<b>Sequence Note</b>: A Novel Subtype A/G/J Recombinant Full-Length HIV Type 1 Genome from Burkina Faso

Oelrichs, Robert; Workman, Cassy; Laukkanen, Tiina; McCutchan, Francine E.; Deacon, Nicholas J.

doi:10.1089/aid.1998.14.1495

Cited by 43 publications

(22 citation statements)

References 17 publications

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“…For instance, the two Indian subtype C sequences were phylogenetically distinct from African subtype C sequences, and the Cambodian E sequence was most similar to a CRF01_AE sequence from a Uruguayan peacekeeper who had been deployed in Cambodia. The subtype G sequences from Burkina Faso were from a heterosexual couple and have been further identified as an A/G/J recombinant or CRF, CRF06_cpx (33). V3 loop peptide sequences were deduced from all nucleotide sequences, and analysis of subtype B V3 loop nucleotide and peptide sequences did not confirm any epidemiological linkage or presence of "founder" viruses in the various patient groups (data not shown).…”

Section: Resultsmentioning

confidence: 99%

Segregation of Human Immunodeficiency Virus Type 1 Subtypes by Risk Factor in Australia

Herring

Wang

et al. 2003

J Clin Microbiol

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The aim of this study was to determine which human immunodeficiency virus type 1 (HIV-1) subtypes were circulating in Australia and to correlate the subtypes with risk factors associated with the acquisition of HIV-1 infection. DNA was extracted from peripheral blood mononuclear cells, and HIV-1 env genes were amplified and subtyped using heteroduplex mobility analysis, with selected samples sequenced and phylogenetic analysis performed. The HIV-1 env subtypes were determined for 141 samples, of which 40 were from female patients and 101 were from male patients; 13 samples were from children. Forty-seven patients were infected by homosexual or bisexual contact, 46 were infected through heterosexual contact, 21 were infected from injecting drug use (IDU), 13 were infected by vertical transmission, 8 were infected from nosocomial exposure, and 6 were infected by other modes of transmission, including exposure to blood products, ritualistic practices, and two cases of intrafamilial transmission. Five subtypes were detected; B (n ‫؍‬ 104), A (n ‫؍‬ 5), C (n ‫؍‬ 17), E (CRF01_AE; n ‫؍‬ 13), and G (n ‫؍‬ 2). Subtype B predominated in HIV-1 acquired homosexually (94% of cases) and by IDU (100%), whereas non-subtype B infections were mostly seen in heterosexually (57%) or vertically (22%) acquired HIV-1 infections and were usually imported from Africa and Asia. Subtype B strains of group M viruses predominate in Australia in HIV-1 transmitted by homosexual or bisexual contact and IDU. However, non-B subtypes have been introduced, mostly acquired via heterosexual contact.

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Section: Resultsmentioning

confidence: 99%

Segregation of Human Immunodeficiency Virus Type 1 Subtypes by Risk Factor in Australia

Herring

Wang

et al. 2003

J Clin Microbiol

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“…Interestingly, two groups of three sequences each were highly homologous to the MAL (A/K) [23] and the 99GR303 (G/A/K) [24] isolates, respectively.…”

Section: Analysis Of Recombinant Hiv-1 Variantsmentioning

confidence: 99%

Changing patterns in HIV‐1 non‐B clade prevalence and diversity in Italy over three decades^*

et al. 2010

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BackgroundHIV-1 non-B subtypes have recently entered Western Europe following immigration from other regions. The distribution of non-B clades and their association with demographic factors, over the entire course of the HIV-1 epidemic, have not been fully investigated in Italy. MethodsWe carried out a phylogenetic analysis of HIV-1 pol sequences derived from 3670 patients followed at 50 Italian clinical centres over nearly three decades. ResultsOverall, 417 patients (11.4%) carried non-B subtypes. The prevalence of non-B strains increased from 2.6% in 1980 -1992 to 18.9% in 1993) in a subset of 2479 subjects with a known year of diagnosis. A multivariate analysis on a subset of 1364 patients for whom relevant demographic data were available indicated that African ethnicity, heterosexual route of infection and year of diagnosis were independently associated with non-B HIV-1 infection (P 0.0001). All pure subtypes, except for clade K, and seven circulating recombinant forms were detected, accounting for 56.6 and 34.1% of the non-B infections, respectively. The F1 subtype was the most prevalent non-B clade among Europeans and was acquired heterosexually in half of this patient population. Unique recombinant forms accounted for 9.4% of the non-B sequences and showed a B/F1 recombination pattern in one-third of cases. ConclusionsThe circulation of non-B clades has significantly increased in Italy in association with demographic changes. Spread of the F1 subtype and B/F recombinants appears to predominate, which may result in a redistribution of the relative proportions of the different strains, and this could lead to overlapping epidemics. Thus, the HIV-1 landscape in Italy may in future be distinct from that of the rest of Europe. IntroductionNine discrete lineages of group M HIV-1 (A-D, F-H, J and K) have differentiated during the global pandemic as a result of massive virus replication, the very high error rate of reverse transcriptase (RT) and the selective pressure exerted by the immune system. The highly recombinogenic activity of HIV-1 RT has added further complexity to the global diversity of HIV-1 as 43 circulating recombinant forms (CRFs) have already been characterized and a number of unique recombinant forms (URFs) have been identified world-wide [1][2][3]. Most subtypes and CRFs were originally restricted to specific geographical regions or populations, but their distribution is constantly evolving [4]. In order to monitor the evolution of the global pandemic, it is convenient and effective to assign viral clades, which allow evaluation of the local epidemiological trends that result from social changes and migration flows. [6][7][8][9][10][11][12][13]. The recent epidemiology of HIV-1 infection in Western European countries with large immigrant communities has been characterized by increasing genetic diversity and a marked rise in non-B subtype strains among newly diagnosed individuals [14][15][16][17]. It has been assumed that most non-B subtype infections in Western Europe are linked to migration ...

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“…CRF06_cpx was first described in 1996 in a patient from Burkina Faso residing in Australia (Oelrichs et al, 1998); it has since been detected at a lower prevalence in other West African countries (Mali, Côte d'Ivoire, Ghana, Benin, Senegal, etc. ) as well as in Nigeria and Niger.…”

Section: Introductionmentioning

confidence: 99%

Reconstructing the HIV-1 CRF02_AG and CRF06_cpx epidemics in Burkina Faso and West Africa using early samples

Yebra

Kalish

Brown

2016

Infection, Genetics and Evolution

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Sequence Note: A Novel Subtype A/G/J Recombinant Full-Length HIV Type 1 Genome from Burkina Faso

Cited by 43 publications

References 17 publications

Segregation of Human Immunodeficiency Virus Type 1 Subtypes by Risk Factor in Australia

Segregation of Human Immunodeficiency Virus Type 1 Subtypes by Risk Factor in Australia

Changing patterns in HIV‐1 non‐B clade prevalence and diversity in Italy over three decades^*

Reconstructing the HIV-1 CRF02_AG and CRF06_cpx epidemics in Burkina Faso and West Africa using early samples

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Sequence Note: A Novel Subtype A/G/J Recombinant Full-Length HIV Type 1 Genome from Burkina Faso

Cited by 43 publications

References 17 publications

Segregation of Human Immunodeficiency Virus Type 1 Subtypes by Risk Factor in Australia

Segregation of Human Immunodeficiency Virus Type 1 Subtypes by Risk Factor in Australia

Changing patterns in HIV‐1 non‐B clade prevalence and diversity in Italy over three decades*

Reconstructing the HIV-1 CRF02_AG and CRF06_cpx epidemics in Burkina Faso and West Africa using early samples

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Changing patterns in HIV‐1 non‐B clade prevalence and diversity in Italy over three decades^*