Evidence map›Paper›PMID 28187204›Full record

ArticlePloS one2017

Differentiating founder and chronic HIV envelope sequences.

John M Murray, Stephen Maher, Talia Mota, Kazuo Suzuki, Anthony D Kelleher, Rob J Center, Damian Purcell

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

Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.1field-weighted citation impact, top 56% 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

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Article
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.

John M MurraySchool of Mathematics and Statistics, UNSW Sydney, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0001-9314-2283
Stephen MaherSchool of Mathematics and Statistics, UNSW Sydney, Sydney, New South Wales, Australia.
Talia MotaDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
Kazuo SuzukiThe Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.
Anthony D KelleherThe Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.
Rob J CenterDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.ORCID http://orcid.org/0000-0002-4466-1922
Damian PurcellDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.ORCID http://orcid.org/0000-0002-4485-1726
UNSW Sydney · AUThe University of Melbourne · AUZuse Institute Berlin · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Significant progress has been made in characterizing broadly neutralizing antibodies against the HIV envelope glycoprotein Env, but an effective vaccine has proven elusive. Vaccine development would be facilitated if common features of early founder virus required for transmission could be identified. Here we employ a combination of bioinformatic and operations research methods to determine the most prevalent features that distinguish 78 subtype B and 55 subtype C founder Env sequences from an equal number of chronic sequences. There were a number of equivalent optimal networks (based on the fewest covarying amino acid (AA) pairs or a measure of maximal covariance) that separated founders from chronics: 13 pairs for subtype B and 75 for subtype C. Every subtype B optimal solution contained the founder pairs 178-346 Asn-Val, 232-236 Thr-Ser, 240-340 Lys-Lys, 279-315 Asp-Lys, 291-792 Ala-Ile, 322-347 Asp-Thr, 535-620 Leu-Asp, 742-837 Arg-Phe, and 750-836 Asp-Ile; the most common optimal pairs for subtype C were 644-781 Lys-Ala (74 of 75 networks), 133-287 Ala-Gln (73/75) and 307-337 Ile-Gln (73/75). No pair was present in all optimal subtype C solutions highlighting the difficulty in targeting transmission with a single vaccine strain. Relative to the size of its domain (0.35% of Env), the α4β7 binding site occurred most frequently among optimal pairs, especially for subtype C: 4.2% of optimal pairs (1.2% for subtype B). Early sequences from 5 subtype B pre-seroconverters each exhibited at least one clone containing an optimal feature 553-624 (Ser-Asn), 724-747 (Arg-Arg), or 46-293 (Arg-Glu).

Indexed as

Binding Sitesenv Gene Products, Human Immunodeficiency VirusFounder EffectPolymorphism, GeneticProtein Bindingenv Gene Products, Human Immunodeficiency Virus

Identifiers

PMID28187204
PMCPMC5302377
OpenAlexW2586724298

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.