id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-315760-9g8901v6	Teng, Xufei	Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades	2020-08-30		.txt	text/plain	3532	182	59	Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. We have further examined the compositional subtleties among the clades and clusters with 304 a focus on G+C and purine content variability as both contents appear drifting toward optima 305 in SARS-CoV-2 and its relatives ( Figure 5C and 5D).	./cache/cord-315760-9g8901v6.txt	./txt/cord-315760-9g8901v6.txt