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

Journal Article · · Retrovirology
 [1];  [2];  [3];  [2];  [2];  [2];  [2];  [4];  [2];  [5];  [2]
  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; DOE/OSTI
  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
+ Show Author Affiliations
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.
Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1626608
Journal Information:
Retrovirology, Journal Name: Retrovirology Journal Issue: 1 Vol. 7; ISSN 1742-4690
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (42)

Differences in Chemokine Coreceptor Usage between Genetic Subtypes of HIV-1 journal February 1998
Full Genome Sequences of Human Immunodeficiency Virus Type 1 Subtypes G and A/G Intersubtype Recombinants journal July 1998
Estimating the pattern of nucleotide substitution journal July 1994
Comparative performance of the REGA subtyping tool version 2 versus version 1 journal April 2010
Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys journal February 2010
Human Immunodeficiency Virus Type 1 Subtypes Differ in Disease Progression journal January 1999
Effect of Human Immunodeficiency Virus (HIV) Type 1 Envelope Subtypes A and D on Disease Progression in a Large Cohort of HIV‐1–Positive Persons in Uganda journal May 2002
No Difference in Clinical Progression between Patients Infected with the Predominant Human Immunodeficiency Virus Type 1 Circulating Recombinant Form (CRF) 02_AG Strain and Patients Not Infected with CRF02_AG, in Western and West‐Central Africa: A Four‐Year Prospective Multicenter Study journal August 2002
Effect of Human Immunodeficiency Virus Type 1 (HIV‐1) Subtype on Disease Progression in Persons from Rakai, Uganda, with Incident HIV‐1 Infection journal March 2008
Study of HIV Type 1 gag/env Variability in The Gambia, Using a Multiplex DNA Polymerase Chain Reaction journal November 2000
Twenty Years of Prospective Molecular Epidemiology in Senegal: Changes in HIV Diversity journal October 2007
Clustal W and Clustal X version 2.0 journal September 2007
Survival of HIV-1 and HIV-2 perinatally infected children in The Gambia journal November 2003
Surprisingly High Prevalence of Subtype C and Specific HIV-1 Subtype/CRF Distribution in Men Having Sex With Men in Senegal journal October 2009
Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form journal June 2007
CCR5- and CXCR4-Tropic Subtype C Human Immunodeficiency Virus Type 1 Isolates Have a Lower Level of Pathogenic Fitness than Other Dominant Group M Subtypes: Implications for the Epidemic journal March 2009
Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing journal February 2008
Unprecedented Degree of Human Immunodeficiency Virus Type 1 (HIV-1) Group M Genetic Diversity in the Democratic Republic of Congo Suggests that the HIV-1 Pandemic Originated in Central Africa journal November 2000
Molecular Epidemiology of Human Immunodeficiency Virus Type 1 Sub-Subtype A3 in Senegal from 1988 to 2001 journal November 2004
Comprehensive Cross-Clade Neutralization Analysis of a Panel of Anti-Human Immunodeficiency Virus Type 1 Monoclonal Antibodies journal December 2004
The predominance of Human Immunodeficiency Virus type 1 (HIV-1) circulating recombinant form 02 (CRF02_AG) in West Central Africa may be related to its replicative fitness journal July 2006
Differences in resistance mutations among HIV-1 non-subtype B infections: a systematic review of evidence (1996-2008) journal February 2009
The Sequence Manipulation Suite: JavaScript Programs for Analyzing and Formatting Protein and DNA Sequences journal June 2000
Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys journal February 2010
HIV‐1 Subtype D Infection Is Associated with Faster Disease Progression than Subtype A in Spite of Similar Plasma HIV‐1 Loads journal April 2007
Signature Nucleotide Polymorphisms at Positions 64 and 65 in Reverse Transcriptase Favor the Selection of the K65R Resistance Mutation in HIV‐1 Subtype C
  • Invernizzi, Cédric F.; Coutsinos, Dimitrios; Oliveira, Maureen
  • The Journal of Infectious Diseases, Vol. 200, Issue 8 https://doi.org/10.1086/605894
journal October 2009
Sequence Note: HIV Type 1 A/J Recombinant with a Pronounced pol Gene Mosaicism journal July 2000
Sequence Note : Complex Mosaic Structure of the Partial Envelope Sequence from a Gambian HIV Type 1 Isolate journal January 1996
MRBAYES: Bayesian inference of phylogenetic trees journal August 2001
Sixteen years of HIV surveillance in a West African research clinic reveals divergent epidemic trends of HIV-1 and HIV-2 journal March 2006
Regional differences in HIV trends in The Gambia: results from sentinel surveillance among pregnant women journal January 2003
Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form journal June 2007
CCR5- and CXCR4-Tropic Subtype C Human Immunodeficiency Virus Type 1 Isolates Have a Lower Level of Pathogenic Fitness than Other Dominant Group M Subtypes: Implications for the Epidemic journal March 2009
Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing journal February 2008
Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination journal January 1999
Characterization of V3 Sequence Heterogeneity in Subtype C Human Immunodeficiency Virus Type 1 Isolates from Malawi: Underrepresentation of X4 Variants journal August 1999
Unprecedented Degree of Human Immunodeficiency Virus Type 1 (HIV-1) Group M Genetic Diversity in the Democratic Republic of Congo Suggests that the HIV-1 Pandemic Originated in Central Africa journal November 2000
Distinct Human Immunodeficiency Virus Type 1 Subtype A Virus Circulating in West Africa: Sub-Subtype A3 journal November 2004
Molecular Epidemiology of Human Immunodeficiency Virus Type 1 Sub-Subtype A3 in Senegal from 1988 to 2001 journal November 2004
Comprehensive Cross-Clade Neutralization Analysis of a Panel of Anti-Human Immunodeficiency Virus Type 1 Monoclonal Antibodies journal December 2004
The role of recombination in the emergence of a complex and dynamic HIV epidemic journal March 2010
Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection. journal March 2008

Cited By (3)

HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation journal March 2018
Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa journal November 2016
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