id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-312524-ee5xw1r8	Moustafa, Ahmed M.	Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread	2020-06-08		.txt	text/plain	2058	129	61	Here we present a rapid, whole genome, allele-based method (GNUVID) for assigning sequence types to sequenced isolates of SARS-CoV-2 sequences. Rapid sequencing of the SARS-CoV-2 pandemic virus has presented an 40 unprecedented opportunity to track the evolution of the virus and to understand the 41 emergence of a new pathogen in near-real time. Our panallelome approach to developing a whole genome (wgMLST) scheme for 58 SARS-CoV-2 uses a modified version of our recently developed tool, WhatsGNU [10], 59 to rapidly assign an allele number to each gene nucleotide sequence in the virus's 60 genome creating a sequence type (ST). We developed the GNU-based Virus IDentification (GNUVID) system as a tool 71 that automatically assigns a number to each unique allele of the 10 open reading 72 frames (ORFs) of SARS-CoV-2 ( Figure 1A) information. When the global region of origin for each genome sequence was mapped to 102 each CC there was a strong association of some CCs with certain geographical 103 locations.	./cache/cord-312524-ee5xw1r8.txt	./txt/cord-312524-ee5xw1r8.txt