Evidence map›Paper›PMID 33055255›Full record

ArticlemSphere2020

Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing.

Bhavna Hora, Naila Gulzar, Yue Chen, Konstantinos Karagiannis, Fangping Cai, Chang Su, Krista Smith, Vahan Simonyan, Sharaf Ali Shah, Manzoor Ahmed and 6 more

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

Article in mSphere, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.1field-weighted citation impact, top 51% 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

1 citing paper in PubMed, 2 citations in OpenAlex.

  1. 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

16 authors at 5 institutions in 2 countries.

Bhavna Hora *Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA.
Naila Gulzar *Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, USA.
Yue ChenDuke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA.
Konstantinos KaragiannisDepartment of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, USA.
Fangping CaiDuke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA.
Chang SuDuke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA.
Krista SmithDepartment of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, USA.
Vahan SimonyanDepartment of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, USA.
Sharaf Ali ShahBridge Consultants Foundation, Karachi, Pakistan.
Manzoor AhmedBridge Consultants Foundation, Karachi, Pakistan.
Ana M SanchezLocus Biosciences, Morrisville, North Carolina, USA.
Mars StoneBlood Systems Research Institute, San Francisco, California, USA.ORCID 0000-0001-5619-2767
Myron S CohenDepartment of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Thomas N DennyDuke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA.
Raja Mazumder *Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, USA.
Feng Gao *Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA fgao@duke.edu.ORCID 0000-0001-8903-0203
Duke Medical Center · USGeorge Washington University · USBridge Consultants Foundation · PKBlood Systems Research Institute · USUniversity of North Carolina at Chapel Hill · US

Funding

NIAID NIH HHS HHSN272201000045CNIAID NIH HHS HHSN272201700061C
6 · The paper itself

Abstract

High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3'-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS.

Indexed as

AlgorithmsGenome, ViralRecombination, GeneticCohort StudiesComputer SimulationGenetic VariationGenotypeHigh-Throughput Nucleotide SequencingHIV-1HIV InfectionsHumansPhylogenyQuasispeciesgenetic recombinationHIV-1quasispeciessequencing

Identifiers

PMID33055255
PMCPMC7565892
OpenAlexW3093219907

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.