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

Meloni, Seema; Kim, Bohye; Sankalé, Jean-Louis; Hamel, Donald J.; Tovanabutra, Sodsai; Mboup, Souleymane; McCutchan, Francine E.; Kanki, Phyllis J.

doi:10.1128/jvi.78.22.12438-12445.2004

Cited by 56 publications

(49 citation statements)

References 35 publications

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“…The distribution of HIV-1 genetic diversity with respect to epidemiological factors such as risk group and geographic location is highly dynamic; novel genetic diversity is continually being generated through mutation and recombination, and travel and migration promote the transfer of diverse viral strains between populations, often across large distances (19,26,37). The speed at which genetic diversity is generated by HIV-1 presents a challenge to standard phylogenetic classification systems, as reflected in the growing number of unclassifiable and complex recombinant sequences being reported (13, 34-36, 38, 44), the proliferation of "sub-subtype" nomenclature (11,23,39,45), and accumulating evidence that at least some of the established groupings are artifacts of sampling (1,2,10).…”

Section: Discussionmentioning

confidence: 99%

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

Gifford

Oliveira

Rambaut

et al. 2007

J Virol

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With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods.

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Section: Discussionmentioning

confidence: 99%

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

Gifford

Oliveira

Rambaut

et al. 2007

J Virol

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“…CRF16_A2D has also achieved a global spread and has been identified in Korea and Argentina (Gomez-Carrillo et al, 2004). Subsubtype A3 has only been recently described (Meloni et al, 2004a), and has thus far only been identified in areas of West and Central Africa (Meloni et al, 2004a;Meloni et al, 2004b). Similarly subsubtype A4 is a relatively new strain, and has only been identified within the Democratic Republic of Congo .…”

Section: The Global Distribution Of Hiv-1 Subtypes and Crfsmentioning

confidence: 99%

HIV Recombination and Pathogenesis – Biological and Epidemiological Implications

Saksena¹,

Lau²,

Dwyer³

et al. 2011

HIV and AIDS - Updates on Biology, Immunology, Epidemiology and Treatment Strategies

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“…However, recent work conducted in our lab revealed that a unique group of viruses within the human immunodeficiency virus type 1 (HIV-1) subtype A radiation is also present in the FSW study population (40,42). Through phylogenetic analyses, we have shown that this subcluster of viruses can be classified as HIV-1 sub-subtype A3 (30). The goal of the current investigation was to understand the distribution and dynamics of HIV-1 A3 in the Dakar FSW cohort.…”

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confidence: 99%

“…Manual adjustments, when necessary, were made by using the MacClade version 4.05 program (Sinauer Associates, Inc., Sunderland, Mass.). For reference A3 sequences, we used AY521629 (DDI579), AY521630 (DDJ360), and AY521631 (DDJ369) (30). Phylogenetic analyses were performed, using the SEQBOOT, DNADIST, NEIGHBOR, and CONSENSE programs in the Phylip version 3.6 package (11).…”

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

Cited by 56 publications

References 35 publications

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

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

HIV Recombination and Pathogenesis – Biological and Epidemiological Implications

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

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