ArticleVirus evolution2018
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Article in Virus evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
61 citing papers in PubMed.
- Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study.The Lancet. Microbe · 2024Trial
- Trial
- Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil.Nature communications · 2021Trial
- Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus.Nature communications · 2021Trial
- Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial.Lancet (London, England) · 2021Trial
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- Unravelling HCV diversity and resistance in Viet Nam: a cross-sectional analysis.The Lancet regional health. Western Pacific · 2026Article
- Multiple Reassortments, Limited Geographic Spread, and Comparable Pathogenicity of Crimean-Congo Hemorrhagic Fever Viruses in Sivas Province, Türkiye.Journal of medical virology · 2026Article
- Reducing mapping reference and lineage bias inMicrobial genomics · 2026Article
- The age and sex dynamics of heterosexual HIV transmission in Zambia: an HPTN 071 (PopART) phylogenetic and modelling study.medRxiv : the preprint server for health sciences · 2026Article
- Detection of HIV-1 Resistance Mutations to Antiretroviral Therapy and Cell Tropism in Russian Patients Using Next-Generation Sequencing.Pathogens (Basel, Switzerland) · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Advancing Precision Public Health: an implementation science framework for HIV Cluster Detection and Response driven by molecular epidemiology.Frontiers in public health · 2026Article
- Respiratory virus genomic epidemiology during post-pandemic re-emergence of influenza in Australia.Virus evolution · 2026Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.BMC bioinformatics · 2025Article
- Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.PLoS pathogens · 2025Article
- Addressing data management and analysis challenges in viral genomics: The Swiss HIV cohort study viral next generation sequencing database.PLOS digital health · 2025Article
- Genetically distinct within-host subpopulations of hepatitis C virus persist after Direct-Acting Antiviral treatment failure.PLoS pathogens · 2025Article
1 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
33 authors.
Funding
Abstract
Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions.
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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.