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Title: HIV-1 subtype distribution in the Gambia and the significant presence of CRF49_cpx, a novel circulating recombinant form

Abstract

Background: Detailed local HIV-1 sequence data are essential for monitoring the HIV epidemic, for maintaining sensitive sequence-based diagnostics, and to aid in designing vaccines. Results: Reported here are full envelope sequences derived from 38 randomly selected HIV-1 infections identified at a Gambian clinic between 1991 and 2009. Special care was taken to generate sequences from circulating viral RNA as uncloned products, either by limiting dilution or single genome amplification polymerase chain reaction (PCR). Within these 38 isolates, eight were subtyped as A and 18 as CRF02_AG. A small number of subtype B, C, D viruses were identified. Surprising, however, was the identification of six isolates with subtype J-like envelopes, a subtype found normally in Central Africa and the Democratic Republic of the Congo (DRC), with gag p24 regions that clustered with subtype A sequences. Near full-length sequence from three of these isolates confirmed that these represent a novel circulating recombinant form of HIV-1, now named CRF49_cpx. Conclusions: This study expands the HIV-1 sequence database from the Gambia and will provide important data for HIV diagnostics, patient care, and vaccine development.

Authors:
 [1];  [2];  [3];  [2];  [2];  [2];  [2];  [4];  [2];  [5];  [2]
+ Show Author Affiliations
  1. Medical Research Council (UK) Labs., Fajara (The Gambia); Univ. College London (United Kingdom). MRC/UCL Centre for Medical Molecular Virology. Division of Infection and Immunity
  2. Medical Research Council (UK) Labs., Fajara (The Gambia)
  3. Univ. College London (United Kingdom). MRC/UCL Centre for Medical Molecular Virology. Division of Infection and Immunity
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Biology & Biophysics
  5. John Radcliffe Hospital, Oxford (United Kingdom). Weatherall Inst. of Molecular Medicine. Medical Research Council Human Immunology Unit
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1626608
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Retrovirology
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 1742-4690
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Virology

Citation Formats

de Silva, Thushan I., Turner, Roxanne, Hue, Stephane, Trikha, Roochi, van Tienen, Carla, Onyango, Clayton, Jaye, Assan, Foley, Brian, Whittle, Hilton, Rowland-Jones, Sarah L., and Cotten, Matthew. HIV-1 subtype distribution in the Gambia and the significant presence of CRF49_cpx, a novel circulating recombinant form. United States: N. p., 2010. Web. doi:10.1186/1742-4690-7-82.
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de Silva, Thushan I., Turner, Roxanne, Hue, Stephane, Trikha, Roochi, van Tienen, Carla, Onyango, Clayton, Jaye, Assan, Foley, Brian, Whittle, Hilton, Rowland-Jones, Sarah L., & Cotten, Matthew. HIV-1 subtype distribution in the Gambia and the significant presence of CRF49_cpx, a novel circulating recombinant form. United States. https://doi.org/10.1186/1742-4690-7-82
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de Silva, Thushan I., Turner, Roxanne, Hue, Stephane, Trikha, Roochi, van Tienen, Carla, Onyango, Clayton, Jaye, Assan, Foley, Brian, Whittle, Hilton, Rowland-Jones, Sarah L., and Cotten, Matthew. Sat . "HIV-1 subtype distribution in the Gambia and the significant presence of CRF49_cpx, a novel circulating recombinant form". United States. https://doi.org/10.1186/1742-4690-7-82. https://www.osti.gov/servlets/purl/1626608.
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@article{osti_1626608,
title = {HIV-1 subtype distribution in the Gambia and the significant presence of CRF49_cpx, a novel circulating recombinant form},
author = {de Silva, Thushan I. and Turner, Roxanne and Hue, Stephane and Trikha, Roochi and van Tienen, Carla and Onyango, Clayton and Jaye, Assan and Foley, Brian and Whittle, Hilton and Rowland-Jones, Sarah L. and Cotten, Matthew},
abstractNote = {Background: Detailed local HIV-1 sequence data are essential for monitoring the HIV epidemic, for maintaining sensitive sequence-based diagnostics, and to aid in designing vaccines. Results: Reported here are full envelope sequences derived from 38 randomly selected HIV-1 infections identified at a Gambian clinic between 1991 and 2009. Special care was taken to generate sequences from circulating viral RNA as uncloned products, either by limiting dilution or single genome amplification polymerase chain reaction (PCR). Within these 38 isolates, eight were subtyped as A and 18 as CRF02_AG. A small number of subtype B, C, D viruses were identified. Surprising, however, was the identification of six isolates with subtype J-like envelopes, a subtype found normally in Central Africa and the Democratic Republic of the Congo (DRC), with gag p24 regions that clustered with subtype A sequences. Near full-length sequence from three of these isolates confirmed that these represent a novel circulating recombinant form of HIV-1, now named CRF49_cpx. Conclusions: This study expands the HIV-1 sequence database from the Gambia and will provide important data for HIV diagnostics, patient care, and vaccine development.},
doi = {10.1186/1742-4690-7-82},
journal = {Retrovirology},
number = 1,
volume = 7,
place = {United States},
year = {Sat Oct 09 00:00:00 EDT 2010},
month = {Sat Oct 09 00:00:00 EDT 2010}
}
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https://doi.org/10.1186/1742-4690-7-82
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    Works referencing / citing this record:

    Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa
    journal, November 2016

    FlatNJ: A Novel Network-Based Approach to Visualize Evolutionary and Biogeographical Relationships
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    Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa
    journal, November 2016

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