Evidence map›Paper›PMID 28027479›Full record

ArticleVirology2017

Characterization of founder viruses in very early SIV rectal transmission.

Zhe Yuan, Fangrui Ma, Andrew J Demers, Dong Wang, Jianqing Xu, Mark G Lewis, Qingsheng Li

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Virology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.7field-weighted citation impact, top 26% of its field
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

5 citing papers in PubMed, 7 citations in OpenAlex.

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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

7 authors at 3 institutions in 2 countries.

Zhe YuanNebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
Fangrui MaNebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
Andrew J DemersNebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
Dong WangDow AgroSciences, LLC, Indianapolis, IN, USA.
Jianqing XuShanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
Mark G LewisBIOQUAL, Inc., Rockville, MD, USA.
Qingsheng LiNebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA. Electronic address: qli@unl.edu.
University of Nebraska–Lincoln · USBioqual · USShanghai Public Health Clinical Center · CN

Funding

Nebraska Center for VirologyP30GM103509 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI WOOD, CHARLES · 2012 to 2014
$3.3M
Improve the safety of an efficacious live-attenuated HIV-1 vaccine through unnatuR01AI111862 · NIAID · UNIVERSITY OF NEBRASKA LINCOLN · PI GUO, JIANTAO, LI, QINGSHENG · 2014 to 2017
$1.9M
The Early Events Determining SIV Rectal TransmissionR01DK087625 · NIDDK · UNIVERSITY OF NEBRASKA LINCOLN · PI LI, QINGSHENG · 2010 to 2013
$1.4M
NIAID NIH HHS R01 AI111862NIDDK NIH HHS R01 DK087625NIGMS NIH HHS P30 GM103509
6 · The paper itself

Abstract

A better understanding of HIV-1 transmission is critical for developing preventative strategies. To that end, we analyzed 524 full-length env sequences of SIVmac251 at 6 and 10 days post intrarectal infection of rhesus macaques. There was no tissue compartmentalization of founder viruses across plasma, rectal and distal lymphatic tissues for most animals; however one animal has evidence of virus tissue compartmentalization. Despite identical viral inoculums, founder viruses were animal-specific, primarily derived from rare variants in the inoculum, and have a founder virus signature that can distinguish dominant founder variants from minor founder or untransmitted variants in the inoculum. Importantly, the sequences of post-transmission defective viruses were phylogenetically associated with competent viral variants in the inoculum and were mainly converted from competent viral variants by frameshift rather than APOBEC mediated mutations, suggesting the converting the transmitted viruses into defective viruses through frameshift mutation is an important component of rectal transmission bottleneck. SIGNIFICANCE: Anorectal receptive intercourse is a common route of HIV-1 transmission and a better understanding of the transmission mechanisms is critical for developing HIV-1 preventative strategies. Here, we report that there is no tissue compartmentalization of founder viruses during very early rectal transmission of SIV in the majority of rhesus macaques and founder viruses are preferentially derived from rare variant in the inoculum. We also found that founder viruses are animal-specific despite identical viral inoculums. After viruses cross the mucosal barriers, the host further reduces viral diversity by converting some of the transmitted functional viruses into defective viruses through frameshift rather than APOBEC derived mutations. To our knowledge, this is the first study of founder viruses at multiple tissue sites during very early rectal transmission.

Indexed as

Virus InternalizationAnimalsDisease Models, AnimalHIV-1HIV InfectionsHumansMacaca mulattaPhylogenyRectumSimian Acquired Immunodeficiency SyndromeSimian Immunodeficiency VirusDefective variantsFounder virus signatureGenetic bottleneckRectal transmissionTissue compartmentalizationVery early virological events

Identifiers

PMID28027479
PMCPMC5276734
OpenAlexW2564729790

What OpenQuestion holds

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Registered trials

None linked

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.