Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage

Journal Article · · Viruses
DOI:https://doi.org/10.3390/v15010128· OSTI ID:1908490
 [1];  [2];  [2];  [2];  [1];  [3];  [4];  [4];  [4];  [5];  [5];  [6];  [1]
  1. Simon Fraser Univ., Burnaby, BC (Canada); British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC (Canada)
  2. British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC (Canada)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. Korle Bu Teaching Hospital, Accra (Ghana)
  5. University of Ghana, Accra (Ghana)
  6. British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC (Canada); Univ. of British Columbia, Vancouver, BC (Canada)
+ Show Author Affiliations
The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.
Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
Canadian Institutes for Health Research; Rideau Hall Foundation (RHF); USDOE
Grant/Contract Number:
89233218CNA000001
OSTI ID:
1908490
Report Number(s):
LA-UR-22-32691
Journal Information:
Viruses, Journal Name: Viruses Journal Issue: 1 Vol. 15; ISSN 1999-4915
Publisher:
MDPICopyright Statement
Country of Publication:
United States
Language:
English

References (77)

Public Health Implications of Antiretroviral Therapy and HIV Drug Resistance journal June 1998
Using a mixed‐methods approach to adapt an HIV stigma reduction intervention to address intersectional stigma faced by men who have sex with men in Ghana journal July 2022
Molecular epidemiology of HIV in Ghana: Dominance of CRF02_AG journal January 2004
Differences in Chemokine Coreceptor Usage between Genetic Subtypes of HIV-1 journal February 1998
Evolutionary trees from DNA sequences: A maximum likelihood approach journal November 1981
Factors Influencing HIV Status Disclosure to Partners Among Antiretroviral Therapy Clients in the Upper East Region, Ghana journal February 2022
Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease journal January 2011
Frequency and implications of HIV superinfection journal July 2013
Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis journal February 2019
Stigma reduction: an essential ingredient to ending AIDS by 2030 journal February 2021
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens journal July 2021
Variability of the human immunodeficiency virus type 1 polymerase gene from treatment naïve patients in Accra, Ghana journal October 2007
Determinants of Unprotected Casual Heterosexual sex in Ghana journal August 2013
Co-receptor tropism and genetic characteristics of the V3 regions in variants of antiretroviral-naive HIV-1 infected subjects journal January 2019
Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing journal October 1993
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960 journal October 2008
Bioinformatics prediction of HIV coreceptor usage journal December 2007
ModelFinder: fast model selection for accurate phylogenetic estimates journal May 2017
The Challenge of HIV-1 Subtype Diversity journal April 2008
Molecular and Clinical Epidemiology of CXCR4‐Using HIV‐1 in a Large Population of Antiretroviral‐Naive Individuals journal August 2005
Web Resources for HIV Type 1 Genotypic-Resistance Test Interpretation journal June 2006
Preexisting Resistance to Nonnucleoside Reverse‐Transcriptase Inhibitors Predicts Virologic Failure of an Efavirenz‐Based Regimen in Treatment‐Naive HIV‐1–Infected Subjects
  • Kuritzkes, Daniel R.; Lalama, Christina M.; Ribaudo, Heather J.
  • The Journal of Infectious Diseases, Vol. 197, Issue 6 https://doi.org/10.1086/528802
journal March 2008
A Computer Program Designed to Screen Rapidly for HIV Type 1 Intersubtype Recombinant Sequences journal November 1995
Retrieval and on-the-fly alignment of sequence fragments from the HIV database journal May 2001
IVA: accuratede novoassembly of RNA virus genomes journal February 2015
Clinical Implications of HIV-1 Minority Variants journal February 2013
Clinical Impact of Pretreatment Human Immunodeficiency Virus Drug Resistance in People Initiating Nonnucleoside Reverse Transcriptase Inhibitor–Containing Antiretroviral Therapy: A Systematic Review and Meta-analysis journal November 2020
Deep Sequencing to Infer HIV-1 Co-Receptor Usage: Application to Three Clinical Trials of Maraviroc in Treatment-Experienced Patients journal December 2010
Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case–control study using centralized ultrasensitive 454 pyrosequencing journal October 2014
Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes journal January 2019
Ultrafast Approximation for Phylogenetic Bootstrap journal February 2013
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes journal July 2003
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis journal April 2016
Genetic diversity of HIV in Africa: impact on diagnosis, treatment, vaccine development and trials journal January 2003
Higher viral load may explain the dominance of CRF02_AG in the molecular epidemiology of HIV in Ghana journal May 2004
HIV subtype diversity worldwide journal January 2019
Technologies for HIV-1 drug resistance testing: inventory and needs journal July 2022
Transmission of HIV-1 minority-resistant variants and response to first-line antiretroviral therapy journal July 2008
Brief Report: HIV-1 Tropism During Primary Infections in France: 1996–2014 journal August 2016
Brief Report: Complete Genome Sequence of CG-0018a-01 Establishes HIV-1 Subtype L journal March 2020
High Prevalence of Unique Recombinant Forms of HIV-1 in Ghana: Molecular Epidemiology From an Antiretroviral Resistance Study journal August 2008
Dynamic HIV-1 genetic recombination and genotypic drug resistance among treatment-experienced adults in northern Ghana journal November 2017
Human immunodeficiency virus type 1 biological variation and coreceptor use: from concept to clinical significance journal October 2011
Resistance development over 144 weeks in treatment-naive patients receiving tenofovir disoproxil fumarate or stavudine with lamivudine and efavirenz in Study 903* journal October 2006
The early spread and epidemic ignition of HIV-1 in human populations journal October 2014
Human Immunodeficiency Virus Type 1 Mutations Selected in Patients Failing Efavirenz Combination Therapy journal September 2000
Evaluation of Eight Different Bioinformatics Tools To Predict Viral Tropism in Different Human Immunodeficiency Virus Type 1 Subtypes journal March 2008
Genotypic Prediction of Human Immunodeficiency Virus Type 1 CRF02-AG Tropism journal July 2009
Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool journal June 2012
Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis journal January 2005
Quality of antiretroviral therapy services in Ghana: Implications for the HIV response in resource-constrained settings journal January 2021
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
Frequent CXCR4 tropism of HIV-1 subtype A and CRF02_AG during late-stage disease - indication of an evolving epidemic in West Africa journal March 2010
Women and HIV in Sub-Saharan Africa journal January 2013
Genetic analysis of HIV-1 Circulating Recombinant Form 02_AG, B and C subtype-specific envelope sequences from Northern India and their predicted co-receptor usage journal December 2009
HIV-1 CRF 02 AG polymerase genes in Southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes journal January 2009
What explains gender inequalities in HIV/AIDS prevalence in sub-Saharan Africa? Evidence from the demographic and health surveys journal November 2016
A gendered analysis of living with HIV/AIDS in the Eastern Region of Ghana journal May 2020
Factors associated with viral suppression and rebound among adult HIV patients on treatment: a retrospective study in Ghana journal May 2022
Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana journal July 2020
Haploflow: strain-resolved de novo assembly of viral genomes journal July 2021
HIV/AIDS in sub-Saharan Africa: Current status, challenges and prospects journal April 2017
Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update journal March 2009
HIV-1 Drug-Resistance Surveillance among Treatment-Experienced and -Naïve Patients after the Implementation of Antiretroviral Therapy in Ghana journal August 2013
HIV Infection and AIDS in Sub-Saharan Africa: Current Status, Challenges and Opportunities journal April 2016
The Tale of Two Epidemics: HIV/AIDS in Ghana and Namibia journal October 2021
Quality of antiretroviral therapy services in Ghana: Implications for the HIV response in resource-constrained settings collection January 2021
Living with HIV in Ghana: Disclosure of status and experiences of persons receiving antiretroviral therapy journal July 2021
Global and Regional Estimates for Subtype-Specific Therapeutic and Prophylactic HIV-1 Vaccines: A Modeling Study journal July 2021
High-level resistance to non-nucleos(t)ide reverse transcriptase inhibitor based first-line antiretroviral therapy in Ghana; A 2017 study journal August 2022
Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping journal June 2020
Migration, sexual networks, and HIV in Agbogbloshie, Ghana journal October 2014
Occurrence of transmitted HIV-1 drug resistance among Drug-naïve pregnant women in selected HIV-care centres in Ghana journal April 2017
Ghana’s HIV epidemic and PEPFAR’s contribution towards epidemic control journal March 2019
HIV Stigma and Status Disclosure in Three Municipalities in Ghana journal June 2021
What explains gender inequalities in HIV/AIDS prevalence in sub-Saharan Africa? Evidence from the demographic and health surveys collection January 2016
Haploflow: strain-resolved de novo assembly of viral genomes collection January 2021

Similar Records

Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola
Journal Article · Sun Jul 31 20:00:00 EDT 2016 · AIDS Research and Human Retroviruses · OSTI ID:1459811
HIV drug resistance during antiretroviral therapy scale-up in Uganda, 2012–19: a population-based, longitudinal study
Journal Article · Fri Dec 26 19:00:00 EST 2025 · The Lancet Microbe · OSTI ID:3007520
HIV-1 subtype distribution in the Gambia and the significant presence of CRF49_cpx, a novel circulating recombinant form
Journal Article · Fri Oct 08 20:00:00 EDT 2010 · Retrovirology · OSTI ID:1626608

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Ghana
HIV
HIV-1
coreceptor usage
molecular epidemiology
pretreatment drug resistance
subtype diversity