ReviewCurrent opinion in HIV and AIDS2019
Phylogenetics in HIV transmission: taking within-host diversity into account.
Review in Current opinion in HIV and AIDS, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed.
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
- Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs.Molecular biology and evolution · 2024Article
- Inferring viral transmission time from phylogenies for known transmission pairs.bioRxiv : the preprint server for biology · 2023Article
- Antiretrovirals to CCR5 CRISPR/Cas9 gene editing - A paradigm shift chasing an HIV cure.Clinical immunology (Orlando, Fla.) · 2023Review
- Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.eLife · 2023Article
- Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference.Open forum infectious diseases · 2023Article
- Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study.Wellcome open research · 2023Article
- Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies.Virus evolution · 2023Article
- Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.PLoS computational biology · 2022Article
- Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.bioRxiv : the preprint server for biology · 2022Article
- Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints.Microbial genomics · 2022Article
- Article
- First complete-genome documentation of HIV-1 intersubtype superinfection with transmissions of diverse recombinants over time to five recipients.PLoS pathogens · 2021Article
- Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.Virus evolution · 2021Article
- Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses.Frontiers in microbiology · 2021Article
- Article
- Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.The lancet. HIV · 2020Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
purpose of reviewWithin-host diversity complicates transmission models because it recognizes that between-host virus phylogenies are not identical to the transmission history among the infected hosts. This review presents the biological and theoretical foundations for recent development in this field, and shows that modern phylodynamic methods are capable of inferring realistic transmission histories from HIV sequence data. RECENT
findingsTransmission of single or multiple genetic variants from a donor's HIV population results in donor-recipient phylogenies with combinations of monophyletic, paraphyletic, and polyphyletic patterns. Large-scale simulations and analyses of many real HIV datasets have established that transmission direction, directness, or common source often can be inferred based on HIV sequence data. Phylodynamic reconstruction of HIV transmissions that include within-host HIV diversity have recently been established and made available in several software packages. SUMMARY: Phylodynamic methods that include realistic features of HIV genetic diversification have come of age, significantly improving inference of key epidemiological parameters. This opens the door to more accurate surveillance and better-informed prevention campaigns.
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