Genetic Analysis of HIV-1 Strains in Rural Eastern Cameroon Indicates the Evolution of Second-Generation Recombinants to Circulating Recombinant Forms

Konings, Frank; Haman, Greg R.; Xue, Ying; Urbanski, Mateusz M.; Hertzmark, Kathryn; Nanfack, Aubin; Achkar, Jacqueline M.; Burda, Sherri; Nyambi, Phillipe N.

doi:10.1097/01.qai.0000219784.81163.2e

Cited by 40 publications

(47 citation statements)

References 32 publications

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“…Unclassified sequences (recombinant and nonrecombinant forms, such as the suggested new cluster within subtype A) were always found linked to Africa, where a clear distinction between subtypes is lost (4,28). This could reflect the huge potential for new HIV variants appearing and spreading in the future (29). For instance, a new possible subsubtype A close to subsubtype A3 could be suggested in individuals from Equatorial Guinea and Mali living in Madrid (Fig.…”

Section: Discussionmentioning

confidence: 99%

Molecular Surveillance of HIV-1 in Madrid, Spain: a Phylogeographic Analysis

González-Alba

Holguín

Garcı́a

et al. 2011

J Virol

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The molecular epidemiology of HIV-1 is constantly changing, mainly as a result of human migratory flows and the high adaptive ability of the virus. In recent years, Spain has become one of Europe's main destinations for immigrants and one of the western European countries with the highest rates of HIV-positive patients. Using a phylogeographic approach, we have analyzed the relationship between HIV-1 variants detected in immigrant and native populations of the urban area of Madrid. Our project was based on two coincidental facts. First, resistance tests were extended to naïve and newly diagnosed patients, and second, the Spanish government legislated the provision of legal status to many immigrants. This allowed us to obtain a large data set (n ‫؍‬ 2,792) from 11 Madrid hospitals of viral pol sequences from the two populations, and with this unique material, we explored the impact of immigration in the epidemiological trends of HIV-1 variants circulating in the largest Spanish city. The prevalence of infections by non-B HIV-1 variants in the studied cohort was 9%, rising to 25% among native Spanish patients. Multiple transmission events involving different lineages and subsubtypes were observed in all the subtypes and recombinant forms studied. Our results also revealed strong social clustering among the most recent immigrant groups, such as Russians and Romanians, but not in those groups who have lived in Madrid for many years. Additionally, we document for the first time the presence of CRF47_BF and CRF38_BF in Europe, and a new BG recombinant form found in Spaniards and Africans is tentatively proposed. These results suggest that the HIV-1 epidemic will evolve toward a more complex epidemiological landscape.

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Section: Discussionmentioning

confidence: 99%

Molecular Surveillance of HIV-1 in Madrid, Spain: a Phylogeographic Analysis

González-Alba

Holguín

Garcı́a

et al. 2011

J Virol

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“…For instance, viruses carrying subtype G sequences at pol could be pure G subtypes or recombinants, and interestingly, 18 of the CRF described (http://www.hiv.lanl.gov/content/sequence /HIV/CRFs/CRFs.html) harbor clade G sequences in partial or complete pol coding regions. Therefore, it is not surprising that CRF may constitute at least 10 to 20% of new HIV-1 infections worldwide and that recombination involving different non-B subtypes is rising where diverse variants cocirculate, particularly in areas where distinct subtypes are highly prevalent (8,12,21,24).…”

Section: Discussionmentioning

confidence: 99%

Reliability of Rapid Subtyping Tools Compared to That of Phylogenetic Analysis for Characterization of Human Immunodeficiency Virus Type 1 Non-B Subtypes and Recombinant Forms

Holguín

López²,

Soriano³

2008

J Clin Microbiol

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Human immunodeficiency virus type 1 (HIV-1) subtyping is often estimated on the basis of pol sequences by using online websites instead of phylogenetic analysis (phy). We evaluated the reliability of distinct rapid subtyping tools versus phy with a large panel of HIV-1 non-B subtypes and circulating recombinant forms (CRF). pol sequences (277 protease [PR] and 171 reverse transcriptase [RT] sequences) previously assigned by phy to eight distinct HIV-1 non-B subtypes were obtained from 277 HIV-infected patients. Phy was run again to identify CRF. Subtyping was then performed using three rapid tools (the Stanford, NCBI, and REGA online tools). Thirty-three additional clade B sequences were tested as controls. New phylogenetic analyses reclassified two-thirds of pol sequences previously assigned to HIV-1 non-B clades as CRF. CRF02_AG variants were correctly assigned by the Stanford and NCBI tools for 92 to 97% and 96 to 99% of PR-RT sequences, respectively, while they were correctly assigned by the REGA tool for only 18 to 32% of PR-RT sequences. The Stanford, NCBI, and REGA tools failed to assign pure non-B clades correctly for 24 to 33%, 35%, and 57 to 64% of PR-RT sequences, respectively. For PR-RT sequences from CRF other than CRF02_AG, discrepancies occurred in 98 to 100%, 18 to 43%, and 80 to 87% of sequences, respectively. The concordance between those tools and phy was almost complete for subtype B assignment. Rapid subtyping tools show relatively low agreement with phy in identifying HIV-1 non-B clades and CRF other than CRF02_AG. The Stanford tool shows the best concordance with phy for the assignment of pure non-B clades, while the NCBI tool performs better at identifying CRF. Before entering routine clinical use, rapid subtyping tools should be optimized and updated periodically. Larger numbers of different non-B subtypes and CRF sequences should be included.

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“…5.5% in adults (2). In Cameroon, where many HIV-1 subtypes circulate (7,11,15,21), vertical transmission of HIV contributes to a majority of the pediatric AIDS cases.…”

Section: /Cd8mentioning

confidence: 99%