SynthesisAIDS (London, England)2011
Designing a genome-based HIV incidence assay with high sensitivity and specificity.
Synthesis in AIDS (London, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis 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.
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
34 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards.Scientific reports · 2017Pooled it
- Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand.PLoS pathogens · 2020Trial
- HIV-1 amino acid changes among participants with virologic failure: associations with first-line efavirenz or atazanavir plus ritonavir and disease status.The Journal of infectious diseases · 2012Trial
- 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
- Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.PLoS pathogens · 2024Article
- Using viral sequence diversity to estimate time of HIV infection in infants.PLoS pathogens · 2023Article
- Microdrop Human Immunodeficiency Virus Sequencing for Incidence and Drug Resistance Surveillance.The Journal of infectious diseases · 2021Article
- Diagnosis of Human Immunodeficiency Virus Infection.Clinical microbiology reviews · 2019Review
- Using Primer-ID Deep Sequencing to Detect Recent Human Immunodeficiency Virus Type 1 Infection.The Journal of infectious diseases · 2018Article
- HIITE: HIV-1 incidence and infection time estimator.Bioinformatics (Oxford, England) · 2018Article
- Estimating time of HIV-1 infection from next-generation sequence diversity.PLoS computational biology · 2017Article
- Observational
- Article
- Enhancement of viral escape in HIV-1 Nef by STEP vaccination.AIDS (London, England) · 2016Article
- Molecular clock of HIV-1 envelope genes under early immune selection.Retrovirology · 2016Article
- SPMM: estimating infection duration of multivariant HIV-1 infections.Bioinformatics (Oxford, England) · 2016Article
- Review
- A Generalized Entropy Measure of Within-Host Viral Diversity for Identifying Recent HIV-1 Infections.Medicine · 2015Article
- Assessing Biases in the Evaluation of Classification Assays for HIV Infection Recency.PloS one · 2015Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
objectiveConsiderable inaccuracy in estimates of HIV incidence has been a serious obstacle to the development of efficient HIV/AIDS prevention and interventions. Accurately distinguishing recent or incident infections from chronic infections enables one to monitor epidemics and evaluate the impact of HIV prevention/intervention trials. However, serological testing has not been able to realize these promises due to a number of critical limitations. Our study is to design a novel scheme of identifying incident infections in a highly accurate manner, based on the characteristics of HIV gene diversification within an infected individual.
methodsWe perform a comprehensive meta-analysis on 5596 full envelope HIV genes generated by single genome amplification-direct sequencing from 182 incident and 43 chronic cases. We devise a binary classification test based on the tail characteristics of the Hamming distance distribution of sequences.
resultsWe identify a clear signature of incident infections, the presence of closely related strains in the sampled HIV envelope gene sequences in each HIV-infected patient, in both single-variant and multivariant transmissions. The sequence similarity used as a biomarker is found to have high specificity and sensitivity, greater than 95%, and is robust to viral and host-specific factors such as the clade of the viral strain, viral load, and the length and location of sequences in the HIV envelope gene.
conclusionBecause of rapid and continuing improvements in sequencing technology and cost, sequence-based incidence assays hold great promise as a means of quantifying HIV incidence from a single blood test.
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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.