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A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses
Published on: August 31, 2014
High genetic diversity of HIV-1 strains in Chad, West Central Africa
Nicole Vidal1, Donato Koyalta, Vincent Richard
1UR36, Laboratoire Retrovirus, IRD, BP 64S01, 34394 Montpellier Cedex 1, France.
Insights
Genetic diversity of HIV-1 in Chad reveals a unique subtype distribution, with notable prevalence of subtype D and CRF11, differing from neighboring regions. This highlights the heterogeneous nature of HIV-1 strains across Africa.
Area of Science:
- Virology
- Genetics
- Epidemiology
Background:
- HIV-1 genetic diversity impacts treatment and prevention strategies.
- Understanding regional subtype distribution is crucial for effective public health interventions.
Purpose of the Study:
- To document the genetic diversity of HIV-1 strains in Chad.
- To identify circulating subtypes and circulating recombinant forms (CRFs) in N'Djamena.
- To compare Chad's HIV-1 genetic landscape with neighboring countries.
Main Methods:
- Analysis of 107 HIV-1 samples from N'Djamena, Chad.
- Sequencing of V3-V5 env and p24 gag regions.
- Phylogenetic tree analyses to determine subtypes and CRFs.
- Nearly full-length genome sequencing for selected strains.
Main Results:
- Four subtypes (A, D, G, F1) and three CRFs (CRF02_AG, CRF11_cpx, CRF01_AE) were identified.
- Subtype D (18.7%) and CRF11_cpx (13.1%) showed high prevalence.
- Subtype distribution in Chad is unique, with lower CRF02_AG, higher CRF11_cpx and subtype D, and absence of CRF06 compared to neighbors.
- Discordant env and gag subtypes were observed in 27% of strains, with recombination events in 15 cases.
Conclusions:
- HIV-1 genetic diversity in Chad is heterogeneous and distinct from surrounding regions.
- The unique subtype profile may be influenced by founder effects.
- Subtype D strains in Chad represent nonrecombinant variants and form a distinct subcluster.
Abstract:
The genetic diversity of HIV-1 strains in Chad was documented with a total of 107 samples from patients attending the general hospital in N'Djamena, the capital city of Chad. The genetic subtypes were identified in the V3-V5 env and p24 gag regions by sequence and phylogenetic tree analyses. Of the 107 strains, 78 had the same subtype/CRF designation between env and gag. Four subtypes and three CRFs were found to cocirculate: subtype A, 20.5%; subtype D, 18.7%; CRF02_AG, 13.1%; CRF11_cpx, 13.1%; subtype G, 3.7%; CRF01_AE, 2.8%; and subtype F1, 0.9%. The remaining 29 strains (27%) had discordant subtypes or CRF designations between env and gag; in 15 of these 29 strains, a CRF was involved in the recombination event, and 10 were subtype G in gag and subtype A in env, forming a separate subcluster within subtypes G and A. Subtype D strains represent almost 20% of the HIV-1 strains circulating in Chad and form a separate subcluster in gag and env. Nearly full-length genome sequencing for two such strains (99TCD-MN011 and 99TCD-MN012) revealed that they represent nonrecombinant subtype D variants. Compared with neighboring countries, the genetic subtype distribution of HIV-1 strains in Chad is unique for several reasons: lower prevalence of CRF02, high prevalence of CRF11 and subtype D, and absence of CRF06. These data clearly show that subtype distribution is very heterogeneous in Africa, probably the result of different founder effects.
