ArticleGenome biology2019
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 767 papers, 1 of them a synthesis that pooled it.
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Who cites it
767 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Local genomic epidemiology investigations of SARS-CoV-2 during the early pandemic response: A global systematic review.Epidemiology and infection · 2026Pooled it
- Tecovirimat treatment of clade II mpox: a virological analysis of a randomised, double-blind, phase 3 trial.The Lancet. Microbe · 2026Trial
- Workflow for Long-Read Amplicon Sequencing of Chikungunya Virus Using Oxford Nanopore Technology.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Global Genomic Surveillance.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Comprehensive genomic characterization of herpes B virus isolated from a wild long-tailed macaque reveals conserved entry mechanisms and zoonotic potential.Emerging microbes & infections · 2026Article
- Rapid and precise amplicon-based genome sequencing to preparedness and response chikungunya virus outbreaks.Emerging microbes & infections · 2026Article
- Multi‑omics insights into uveitis: From mechanisms to precision medicine (Review).International journal of molecular medicine · 2026Review
- The HBV basal core promoter mutation confers a replicative advantage and transcriptionally reprograms hepatocytes toward HCC subtypes.bioRxiv : the preprint server for biology · 2026Article
- Expansion of Dengue Virus Serotype 3 Genetic Diversity and Changing Serotype Composition in Brazil.Pathogens (Basel, Switzerland) · 2026Article
- Virome Diversity in Three Bat Species in Different Environments in Southern Spain.Microorganisms · 2026Article
- HIV-1 integrase inhibitor resistance in viraemic-treated individuals and baseline capsid diversity relevant to future lenacapavir therapy.The Journal of antimicrobial chemotherapy · 2026Article
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- Autochthonous chikungunya virus (CHIKV) outbreak in the province of Modena, Emilia-Romagna region, Italy, August to October 2025: epidemiology, clinical features and virological findings.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Genomic Surveillance Uncovers a Shift in Respiratory Syncytial Virus Subtype Dominance and the Local Expansion of Subclade B.D.E.1.7.Open forum infectious diseases · 2026Article
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- Genomics in containment: BSL-4-compatible workflows enable high-resolution genomic and transcriptomic analyses of Risk Group 4 viruses.iScience · 2026Article
- Molecular and Serological Evidence of Oropouche Virus Circulation in Asymptomatic Blood Donors During the 2023-2024 Outbreak in Manaus, Brazil.The Journal of infectious diseases · 2026Article
- Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary constraints limit additional mammalian adaptation of bovine-derived H5N1 influenza viruses in ferrets.bioRxiv : the preprint server for biology · 2026Article
- Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.Journal of virology · 2026Article
707 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
Abstract
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.
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