<b>Sequence Note</b>: Genetic Variability of HIV Type 1 in Bénin

HEYNDRIC, L.; Janssens, Wouter; Alary, Michel; Fransen, Katrien; Vereecken, Katleen; Coppens, S; Willems, Betty; Davo, N; GUÈDÈMÈ, A.; Baganizi, Enias; Joly, J; Groen, G van der

doi:10.1089/aid.1996.12.1495

Cited by 15 publications

(6 citation statements)

References 7 publications

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“…A comparative analysis of subtype A variants from East and West Africa Although multiple HIV-1 subtypes A, B, and D have been described previously by convenience sampling in Ivory Coast, 10,19 this is the first report of subtype G in this country. To date, other subtype G variants have been reported from Nigeria, 6 Ghana, 8 Benin, 9 Gabon, 20 Mali, 21 Tanzania, 22 Russia, 23 and Uganda. 24,25 Interestingly, the four subtype G strains in this study all had unique V3 loop crowns.…”

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confidence: 99%

Genetic Analysis of Human Immunodeficiency Virus in Abidjan, Ivory Coast Reveals Predominance of HIV Type 1 Subtype A and Introduction of Subtype G

Ellenberger

Pienia̧źek²,

Nkengasong³

et al. 1999

AIDS Research and Human Retroviruses

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To better understand the molecular epidemiology of HIV genetic diversity in Abidjan, Ivory Coast, we performed a genetic analysis of 170 HIV-1-seropositive specimens representing newly diagnosed tuberculosis patients (n = 143) and women monitored in a mother-to-child transmission cohort study (n = 27). Preliminary screening with RFLP presumptively classified 162 (95.3%) of these as subtype A. The envelope region of 108 specimens was subtyped by sequence analysis: 102 (94.4%) were subtype A, 2 (1.9%) were subtype D, and 4 (3.7%) were subtype G. Subtyping gag and env regions of the genome suggested that five of the six nonsubtype A isolates exhibited a potentially mosaic structure. A comparative phylogenetic analysis of HIV-1 subtype A C2V3 from 27 Ivory Coast and 21 Ugandan sequences revealed a striking clustering among Ivory Coast variants, and an independent segregation from Ugandan subtype A. Despite independent clustering with other subtype A specimens, limited variability of the V3 loop apex was observed; the globally predominant V3 motif, GPGQ, represented 90.1% of the HIV-1 strains. This study demonstrates that clade A is the predominant HIV-1 subtype in HIV-seropositive individuals in Abidjan, Ivory Coast and that these strains are phylogenetically distinct from other subtype A strains observed in East Africa.

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confidence: 99%

Genetic Analysis of Human Immunodeficiency Virus in Abidjan, Ivory Coast Reveals Predominance of HIV Type 1 Subtype A and Introduction of Subtype G

Ellenberger

Pienia̧źek²,

Nkengasong³

et al. 1999

AIDS Research and Human Retroviruses

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“…We first conducted a BLAST search to identify a subset of GenBank submitted sequences, which might have originally been classified as subtype A, that would potentially cluster with subsubtype A3 reference sequences. Phylogenetic analyses indicated that a few of the previously characterized sequences from Ivory Coast (AF000450, AF000453, AF000456, AF000466, and AF000475) (9), Equatorial Guinea (AF530014) (34), Niger (AJ429851, AJ429856, AJ429866, AJ429869, and AJ429875) (26), Guinea-Bissau (AF178170, AF178172, AF178184, and AF178195) (3), Nigeria (AF069932, AJ389774, AY653735, and AY653736) (29,37), and Benin (U61862 and U61866) (14) clustered with sub-subtype A3 viruses identified in the Dakar FSW cohort (Fig. 2).…”

Section: Resultsmentioning

confidence: 99%

Molecular Epidemiology of Human Immunodeficiency Virus Type 1 Sub-Subtype A3 in Senegal from 1988 to 2001

Meloni

Sankalé

Hamel

et al. 2004

J Virol

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The global human immunodeficiency virus (HIV)epidemic is characterized by significant genetic diversity in circulating viruses. We have recently characterized a group of viruses that form a distinct sub-subtype within the subtype A radiation, which we have designated HIV type 1 (HIV-1) sub-subtype A, circulating in West Africa. A prospective study of a cohort of female sex workers (FSW) in Dakar, Senegal over an 18-year period indicated that an A3-specific sequence in the C2-V3 region of the env gene was found in 46 HIV-1-infected women. HIV-1 sub-subtype A3 appeared in the FSW population as early as 1988 and continued to be transmitted as of 2001. We also found that HIV-1 A3 is not confined to the FSW cohort in Senegal but is also circulating in the general population in Dakar. Furthermore, analyses of viral sequences from a few other West and Central African countries also demonstrated evidence of HIV-1 A3 sequence in isolates from HIV-1-infected people in Ivory Coast, Nigeria, Niger, Guinea Bissau, Benin, and Equatorial Guinea. Overall, because of the evidence of sub-subtype A3 in the general population in Senegal, as well as in a few neighboring West and Central African countries, along with the increasing incidence of infection with A3-containing viruses in the Dakar high-risk FSW population, we feel that HIV-1 sub-subtype A3 viruses are important to distinguish and monitor.Molecular surveillance has revealed significant heterogeneity in the prevalence and geographic distribution of various subtypes worldwide (5,35,36). For example, subtype B viruses account for an estimated 12.3% of cases globally, but infections with this subtype are primarily seen in the Americas, Western Europe, and Australia (35). Conversely, subtype C viruses were estimated to have caused Ͼ47% of the worldwide infections, with the highest incidence in southern African countries, Ethiopia, and India (35). As with the nonrecombinant subtypes, circulating recombinant forms (CRFs) also show founder effects and uneven geographic distributions. For example, CRF01_AE appears to be the cause of a high proportion of infections in Southeast Asia and seems to be largely confined to that area of the world with relatively little spread into other populations (35). In contrast, CRF02_AG contributes to a major number of new infections in West Africa and appears to be associated with rapidly spreading epidemics in West African countries (3,6,7,28,31,35,37). The underlying causes of the varied geographic distributions are most likely founder effects with other contributing factors, such as human population movements, unregulated commercial sex work, and intravenous drug use.Over the course of an 18-year prospective study monitoring a cohort of female sex workers (FSWs) in Dakar, Senegal, we found that the most prevalent circulating strain in the cohort is CRF02_AG, as seen in other parts of West Africa (2,6,7,28,31,35,37). However, recent work conducted in our lab revealed that a unique group of viruses within the human immunodeficiency virus type 1 (...

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“…The genome of the 99GR303 isolate is a complex recombinant comprising at least five distinct subtypes. Subtypes J and K are extremely rare in Western Africa (Heyndrickx et al , 1996 ; Ishikawa et al , 1996 ; Takehisa et al , 1997 ; Ellenberger et al , 1999 ; McCutchan et al , 1999 ), suggesting that putative recombination events involving these subtypes could have occurred in other geographical regions. The identification of additional mosaic HIV-1 viruses consisting of partial regions that show similarity to this novel sequence could provide further information on how these isolates originated.…”

Section: Full Textmentioning

confidence: 99%

Molecular characterization of a complex, recombinant human immunodeficiency virus type 1 (HIV-1) isolate (A/G/J/K/?): evidence to support the existence of a novel HIV-1 subtype

Paraskevis

Magiorkinis

et al. 2001

Journal of General Virology

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Recombination is one of several factors that contribute to the great genetic diversity of human immunodeficiency virus type 1 (HIV-1). In the current study, analysis of the full-length genome of a novel complex mosaic HIV-1 isolate (99GR303) from a Greek sailor who was possibly infected in Sierra Leone, Africa is presented. The 99GR303 isolate was found to comprise genomic regions belonging to subtypes A, G, J and K as well as of regions of a subtype that remains unclassified. For a partial region of env as well as vpr, no apparent similarity to the known HIV-1 subtypes or to any of the circulating recombinant forms was found. In fact, in the partial env gene, including the C2-V3 region, the 99GR303 isolate formed a new clade, suggesting the existence of an additional HIV-1 subtype. Thus, novel recombinants embody partial genomic regions which may have originated either from subtypes that existed in the past and became extinct or from contemporary subtypes that are extremely rare.

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Sequence Note: Genetic Variability of HIV Type 1 in Bénin

Cited by 15 publications

References 7 publications

Genetic Analysis of Human Immunodeficiency Virus in Abidjan, Ivory Coast Reveals Predominance of HIV Type 1 Subtype A and Introduction of Subtype G

Genetic Analysis of Human Immunodeficiency Virus in Abidjan, Ivory Coast Reveals Predominance of HIV Type 1 Subtype A and Introduction of Subtype G

Molecular Epidemiology of Human Immunodeficiency Virus Type 1 Sub-Subtype A3 in Senegal from 1988 to 2001

Molecular characterization of a complex, recombinant human immunodeficiency virus type 1 (HIV-1) isolate (A/G/J/K/?): evidence to support the existence of a novel HIV-1 subtype

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