Evidence map›Paper›PMID 42827436›Full record

ArticlebioRxiv : the preprint server for biology2026

Ultrasensitive single-genome sequencing reveals strong purifying selection in acute HIV-1 infection.

Adam A Capoferri, Valerie F Boltz, Wei Shao, Clarissa Halpern, Rasmi Thomas, Nittaya Phanuphak, Lydie Trautmann, Sandhya Vasan, Carlo Sacdalan, Somchai Sriplienchan and 4 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Adam A CapoferriHIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.ORCID 0000-0002-6048-2115
Valerie F BoltzHIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Wei ShaoLeidos Biomedical Research, Inc., Frederick National Laboratories for Cancer Research, Frederick, MD, USA.
Clarissa HalpernHIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Rasmi ThomasUS Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA.ORCID 0000-0002-2116-2418
Nittaya PhanuphakInstitute of HIV Research and Innovation (IHRI), Bangkok, Thailand.
Lydie TrautmannUS Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA.
Sandhya VasanUS Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA.
Carlo SacdalanSEARCH Research Foundation, Bangkok, Thailand.ORCID 0000-0002-5839-4837
Somchai SriplienchanSEARCH Research Foundation, Bangkok, Thailand.
John W MellorsDepartment of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
John M CoffinDepartment of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA.
Jason W RauschHIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Mary F KearneyHIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.ORCID 0000-0003-3839-6576

Funding

Ultrasensitive Single-Genome Sequencing to Study HIV Transmission and EvolutionZIABC011699 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI KEARNEY, MARY · 2016 to 2024
$7.1M
Intramural NIH HHS ZIA BC011699
6 · The paper itself

Abstract

HIV transmission from one individual to another occurs by one or a small number of virions followed by spread and genetic diversification into a complex quasispecies. To understand the early events in this process, we investigated how HIV-1 genomes diversify within the first two to three weeks after transmission by use of ultra-deep single subgenomic sequencing of over 10,000 plasma RNA genomes in each of a cohort of 15 individuals in acute infection. This approach confirmed transmission of one or a few transmitted/founder (TF) viral lineages and very limited early divergence from the founder sequences. Most observed variants that differed from the TF included single nucleotide changes attributable to HIV-1 reverse transcriptase (RT) error or host APOBEC3G/F activity. Comparing the number of expected versus observed changes after transmission indicated that most

Identifiers

PMID42827436
PMCPMC13628423

What OpenQuestion holds

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Registered trials

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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.