	24	click	click	VB
cord-002542-f7l4ty2j	474	25	-	-	HYPH
cord-002542-f7l4ty2j	474	26	chemistry	chemistry	NN
cord-002542-f7l4ty2j	474	27	for	for	IN
cord-002542-f7l4ty2j	474	28	next	next	JJ
cord-002542-f7l4ty2j	474	29	-	-	HYPH
cord-002542-f7l4ty2j	474	30	generation	generation	NN
cord-002542-f7l4ty2j	474	31	3	3	CD
cord-002542-f7l4ty2j	474	32	0	0	CD
cord-002542-f7l4ty2j	475	1	-end	-end	:
cord-002542-f7l4ty2j	475	2	sequencing	sequence	VBG
cord-002542-f7l4ty2j	475	3	without	without	IN
cord-002542-f7l4ty2j	475	4	RNA	RNA	NNP
cord-002542-f7l4ty2j	475	5	enrichment	enrichment	NN
cord-002542-f7l4ty2j	475	6	or	or	CC
cord-002542-f7l4ty2j	475	7	fragmentation	fragmentation	NN
cord-002542-f7l4ty2j	476	1	Cutadapt	Cutadapt	NNP
cord-002542-f7l4ty2j	476	2	removes	remove	VBZ
cord-002542-f7l4ty2j	476	3	adapter	adapter	NN
cord-002542-f7l4ty2j	476	4	sequences	sequence	NNS
cord-002542-f7l4ty2j	476	5	from	from	IN
cord-002542-f7l4ty2j	476	6	high	high	JJ
cord-002542-f7l4ty2j	476	7	-	-	HYPH
cord-002542-f7l4ty2j	476	8	throughput	throughput	NN
cord-002542-f7l4ty2j	476	9	sequencing	sequencing	NN
cord-002542-f7l4ty2j	476	10	reads	read	VBZ
cord-002542-f7l4ty2j	476	11	Ultrafast	ultrafast	NN
cord-002542-f7l4ty2j	476	12	and	and	CC
cord-002542-f7l4ty2j	476	13	memory	memory	NN
cord-002542-f7l4ty2j	476	14	-	-	HYPH
cord-002542-f7l4ty2j	476	15	efficient	efficient	JJ
cord-002542-f7l4ty2j	476	16	alignment	alignment	NN
cord-002542-f7l4ty2j	476	17	of	of	IN
cord-002542-f7l4ty2j	476	18	short	short	JJ
cord-002542-f7l4ty2j	476	19	DNA	dna	NN
cord-002542-f7l4ty2j	476	20	sequences	sequence	NNS
cord-002542-f7l4ty2j	476	21	to	to	IN
cord-002542-f7l4ty2j	476	22	the	the	DT
cord-002542-f7l4ty2j	476	23	human	human	JJ
cord-002542-f7l4ty2j	476	24	genome	genome	NN
cord-002542-f7l4ty2j	476	25	Poretools	Poretools	NNP
cord-002542-f7l4ty2j	476	26	:	:	:
cord-002542-f7l4ty2j	476	27	a	a	DT
cord-002542-f7l4ty2j	476	28	toolkit	toolkit	NN
cord-002542-f7l4ty2j	476	29	for	for	IN
cord-002542-f7l4ty2j	476	30	analyzing	analyze	VBG
cord-002542-f7l4ty2j	476	31	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	476	32	sequence	sequence	NN
cord-002542-f7l4ty2j	476	33	data	data	NNP
cord-002542-f7l4ty2j	476	34	Tablet	Tablet	NNP
cord-002542-f7l4ty2j	476	35	-	-	HYPH
cord-002542-f7l4ty2j	476	36	next	next	JJ
cord-002542-f7l4ty2j	476	37	generation	generation	NN
cord-002542-f7l4ty2j	476	38	sequence	sequence	NN
cord-002542-f7l4ty2j	476	39	assembly	assembly	NN
cord-002542-f7l4ty2j	476	40	visualization	visualization	NN
cord-002542-f7l4ty2j	477	1	The	the	DT
cord-002542-f7l4ty2j	477	2	Sequence	Sequence	NNP
cord-002542-f7l4ty2j	477	3	Alignment	Alignment	NNP
cord-002542-f7l4ty2j	477	4	/	/	SYM
cord-002542-f7l4ty2j	477	5	Map	Map	NNP
cord-002542-f7l4ty2j	477	6	format	format	NN
cord-002542-f7l4ty2j	477	7	and	and	CC
cord-002542-f7l4ty2j	477	8	SAMtools	samtool	NNS
cord-002542-f7l4ty2j	477	9	Measuring	measure	VBG
cord-002542-f7l4ty2j	477	10	HCV	HCV	NNP
cord-002542-f7l4ty2j	477	11	infectivity	infectivity	NN
cord-002542-f7l4ty2j	477	12	produced	produce	VBN
cord-002542-f7l4ty2j	477	13	in	in	IN
cord-002542-f7l4ty2j	477	14	cell	cell	NN
cord-002542-f7l4ty2j	477	15	culture	culture	NN
cord-002542-f7l4ty2j	477	16	and	and	CC
cord-002542-f7l4ty2j	477	17	in	in	IN
cord-002542-f7l4ty2j	477	18	vivo	vivo	NNP
cord-002542-f7l4ty2j	477	19	Plaque	Plaque	NNP
cord-002542-f7l4ty2j	477	20	assay	assay	NN
cord-002542-f7l4ty2j	477	21	for	for	IN
cord-002542-f7l4ty2j	477	22	black	black	JJ
cord-002542-f7l4ty2j	477	23	beetle	beetle	NN
cord-002542-f7l4ty2j	477	24	virus	virus	NN
cord-002542-f7l4ty2j	477	25	High	high	JJ
cord-002542-f7l4ty2j	477	26	-	-	HYPH
cord-002542-f7l4ty2j	477	27	fidelity	fidelity	NN
cord-002542-f7l4ty2j	477	28	mass	mass	NN
cord-002542-f7l4ty2j	477	29	analysis	analysis	NN
cord-002542-f7l4ty2j	477	30	unveils	unveil	VBZ
cord-002542-f7l4ty2j	477	31	heterogeneity	heterogeneity	NN
cord-002542-f7l4ty2j	477	32	in	in	IN
cord-002542-f7l4ty2j	477	33	intact	intact	JJ
cord-002542-f7l4ty2j	477	34	ribosomal	ribosomal	JJ
cord-002542-f7l4ty2j	477	35	particles	particle	NNS
cord-002542-f7l4ty2j	477	36	Replication	replication	NN
cord-002542-f7l4ty2j	477	37	of	of	IN
cord-002542-f7l4ty2j	477	38	flock	flock	NN
cord-002542-f7l4ty2j	477	39	house	house	NN
cord-002542-f7l4ty2j	477	40	virus	virus	NN
cord-002542-f7l4ty2j	477	41	RNAs	rna	NNS
cord-002542-f7l4ty2j	477	42	from	from	IN
cord-002542-f7l4ty2j	477	43	primary	primary	JJ
cord-002542-f7l4ty2j	477	44	transcripts	transcript	NNS
cord-002542-f7l4ty2j	477	45	made	make	VBN
cord-002542-f7l4ty2j	477	46	in	in	IN
cord-002542-f7l4ty2j	477	47	cells	cell	NNS
cord-002542-f7l4ty2j	477	48	by	by	IN
cord-002542-f7l4ty2j	477	49	RNA	RNA	NNP
cord-002542-f7l4ty2j	477	50	polymerase	polymerase	NN
cord-002542-f7l4ty2j	477	51	II	II	NNP
cord-002542-f7l4ty2j	477	52	Packaging	Packaging	NNP
cord-002542-f7l4ty2j	477	53	host	host	NN
cord-002542-f7l4ty2j	477	54	RNAs	rna	NNS
cord-002542-f7l4ty2j	477	55	in	in	IN
cord-002542-f7l4ty2j	477	56	small	small	JJ
cord-002542-f7l4ty2j	477	57	RNA	RNA	NNP
cord-002542-f7l4ty2j	477	58	viruses	virus	NNS
cord-002542-f7l4ty2j	477	59	:	:	:
cord-002542-f7l4ty2j	478	1	An	an	DT
cord-002542-f7l4ty2j	478	2	inevitable	inevitable	JJ
cord-002542-f7l4ty2j	478	3	consequence	consequence	NN
cord-002542-f7l4ty2j	478	4	of	of	IN
cord-002542-f7l4ty2j	478	5	an	an	DT
cord-002542-f7l4ty2j	478	6	error	error	NN
cord-002542-f7l4ty2j	478	7	-	-	HYPH
cord-002542-f7l4ty2j	478	8	prone	prone	JJ
cord-002542-f7l4ty2j	478	9	polymerase	polymerase	NN
cord-002542-f7l4ty2j	478	10	?	?	.
cord-002542-f7l4ty2j	479	1	Double	double	JJ
cord-002542-f7l4ty2j	479	2	indexing	indexing	NN
cord-002542-f7l4ty2j	479	3	overcomes	overcome	VBZ
cord-002542-f7l4ty2j	479	4	inaccuracies	inaccuracy	NNS
cord-002542-f7l4ty2j	479	5	in	in	IN
cord-002542-f7l4ty2j	479	6	multiplex	multiplex	JJ
cord-002542-f7l4ty2j	479	7	sequencing	sequencing	NN
cord-002542-f7l4ty2j	479	8	on	on	IN
cord-002542-f7l4ty2j	479	9	the	the	DT
cord-002542-f7l4ty2j	479	10	Illumina	Illumina	NNP
cord-002542-f7l4ty2j	479	11	platform	platform	NN
cord-002542-f7l4ty2j	479	12	Common	common	JJ
cord-002542-f7l4ty2j	479	13	contaminants	contaminant	NNS
cord-002542-f7l4ty2j	479	14	in	in	IN
cord-002542-f7l4ty2j	479	15	next	next	JJ
cord-002542-f7l4ty2j	479	16	-	-	HYPH
cord-002542-f7l4ty2j	479	17	generation	generation	NN
cord-002542-f7l4ty2j	479	18	sequencing	sequencing	NN
cord-002542-f7l4ty2j	479	19	that	that	WDT
cord-002542-f7l4ty2j	479	20	hinder	hinder	VBP
cord-002542-f7l4ty2j	479	21	discovery	discovery	NN
cord-002542-f7l4ty2j	479	22	of	of	IN
cord-002542-f7l4ty2j	479	23	low	low	JJ
cord-002542-f7l4ty2j	479	24	-	-	HYPH
cord-002542-f7l4ty2j	479	25	abundance	abundance	NN
cord-002542-f7l4ty2j	479	26	microbes	microbe	NNS
cord-002542-f7l4ty2j	479	27	Generation	generation	NN
cord-002542-f7l4ty2j	479	28	and	and	CC
cord-002542-f7l4ty2j	479	29	selection	selection	NN
cord-002542-f7l4ty2j	479	30	of	of	IN
cord-002542-f7l4ty2j	479	31	coronavirus	coronavirus	NN
cord-002542-f7l4ty2j	479	32	defective	defective	JJ
cord-002542-f7l4ty2j	479	33	interfering	interfere	VBG
cord-002542-f7l4ty2j	479	34	RNA	RNA	NNP
cord-002542-f7l4ty2j	479	35	with	with	IN
cord-002542-f7l4ty2j	479	36	large	large	JJ
cord-002542-f7l4ty2j	479	37	open	open	JJ
cord-002542-f7l4ty2j	479	38	reading	reading	NN
cord-002542-f7l4ty2j	479	39	frame	frame	NN
cord-002542-f7l4ty2j	479	40	by	by	IN
cord-002542-f7l4ty2j	479	41	RNA	RNA	NNP
cord-002542-f7l4ty2j	479	42	recombination	recombination	NN
cord-002542-f7l4ty2j	479	43	and	and	CC
cord-002542-f7l4ty2j	479	44	possible	possible	JJ
cord-002542-f7l4ty2j	479	45	editing	edit	VBG
cord-002542-f7l4ty2j	479	46	Flock	Flock	NNP
cord-002542-f7l4ty2j	479	47	house	house	NN
cord-002542-f7l4ty2j	479	48	virus	virus	NN
cord-002542-f7l4ty2j	479	49	replicates	replicate	VBZ
cord-002542-f7l4ty2j	479	50	and	and	CC
cord-002542-f7l4ty2j	479	51	expresses	express	VBZ
cord-002542-f7l4ty2j	479	52	green	green	JJ
cord-002542-f7l4ty2j	479	53	fluorescent	fluorescent	JJ
cord-002542-f7l4ty2j	479	54	protein	protein	NN
cord-002542-f7l4ty2j	479	55	in	in	IN
cord-002542-f7l4ty2j	479	56	mosquitoes	mosquito	NNS
cord-002542-f7l4ty2j	479	57	Long	long	JJ
cord-002542-f7l4ty2j	479	58	-	-	HYPH
cord-002542-f7l4ty2j	479	59	distance	distance	NN
cord-002542-f7l4ty2j	479	60	base	base	NN
cord-002542-f7l4ty2j	479	61	pairing	pair	VBG
cord-002542-f7l4ty2j	479	62	in	in	IN
cord-002542-f7l4ty2j	480	1	flock	flock	NNP
cord-002542-f7l4ty2j	480	2	house	house	NNP
cord-002542-f7l4ty2j	480	3	virus	virus	NN
cord-002542-f7l4ty2j	480	4	RNA1	RNA1	NNP
cord-002542-f7l4ty2j	480	5	regulates	regulate	VBZ
cord-002542-f7l4ty2j	480	6	subgenomic	subgenomic	NNP
cord-002542-f7l4ty2j	480	7	RNA3	RNA3	NNP
cord-002542-f7l4ty2j	480	8	synthesis	synthesis	NN
cord-002542-f7l4ty2j	480	9	and	and	CC
cord-002542-f7l4ty2j	480	10	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	480	11	replication	replication	NN
cord-002542-f7l4ty2j	480	12	Requirements	requirement	NNS
cord-002542-f7l4ty2j	480	13	for	for	IN
cord-002542-f7l4ty2j	480	14	the	the	DT
cord-002542-f7l4ty2j	480	15	self	self	NN
cord-002542-f7l4ty2j	480	16	-	-	HYPH
cord-002542-f7l4ty2j	480	17	directed	direct	VBN
cord-002542-f7l4ty2j	480	18	replication	replication	NN
cord-002542-f7l4ty2j	480	19	of	of	IN
cord-002542-f7l4ty2j	480	20	flock	flock	NN
cord-002542-f7l4ty2j	480	21	house	house	NN
cord-002542-f7l4ty2j	480	22	virus	virus	NN
cord-002542-f7l4ty2j	481	1	RNA	RNA	NNP
cord-002542-f7l4ty2j	481	2	1	1	CD
cord-002542-f7l4ty2j	481	3	Replication	Replication	NNP
cord-002542-f7l4ty2j	481	4	of	of	IN
cord-002542-f7l4ty2j	481	5	the	the	DT
cord-002542-f7l4ty2j	481	6	RNA	RNA	NNP
cord-002542-f7l4ty2j	481	7	segments	segment	NNS
cord-002542-f7l4ty2j	481	8	of	of	IN
cord-002542-f7l4ty2j	481	9	a	a	DT
cord-002542-f7l4ty2j	481	10	bipartite	bipartite	JJ
cord-002542-f7l4ty2j	481	11	viral	viral	JJ
cord-002542-f7l4ty2j	481	12	genome	genome	NN
cord-002542-f7l4ty2j	481	13	is	be	VBZ
cord-002542-f7l4ty2j	481	14	coordinated	coordinate	VBN
cord-002542-f7l4ty2j	481	15	by	by	IN
cord-002542-f7l4ty2j	481	16	a	a	DT
cord-002542-f7l4ty2j	481	17	transactivating	transactivate	VBG
cord-002542-f7l4ty2j	481	18	subgenomic	subgenomic	NNP
cord-002542-f7l4ty2j	481	19	RNA	RNA	NNP
cord-002542-f7l4ty2j	482	1	The	the	DT
cord-002542-f7l4ty2j	482	2	cis	cis	NNP
cord-002542-f7l4ty2j	482	3	-	-	HYPH
cord-002542-f7l4ty2j	482	4	acting	act	VBG
cord-002542-f7l4ty2j	482	5	replication	replication	NN
cord-002542-f7l4ty2j	482	6	signal	signal	NN
cord-002542-f7l4ty2j	482	7	at	at	IN
cord-002542-f7l4ty2j	482	8	the	the	DT
cord-002542-f7l4ty2j	482	9	3	3	CD
cord-002542-f7l4ty2j	482	10	'	'	NN
cord-002542-f7l4ty2j	482	11	end	end	NN
cord-002542-f7l4ty2j	482	12	of	of	IN
cord-002542-f7l4ty2j	482	13	Flock	Flock	NNP
cord-002542-f7l4ty2j	482	14	House	House	NNP
cord-002542-f7l4ty2j	482	15	virus	virus	NN
cord-002542-f7l4ty2j	482	16	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	482	17	is	be	VBZ
cord-002542-f7l4ty2j	482	18	RNA3-dependent	RNA3-dependent	NNP
cord-002542-f7l4ty2j	482	19	A	a	DT
cord-002542-f7l4ty2j	482	20	3	3	CD
cord-002542-f7l4ty2j	482	21	'	'	''
cord-002542-f7l4ty2j	482	22	terminal	terminal	JJ
cord-002542-f7l4ty2j	482	23	stem	stem	NN
cord-002542-f7l4ty2j	482	24	-	-	HYPH
cord-002542-f7l4ty2j	482	25	loop	loop	NN
cord-002542-f7l4ty2j	482	26	structure	structure	NN
cord-002542-f7l4ty2j	482	27	in	in	IN
cord-002542-f7l4ty2j	483	1	Nodamura	Nodamura	NNP
cord-002542-f7l4ty2j	483	2	virus	virus	NN
cord-002542-f7l4ty2j	483	3	RNA2	RNA2	NNP
cord-002542-f7l4ty2j	483	4	forms	form	VBZ
cord-002542-f7l4ty2j	483	5	an	an	DT
cord-002542-f7l4ty2j	483	6	essential	essential	JJ
cord-002542-f7l4ty2j	483	7	cis	cis	NN
cord-002542-f7l4ty2j	483	8	-	-	HYPH
cord-002542-f7l4ty2j	483	9	acting	act	VBG
cord-002542-f7l4ty2j	483	10	signal	signal	NN
cord-002542-f7l4ty2j	483	11	for	for	IN
cord-002542-f7l4ty2j	483	12	RNA	rna	NN
cord-002542-f7l4ty2j	483	13	replication	replication	NN
cord-002542-f7l4ty2j	483	14	Characterization	characterization	NN
cord-002542-f7l4ty2j	483	15	and	and	CC
cord-002542-f7l4ty2j	483	16	template	template	NN
cord-002542-f7l4ty2j	483	17	properties	property	NNS
cord-002542-f7l4ty2j	483	18	of	of	IN
cord-002542-f7l4ty2j	483	19	RNA	RNA	NNP
cord-002542-f7l4ty2j	483	20	dimers	dimer	NNS
cord-002542-f7l4ty2j	483	21	generated	generate	VBN
cord-002542-f7l4ty2j	483	22	during	during	IN
cord-002542-f7l4ty2j	483	23	flock	flock	NN
cord-002542-f7l4ty2j	483	24	house	house	NNP
cord-002542-f7l4ty2j	483	25	virus	virus	NN
cord-002542-f7l4ty2j	483	26	RNA	RNA	NNP
cord-002542-f7l4ty2j	483	27	replication	replication	NN
cord-002542-f7l4ty2j	484	1	The	the	DT
cord-002542-f7l4ty2j	484	2	Oxford	Oxford	NNP
cord-002542-f7l4ty2j	484	3	Nanopore	Nanopore	NNP
cord-002542-f7l4ty2j	484	4	MinION	minion	NN
cord-002542-f7l4ty2j	484	5	:	:	:
cord-002542-f7l4ty2j	484	6	delivery	delivery	NN
cord-002542-f7l4ty2j	484	7	of	of	IN
cord-002542-f7l4ty2j	484	8	nanopore	nanopore	NNP
cord-002542-f7l4ty2j	484	9	sequencing	sequence	VBG
cord-002542-f7l4ty2j	484	10	to	to	IN
cord-002542-f7l4ty2j	484	11	the	the	DT
cord-002542-f7l4ty2j	484	12	genomics	genomic	NNS
cord-002542-f7l4ty2j	484	13	community	community	NN
cord-002542-f7l4ty2j	484	14	Continuous	continuous	JJ
cord-002542-f7l4ty2j	484	15	influenza	influenza	NN
cord-002542-f7l4ty2j	484	16	virus	virus	NN
cord-002542-f7l4ty2j	484	17	production	production	NN
cord-002542-f7l4ty2j	484	18	in	in	IN
cord-002542-f7l4ty2j	484	19	cell	cell	NN
cord-002542-f7l4ty2j	484	20	culture	culture	NN
cord-002542-f7l4ty2j	484	21	shows	show	VBZ
cord-002542-f7l4ty2j	484	22	a	a	DT
cord-002542-f7l4ty2j	484	23	periodic	periodic	JJ
cord-002542-f7l4ty2j	484	24	accumulation	accumulation	NN
cord-002542-f7l4ty2j	484	25	of	of	IN
cord-002542-f7l4ty2j	484	26	defective	defective	JJ
cord-002542-f7l4ty2j	484	27	interfering	interfere	VBG
cord-002542-f7l4ty2j	484	28	particles	particle	NNS
cord-002542-f7l4ty2j	484	29	Nonhomologous	Nonhomologous	NNP
cord-002542-f7l4ty2j	484	30	RNA	RNA	NNP
cord-002542-f7l4ty2j	484	31	recombination	recombination	NN
cord-002542-f7l4ty2j	484	32	in	in	IN
cord-002542-f7l4ty2j	484	33	tombusviruses	tombusviruse	NNS
cord-002542-f7l4ty2j	484	34	:	:	:
cord-002542-f7l4ty2j	484	35	generation	generation	NN
cord-002542-f7l4ty2j	484	36	and	and	CC
cord-002542-f7l4ty2j	484	37	evolution	evolution	NN
cord-002542-f7l4ty2j	484	38	of	of	IN
cord-002542-f7l4ty2j	484	39	defective	defective	JJ
cord-002542-f7l4ty2j	484	40	interfering	interfere	VBG
cord-002542-f7l4ty2j	484	41	RNAs	rna	NNS
cord-002542-f7l4ty2j	484	42	by	by	IN
cord-002542-f7l4ty2j	484	43	stepwise	stepwise	JJ
cord-002542-f7l4ty2j	484	44	deletions	deletion	NNS
cord-002542-f7l4ty2j	485	1	Massive	massive	JJ
cord-002542-f7l4ty2j	485	2	genomic	genomic	JJ
cord-002542-f7l4ty2j	485	3	rearrangement	rearrangement	NN
cord-002542-f7l4ty2j	485	4	acquired	acquire	VBN
cord-002542-f7l4ty2j	485	5	in	in	IN
cord-002542-f7l4ty2j	485	6	a	a	DT
cord-002542-f7l4ty2j	485	7	single	single	JJ
cord-002542-f7l4ty2j	485	8	catastrophic	catastrophic	JJ
cord-002542-f7l4ty2j	485	9	event	event	NN
cord-002542-f7l4ty2j	485	10	during	during	IN
cord-002542-f7l4ty2j	485	11	cancer	cancer	NN
cord-002542-f7l4ty2j	485	12	development	development	NN
cord-002542-f7l4ty2j	485	13	Role	role	NN
cord-002542-f7l4ty2j	485	14	of	of	IN
cord-002542-f7l4ty2j	485	15	Mitochondrial	mitochondrial	JJ
cord-002542-f7l4ty2j	485	16	Membrane	membrane	NN
cord-002542-f7l4ty2j	485	17	Spherules	Spherules	NNPS
cord-002542-f7l4ty2j	485	18	in	in	IN
cord-002542-f7l4ty2j	485	19	Flock	Flock	NNP
cord-002542-f7l4ty2j	485	20	House	House	NNP
cord-002542-f7l4ty2j	485	21	Virus	Virus	NNP
cord-002542-f7l4ty2j	485	22	Replication	replication	NN
cord-002542-f7l4ty2j	486	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	486	2	thank	thank	VBP
cord-002542-f7l4ty2j	486	3	Thomas	Thomas	NNP
cord-002542-f7l4ty2j	486	4	Wood	Wood	NNP
cord-002542-f7l4ty2j	486	5	,	,	,
cord-002542-f7l4ty2j	486	6	Steve	Steve	NNP
cord-002542-f7l4ty2j	486	7	Widen	Widen	NNP
cord-002542-f7l4ty2j	486	8	and	and	CC
cord-002542-f7l4ty2j	486	9	Jill	Jill	NNP
cord-002542-f7l4ty2j	486	10	Thomson	Thomson	NNP
cord-002542-f7l4ty2j	486	11	from	from	IN
cord-002542-f7l4ty2j	486	12	the	the	DT
cord-002542-f7l4ty2j	486	13	UTMB	UTMB	NNP
cord-002542-f7l4ty2j	486	14	Next	Next	NNP
cord-002542-f7l4ty2j	486	15	-	-	HYPH
cord-002542-f7l4ty2j	486	16	Generation	Generation	NNP
cord-002542-f7l4ty2j	486	17	Sequencing	Sequencing	NNP
cord-002542-f7l4ty2j	486	18	core	core	NN
cord-002542-f7l4ty2j	486	19	and	and	CC
cord-002542-f7l4ty2j	486	20	Gillian	Gillian	NNP
cord-002542-f7l4ty2j	486	21	Lynch	Lynch	NNP
cord-002542-f7l4ty2j	486	22	from	from	IN
cord-002542-f7l4ty2j	486	23	the	the	DT
cord-002542-f7l4ty2j	486	24	SCSB	SCSB	NNP
cord-002542-f7l4ty2j	486	25	computing	computing	NN
cord-002542-f7l4ty2j	486	26	facility	facility	NN
cord-002542-f7l4ty2j	486	27	for	for	IN
cord-002542-f7l4ty2j	486	28	support	support	NN
cord-002542-f7l4ty2j	486	29	.	.	.
cord-002542-f7l4ty2j	487	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	487	2	are	be	VBP
cord-002542-f7l4ty2j	487	3	indebted	indebted	JJ
cord-002542-f7l4ty2j	487	4	to	to	IN
cord-002542-f7l4ty2j	487	5	Mariano	Mariano	NNP
cord-002542-f7l4ty2j	487	6	Garcia	Garcia	NNP
cord-002542-f7l4ty2j	487	7	-	-	HYPH
cord-002542-f7l4ty2j	487	8	Blanco	Blanco	NNP
cord-002542-f7l4ty2j	487	9	and	and	CC
cord-002542-f7l4ty2j	487	10	Shelton	Shelton	NNP
cord-002542-f7l4ty2j	487	11	Bradrick	Bradrick	NNP
cord-002542-f7l4ty2j	487	12	and	and	CC
cord-002542-f7l4ty2j	487	13	the	the	DT
cord-002542-f7l4ty2j	487	14	members	member	NNS
cord-002542-f7l4ty2j	487	15	of	of	IN
cord-002542-f7l4ty2j	487	16	their	-PRON-	PRP$
cord-002542-f7l4ty2j	487	17	lab	lab	NN
cord-002542-f7l4ty2j	487	18	for	for	IN
cord-002542-f7l4ty2j	487	19	sharing	share	VBG
cord-002542-f7l4ty2j	487	20	lab	lab	NN
cord-002542-f7l4ty2j	487	21	space	space	NN
cord-002542-f7l4ty2j	487	22	,	,	,
cord-002542-f7l4ty2j	487	23	helpful	helpful	JJ
cord-002542-f7l4ty2j	487	24	discussions	discussion	NNS
cord-002542-f7l4ty2j	487	25	and	and	CC
cord-002542-f7l4ty2j	487	26	other	other	JJ
cord-002542-f7l4ty2j	487	27	research	research	NN
cord-002542-f7l4ty2j	487	28	support	support	NN
cord-002542-f7l4ty2j	487	29	.	.	.
cord-002542-f7l4ty2j	488	1	We	-PRON-	PRP
cord-002542-f7l4ty2j	488	2	thank	thank	VBP
cord-002542-f7l4ty2j	488	3	Eric	Eric	NNP
cord-002542-f7l4ty2j	488	4	Wagner	Wagner	NNP
cord-002542-f7l4ty2j	488	5	,	,	,
cord-002542-f7l4ty2j	488	6	Jack	Jack	NNP
cord-002542-f7l4ty2j	488	7	Johnson	Johnson	NNP
cord-002542-f7l4ty2j	488	8	and	and	CC
cord-002542-f7l4ty2j	488	9	Bruce	Bruce	NNP
cord-002542-f7l4ty2j	488	10	Torbett	Torbett	NNP
cord-002542-f7l4ty2j	488	11	for	for	IN
cord-002542-f7l4ty2j	488	12	support	support	NN
cord-002542-f7l4ty2j	488	13	and	and	CC
cord-002542-f7l4ty2j	488	14	advice	advice	NN
cord-002542-f7l4ty2j	488	15	.	.	.
cord-002542-f7l4ty2j	489	1	Visualization	visualization	NN
cord-002542-f7l4ty2j	489	2	:	:	:
cord-002542-f7l4ty2j	489	3	AR	AR	NNP
cord-002542-f7l4ty2j	489	4	EJ	EJ	NNP
cord-002542-f7l4ty2j	489	5	.	.	.
cord-002542-f7l4ty2j	490	1	Writing	write	VBG
cord-002542-f7l4ty2j	490	2	-review	-review	:
cord-002542-f7l4ty2j	490	3	&	&	CC
cord-002542-f7l4ty2j	490	4	editing	editing	NN
cord-002542-f7l4ty2j	490	5	:	:	:
cord-002542-f7l4ty2j	490	6	AR	AR	NNP
cord-002542-f7l4ty2j	490	7	EJ	EJ	NNP
cord-002542-f7l4ty2j	490	8	.	.	.