About: Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission

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About: Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission
Creator	Chen-Harris, Haiyin Vanier, Gilda Lao, Victoria Messenger, Sharon Allen, Jonathan Borucki, Monica Wadford, Debra
source	PMC
abstract	One of the hurdles to understanding the role of viral quasispecies in RNA virus cross-species transmission (CST) events is the need to analyze a densely sampled outbreak using deep sequencing in order to measure the amount of mutation occurring on a small time scale. In 2009, the California Department of Public Health reported a dramatic increase (350) in the number of gray foxes infected with a rabies virus variant for which striped skunks serve as a reservoir host in Humboldt County. To better understand the evolution of rabies, deep-sequencing was applied to 40 unpassaged rabies virus samples from the Humboldt outbreak. For each sample, approximately 11 kb of the 12 kb genome was amplified and sequenced using the Illumina platform. Average coverage was 17,448 and this allowed characterization of the rabies virus population present in each sample at unprecedented depths. Phylogenetic analysis of the consensus sequence data demonstrated that samples clustered according to date (1995 vs. 2009) and geographic location (northern vs. southern). A single amino acid change in the G protein distinguished a subset of northern foxes from a haplotype present in both foxes and skunks, suggesting this mutation may have played a role in the observed increased transmission among foxes in this region. Deep-sequencing data indicated that many genetic changes associated with the CST event occurred prior to 2009 since several nonsynonymous mutations that were present in the consensus sequences of skunk and fox rabies samples obtained from 20032010 were present at the sub-consensus level (as rare variants in the viral population) in skunk and fox samples from 1995. These results suggest that analysis of rare variants within a viral population may yield clues to ancestral genomes and identify rare variants that have the potential to be selected for if environment conditions change.
has issue date	2013-11-21(xsd:dateTime)
bibo:doi	10.1371/journal.pntd.0002555
bibo:pmid	24278493
has license	cc0
sha1sum (hex)	e5526afbb4d770dabb8c34da47c1267ee3342959
schema:url	https://doi.org/10.1371/journal.pntd.0002555
resource representing a document's title	Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission
has PubMed Central identifier	PMC3836733
has PubMed identifier	24278493
schema:publication	PLoS Negl Trop Dis
resource representing a document's body	covid:e5526afbb4d770dabb8c34da47c1267ee3342959#body_text
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