Evidence map›Paper›PMID 41279611›Full record

ArticlebioRxiv : the preprint server for biology2025

Long-Read Deep Sequencing Reveals High Rates of Multilineage Transmission and Rapid Viral Population Changes in Acute HIV Infection.

James I Mullins, Wenjie Deng, Elena E Giorgi, Craig A Magaret, Morgane Rolland, Tanmoy Bhattacharya, Dylan H Westfall, Anna E J Yssel, Roger E Bumgarner, Ben Murrell and 23 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

5 · Who and what money

Authors and funding

33 authors.

James I MullinsDepartment of Microbiology, University of Washington, Seattle, WA, US.ORCID 0000-0002-4461-8158
Wenjie DengDepartment of Microbiology, University of Washington, Seattle, WA, US.
Elena E GiorgiVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
Craig A MagaretVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
Morgane RollandHenry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, US.
Tanmoy BhattacharyaTheoretical Division, Los Alamos National Laboratory, Los Alamos, NM, US.
Dylan H WestfallDepartment of Microbiology, University of Washington, Seattle, WA, US.
Anna E J YsselInstitute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.
Roger E BumgarnerDepartment of Microbiology, University of Washington, Seattle, WA, US.
Ben MurrellDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE.
Thumbi Ndung'uAfrican Health Research Institute, University of KwaZulu Natal, Durban, ZA.
Merlin L RobbHenry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, US.
Raabya RossenkhanVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
Paul T EdlefsenVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
Krista L DongRagon Institute of Mass General Brigham, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, US.
Lennie ChenDepartment of Microbiology, University of Washington, Seattle, WA, US.
Asanda Gwashu-NyangiriInstitute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.
Hong ZhaoDepartment of Microbiology, University of Washington, Seattle, WA, US.
Ruwayhida ThebusInstitute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.
Fredrick SaweKenya Medical Research Institute, Walter Reed Army Institute of Research-Africa, Nairobi, KE.
Sorachai NitayaphanArmed Forces Research Institute of Medical Sciences, Bangkok, TH.
Talita YorkInstitute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.
David MattenInstitute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.
Hugh MurrellInstitute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.
Alec P PankowDepartment of Microbiology, University of Washington, Seattle, WA, US.
Michal JuraskaVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
James LudwigVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
John HuralVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
Myron S CohenUniversity of North Carolina, Chapel Hill, NC, US.
Lawrence CoreyVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
M Juliana McElrathVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
Peter B GilbertVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.
Carolyn WilliamsonInstitute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.

Funding

LOC: HIV Vaccine Trials NetworkUM1AI068614 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI Dan H. Barouch, Lawrence Corey · 2011 to 2026
$1175.6M
LC: HIV Vaccine Trials NetworkUM1AI068618 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI Margaret Juliana McElrath · 2011 to 2026
$483.6M
SDMC: HIV Vaccine Trials NetworkUM1AI068635 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI Peter B. Gilbert, Yunda Huang · 2011 to 2026
$385.9M
The impact of HIV viral diversity and cellular immunity on HIV pathogenesisP30AI060354 · NIAID · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI ARTHUR Y KIM · 2004 to 2026
$94.4M
Gates Foundation INV-016189Gates Foundation INV-033558NIAID NIH HHS P30 AI060354NIAID NIH HHS UM1 AI068614NIAID NIH HHS UM1 AI068618NIAID NIH HHS UM1 AI068635Wellcome Trust
6 · The paper itself

Abstract

Understanding the selective forces acting upon HIV early in infection is crucial to design prevention strategies. By leveraging deep sequencing and the short diagnostic intervals of the FRESH and RV217 cohorts (median 4 days) between the last-negative and first-positive RNA tests, we captured a precise and early snapshot of acute HIV infection. The frequency of multiple transmitted viruses of 38% in these as well as placebo recipients from the AMP trials was higher than previously published, with the true frequency likely to be higher. The relative abundance of lineages fluctuated substantially over time in two-thirds of the multilineage infections, generating uncertainty in identifying the specific viruses that were transmitted and founding the infection. Viral populations exhibited diversity and selection on the Gag and Env proteins at the earliest times examined, with sites inferred to be undergoing negative selection most evident. These data may help explain vaccination failures and provide new targets for prevention.

Identifiers

PMID41279611
PMCPMC12632927

What OpenQuestion holds

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LicenceCC BY
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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.