An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
Amplicon sequencing
Intrahost evolution
SNP calling
Viral sequencing
West Nile
Zika
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
08 01 2019
08 01 2019
Historique:
received:
04
08
2018
accepted:
26
12
2018
entrez:
10
1
2019
pubmed:
10
1
2019
medline:
9
3
2019
Statut:
epublish
Résumé
How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using PrimalSeq to measure virus diversity using Illumina and compare the results to Oxford Nanopore sequencing. We demonstrate the utility of PrimalSeq by measuring Zika and West Nile virus diversity from varied sample types and show that the accumulation of genetic diversity is influenced by experimental and biological systems.
Identifiants
pubmed: 30621750
doi: 10.1186/s13059-018-1618-7
pii: 10.1186/s13059-018-1618-7
pmc: PMC6325816
doi:
Types de publication
Evaluation Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
8Subventions
Organisme : NIAID NIH HHS
ID : R21 AI129479
Pays : United States
Organisme : NIAID NIH HHS
ID : U19 AI135995
Pays : United States
Organisme : Medical Research Council
ID : MR/L015080/1
Pays : United Kingdom
Organisme : NIH HHS
ID : P51 OD011107
Pays : United States
Organisme : NIAID NIH HHS
ID : R21AI137690
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001114
Pays : United States
Organisme : Medical Research Council
ID : MR/M501621/1
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : T32 AI007244
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI099210
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1TR002550
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI137690
Pays : United States
Organisme : NCEZID CDC HHS
ID : U01 CK000516
Pays : United States
Organisme : NIAID NIH HHS
ID : HHSN272201400048C
Pays : United States
Organisme : NIAID NIH HHS
ID : U19AI135995
Pays : United States
Organisme : Medical Research Council
ID : MC_PC_15100
Pays : United Kingdom
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