Evidence map›Paper›PMID 32764600›Full record

ArticleScientific reports2020

Genetic variability of the U5 and downstream sequence of major HIV-1 subtypes and circulating recombinant forms.

Christelle Mbondji-Wonje, Ming Dong, Jiangqin Zhao, Xue Wang, Aubin Nanfack, Viswanath Ragupathy, Ana M Sanchez, Thomas N Denny, Indira Hewlett

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

Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.4field-weighted citation impact, top 40% 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

4 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
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  4. Review
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

9 authors at 4 institutions in 2 countries.

Christelle Mbondji-WonjeLaboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA. christelle.mbondji@fda.hhs.gov.
Ming DongU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Jiangqin ZhaoLaboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
Xue WangLaboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
Aubin NanfackChantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.
Viswanath RagupathyLaboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
Ana M SanchezDuke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
Thomas N DennyDuke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
Indira HewlettLaboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA. Indira.Hewlett@fda.hhs.gov.
Center for Biologics Evaluation and Research · USDuke Medical Center · USCentre International De Reference Chantal Biya · CMHenry M. Jackson Foundation · US

Funding

NIAID NIH HHS HHSN272201700061C
6 · The paper itself

Abstract

The critical role of the regulatory elements at the 5' end of the HIV-1 genome in controlling the life cycle of HIV-1 indicates that this region significantly influences virus fitness and its biological properties. In this study, we performed a detailed characterization of strain-specific variability of sequences from the U5 to upstream of the gag gene start codon of diverse HIV-1 strains by using next-generation sequencing (NGS) techniques. Overall, we found that this region of the HIV-1 genome displayed a low degree of intra-strain variability. On the other hand, inter-strain variability was found to be as high as that reported for gag and env genes (13-17%). We observed strain-specific single point and clustered mutations in the U5, PBS, and gag leader sequences (GLS), generating potential strain-specific transcription factor binding sites (TFBS). Using an infrared gel shift assay, we demonstrated the presence of potential TFBS such as E-box in CRF22_01A, and Stat 6 in subtypes A and G, as well as in their related CRFs. The strain-specific variation found in the sequence corresponding at the RNA level to functional domains of the 5' UTR, could also potentially impact the secondary/tertiary structural rearrangement of this region. Thus, the variability observed in this 5' end of the genomic region of divergent HIV-1 strains strongly suggests that functions of this region might be affected in a strain-specific manner. Our findings provide new insights into DNA-protein interactions that regulate HIV-1 replication and the influence of strain characterization on the biology of HIV-1 infection.

Indexed as

5' Untranslated RegionsBinding Sitesgag Gene Products, Human Immunodeficiency VirusGenetic VariationHigh-Throughput Nucleotide SequencingHIV-1Recombination, GeneticRNA, ViralSpecies SpecificityTranscription Factors5' Untranslated Regionsgag Gene Products, Human Immunodeficiency VirusRNA, ViralTranscription Factors

Identifiers

PMID32764600
PMCPMC7411029
OpenAlexW3047015956

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.