ArticleFrontiers in microbiology2012
Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.
Article in Frontiers in microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
120 citing papers in PubMed, 2 syntheses or guidelines pooled it, 249 citations in OpenAlex.
- A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing.Briefings in bioinformatics · 2020Guideline
- Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact.The Journal of infectious diseases · 2020Pooled it
- Trial
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- BonoboFlow: viral genome assembly and haplotype reconstruction from nanopore reads.Bioinformatics advances · 2025Article
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.Molecular biology and evolution · 2024Article
- The impact of integrated hepatitis B virus DNA on oncogenesis and antiviral therapy.Biomarker research · 2024Review
- Correlated Allele Frequency Changes Reveal Clonal Structure and Selection in Temporal Genetic Data.Molecular biology and evolution · 2024Article
- An amplicon-based protocol for whole-genome sequencing of human respiratory syncytial virus subgroup A.Biology methods & protocols · 2024Article
- High Prevalence of a Novel Circovirus in the European Hedgehog (Transboundary and emerging diseases · 2024Article
- Genomic characterisation of respiratory syncytial virus: a novel system for whole genome sequencing and full-length G and F gene sequences.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2023Article
- Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia.Microbial genomics · 2023Article
- Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics.Diagnostics (Basel, Switzerland) · 2023Review
- Article
- Article
- From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol.Vaccines · 2022Article
- Review
- Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples.Virus evolution · 2022Article
- What sequencing technologies can teach us about innate immunity.Immunological reviews · 2022Review
60 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency virus) and HCV (hepatitis C virus), exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing (NGS) technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different NGS platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants (SNVs) to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of NGS to estimate viral diversity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.