id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-317595-siwzjeea	Forni, Diego	Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV	2018-05-01		.txt	text/plain	9944	505	49	Herein, we apply an evolutionary approach to shed light into HCV origin, to analyze its adaptation to human populations, and to verify if the emergence of drug-resistant variants is a result of positive selection. We used Single-Likelihood Ancestor Counting (SLAC) and fixed effects likelihood (FEL) (Kosakovsky Pond and Frost, 2005) to calculate the rates of nonsynonymous and synonymous changes at each site in the structural and in the non-structural region alignments (analyses were performed on alignments split on the basis of the recombination breakpoint detected by GARD). The observation that the positively selected sites are involved in HCV binding and infectivity suggests that hepaciviruses contributed to shape the genetic diversity of CD81 in bats. Using an evolutionary model that accounts for variation in the pressure of natural selection across sites and branches, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago, with a lower bound estimate of ∼5200 years before present.	./cache/cord-317595-siwzjeea.txt	./txt/cord-317595-siwzjeea.txt