Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies.
Dengue
evolution
intra-host variants
passage
Journal
The Journal of general virology
ISSN: 1465-2099
Titre abrégé: J Gen Virol
Pays: England
ID NLM: 0077340
Informations de publication
Date de publication:
03 2021
03 2021
Historique:
pubmed:
17
2
2021
medline:
15
7
2021
entrez:
16
2
2021
Statut:
ppublish
Résumé
Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loads, there might not be enough genetic material for deep sequencing and iSNV determination. Isolation of the virus from clinical samples with low-passage number increases viral load, but few studies have investigated how dengue virus (DENV) culture isolation from a clinical sample impacts the consensus sequence and the intra-host virus population frequencies. In this study, we investigate consensus and iSNV frequency differences between DENV sequenced directly from clinical samples and their corresponding low-passage isolates. Twenty five DENV1 and DENV2 positive sera and their corresponding viral isolates (
Identifiants
pubmed: 33591246
doi: 10.1099/jgv.0.001553
pmc: PMC8515859
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIAID NIH HHS
ID : P01 AI034533
Pays : United States
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