High Genetic Diversity of HIV-1 Strains in Chad, West Central Africa

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.

Genetic Diversity of HIV Type 1 in Likasi, Southeast of the Democratic Republic of Congo

“…[2][3][4][5][6][7] The proportion of CRF02_AG among subtype A strains based on env sequences decreases from west to central Africa, with an absence of CRF02_AG in the Democratic Republic of Congo (DRC). 2,8,9 The profile of HIV-1 endemic in DRC, such as high number of cocirculating HIV-1 subtypes, possible recombinant viruses, and unclassified strains, is consistent with that of an old and mature epidemic of HIV-1. 5 The DRC is bordered on the southeast by Zambia.…”

“…This is higher than that reported in other regions of the country (29-44%). 5,8,15 In Lubumbashi, a city on the southeast border of the DRC with Zambia, subtype C was reported to be predominant (51.9%), followed by subtype A (22.1%). 15 Our data highlight a high prevalence of subtype A (37.0% and 52.5%) and low prevalence of subtype C (7.4% and 12.5%) in Likasi based on env-C2V3 and pol-IN analyses, respectively.…”

Evidence of intratypic recombination in natural populations of hepatitis C virus

“…The recombination breakpoint for non-segmented positive-strand RNA viruses, such as polioviruses and other picornaviruses (Santti et al, 1999;Guillot et al, 2000;Kew et al, 2002), as well as members of the family Flaviviridae, are often located in the part of the genome encoding the non-structural proteins but sometimes in genes encoding structural proteins (CostaMattioli et al, 2003;Martin et al, 2002). Moreover, several possible recombination breakpoints have been identified in other RNA viruses, such as human immunodeficiency virus (HIV), and many more are being reported (Onafuwa et al, 2003;Vidal et al, 2003;Strimmer et al, 2003;Najera et al, 2002). The recombination point in our recombinant strain was situated in the NS5B region (see Figs 2 and 3).…”

Phylogenetic Surveillance of Viral Genetic Diversity and the Evolving Molecular Epidemiology of Human Immunodeficiency Virus Type 1

“…Although broad diversity is concentrated in areas of West and Central Africa, where infection is longest established (24,(40)(41)(42)46), it is increasingly evident elsewhere as infection expands globally (9,13,14,28,30,34,44).…”