Sequence Note: Identification of All HIV Type 1 Group M Subtypes in Senegal, a Country with Low and Stable Seroprevalence

Touré-Kâne, Coumba; Montavon, Céline; Faye, Mame Awa; Mandoumb, Pape; Eacute,; Sow, Papa Salif; Ndoye, Ibra; Gaye-Diallo, Aïssatou; Delaporte, Eric; Peeters, Martine; Mboup, Souleymane

doi:10.1089/088922200309025

Cited by 63 publications

(39 citation statements)

References 25 publications

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“…Indeed, in western Africa, 80% of the subtype A samples can be detected with the specific subtype A primers (42), and HMA was able to identify the genetic subtype for more than 90% of the samples (43,58). In the DRC, only 45% of the subtype A samples could be detected with the subtype A-specific primers, and less than 50% could be identified by HMA.…”

Section: Discussionmentioning

confidence: 99%

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

Vidal¹,

Peeters²,

Mulanga-Kabeya³

et al. 2000

J Virol

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287

187

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The purpose of this study was to document the genetic diversity of human immunodeficiency virus type 1 (HIV-1) in the Democratic Republic of Congo (DRC; formerly Zaire). A total of 247 HIV-1-positive samples, collected during an epidemiologic survey conducted in 1997 in three regions (Kinshasa [the capital], Bwamanda [in the north], and Mbuyi-Maya [in the south]), were genetically characterized in the env V3-V5 region. All known subtypes were found to cocirculate, and for 6% of the samples the subtype could not be identified. Subtype A is predominant, with prevalences decreasing from north to south (69% in the north, 53% in the capital city, and 46% in the south). Subtype C, D, G, and H prevalences range from 7 to 9%, whereas subtype F, J, K, and CRF01-AE strains represent 2 to 4% of the samples; only one subtype B strain was identified. The highest prevalence (25%) of subtype C was in the south, and CRF01-AE was seen mainly in the north. The high intersubtype variability among the V3-V5 sequences is the most probable reason for the low (45%) efficiency of subtype A-specific PCR and HMA (heteroduplex mobility assay). Eighteen (29%) of 62 samples had discordant subtype designations between env and gag. Sequence analysis of the entire envelope from 13 samples confirmed the high degree of diversity and complexity of HIV-1 strains in the DRC; 9 had a complex recombinant structure in gp160, involving fragments of known and unknown subtypes. Interestingly, the unknown fragments from the different strains did not cluster together. Overall, the high number of HIV-1 subtypes cocirculating, the high intrasubtype diversity, and the high numbers of possible recombinant viruses as well as different unclassified strains are all in agreement with an old and mature epidemic in the DRC, suggesting that this region is the epicenter of HIV-1 group M.

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Section: Discussionmentioning

confidence: 99%

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

Vidal¹,

Peeters²,

Mulanga-Kabeya³

et al. 2000

J Virol

Self Cite

287

187

View full text Add to dashboard Cite

show abstract

“…The vast majority of HIV-1 infections in sub-Saharan Africa are caused by subtypes A and C (30). The HIV-1 subtype A epidemic, including CRF02_AG-IbNg-like strains (20,21,35,55,70,75,77,79,102,108), dominates in West, Central, and East Africa and reached a plateau at the prevalence rate of 1.5 to 14% by the 1990s (111,112). In contrast, countries in southern Africa and the horn of Africa have experienced the greatest burden of the AIDS epidemic caused predominantly by HIV-1 subtype C (HIV-1C).…”

mentioning

confidence: 99%

Identification of Human Immunodeficiency Virus Type 1 Subtype C Gag-, Tat-, Rev-, and Nef-Specific Elispot-Based Cytotoxic T-Lymphocyte Responses for AIDS Vaccine Design

Novitsky

Rybak

McLane

et al. 2001

J Virol

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“…HIV-1 infection in West Africa is principally due to CRF02AG (2,4,6,19,22,23,25). Recent work conducted in our laboratory revealed that a distinct group of viruses within the HIV-1A subtype radiation is also present in Senegal (30,32,35). Phylogenetic analyses indicated that this group of viruses, which we previously referred to as HIV-1A subcluster 2, differed from sub-subtypes A1 and A2 (30,32).…”

mentioning

confidence: 73%

Distinct Human Immunodeficiency Virus Type 1 Subtype A Virus Circulating in West Africa: Sub-Subtype A3

Meloni

Kim

Sankalé

et al. 2004

J Virol

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Phylogenetic analyses demonstrate significant diversity in worldwide circulating strains of human immunodeficiency virus type 1 (HIV-1). Detailed studies have revealed a complex pattern of intersubtype recombinations, as well as evidence of sub-subtypes circulating in various populations. In this study, we characterized an HIV-1 strain that had previously been identified as a distinct subcluster within the subtype A radiation based on partial sequence data. These viruses were of particular interest given that we recently found that their prevalence was significantly higher in dually infected individuals compared to women who were singly infected with HIV-1. Five viruses isolated from commercial sex workers in Dakar, Senegal, were full-length PCR amplified and sequenced. Phylogenetic analyses indicated that, whereas three of these viruses were closely related and clustered overall within the HIV-1 subtype A radiation, they were distinct from previously characterized sub-subtype A1 and A2 viruses. The clustering pattern was maintained in the individual gag, pol, and env regions of the genome. Distance calculations between these viruses, which we termed A3, and other reference sub-subtype A1 and A2 viruses fell in the range of distances between previously characterized sub-subtype groups. In addition, we found evidence of two A3-containing recombinants in our cohort. These recombinants are mosaics composed of sequence from both sub-subtype A3 and CRF02AG, the major circulating recombinant form in this West African population. Based on phylogenetic analyses, we propose that the group of viruses found in the Dakar sex worker cohort, previously referred to as HIV-1 A subcluster 2, be referred to as HIV-1 sub-subtype A3.

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Sequence Note: Identification of All HIV Type 1 Group M Subtypes in Senegal, a Country with Low and Stable Seroprevalence

Cited by 63 publications

References 25 publications

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

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

Identification of Human Immunodeficiency Virus Type 1 Subtype C Gag-, Tat-, Rev-, and Nef-Specific Elispot-Based Cytotoxic T-Lymphocyte Responses for AIDS Vaccine Design

Distinct Human Immunodeficiency Virus Type 1 Subtype A Virus Circulating in West Africa: Sub-Subtype A3

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