Near Full-Length Genome Characterization of a Newly Identified HIV Type 1 Subtype F Variant Circulating in St. Petersburg, Russia

Fernández-García, Aurora; Cuevas, Maria Teresa; Vinogradova, A. I.; Rakhmanova, Aza; Pérez-Álvarez, Lucı́a; Castro, R. Ojea de; Osmanov, Saladin; Thomson, Michael M.

doi:10.1089/aid.2009.0140

Cited by 9 publications

(5 citation statements)

References 17 publications

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“…Donor samples were collected between 2009 and 2011, and included a mix of supernatants obtained from recently infected (Fiebig IV and V) and chronically infected individuals as defined by the contributing laboratory. Thirty-three viral supernatants were obtained from the Centre for AIDS Reagents, NIBSC HPA UK, supported by the EC FP6/7 Europrise Network of Excellence, and NGIN consortia and the Bill and Melinda Gates GHRCCAVD Project and were donated by Lucia Pérez Alvarez (Instituto de Salud Carlos III) (Fernandez-Garcia et al, 2009; Cuevas et al, 2010; Fernandez-Garcia et al, 2010; Delgado et al, 2012; Thomson et al, 2012; Diez-Fuertes et al, 2013). Twenty-three culture supernatants from donors in Cameroon, Spain, USA and Germany were kindly provided by Indira Hewlett (CBER, FDA) (Vallejo et al, 2003; Ragupathy et al, 2011; Zhao et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

Development of a contemporary globally diverse HIV viral panel by the EQAPOL program

Sánchez

DeMarco

Hora

et al. 2014

Journal of Immunological Methods

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The significant diversity among HIV-1 variants poses serious challenges for vaccine development and for developing sensitive assays for screening, surveillance, diagnosis and clinical management. Recognizing a need to develop a panel of HIV representing the current genetic and geographic diversity NIH/NIAID contracted the External Quality Assurance Program Oversight Laboratory (EQAPOL) to isolate, characterize and establish panels of HIV-1 strains representing global diverse subtypes and circulating recombinant forms (CRFs), and to make them available to the research community. HIV-positive plasma specimens and previously established isolates were collected through a variety of collaborations with a preference for samples from acutely/recently infected persons diagnosed since 2009. Source specimens were cultured to high-titer/high-volume using well-characterized cryopreserved PBMCs from healthy donors. Panel samples were stored as neat culture supernatant or diluted into defibrinated plasma. Characterization for the final expanded virus stocks included viral load, p24 antigen, infectivity (TCID), sterility, coreceptor usage, and near full-length genome sequencing. Viruses are made available to approved, interested laboratories using an online ordering application. The current EQAPOL Viral Diversity panel includes over 101 viral specimens representing 6 subtypes (A, B, C, D, F, and G), 2 sub-subtypes (F1 and F2), 7 CRFs (01, 02, 04, 14, 22, 24, and 47), 19 URFs and 3 group O viruses from 22 countries. The EQAPOL Viral Diversity panel is an invaluable collection of well-characterized reagents that are available to the scientific community, including researchers, epidemiologists, and commercial manufacturers of diagnostics and pharmaceuticals to support HIV research and diagnostic and vaccine development.

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Section: Methodsmentioning

confidence: 99%

Development of a contemporary globally diverse HIV viral panel by the EQAPOL program

Sánchez

DeMarco

Hora

et al. 2014

Journal of Immunological Methods

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“…Pure clade E has never been isolated but rather appears as an A/E mosaic which has been detected in Thailand, the Philippines, China and Central Africa [14,15]. Subtype F has been reported in Central Africa [17,18], South America [19] and Eastern Europe [20,21] while G and A/G recombinants have been observed in Western and Eastern Africa as well as in central Europe [15]. Subtypes H and J were described in Central Africa [22,23,24]) and in Angola [25,26]).…”

Section: Introductionmentioning

confidence: 99%

Phylogeny of partial gag, pol and env genes show predominance of HIV-1G and CRF02_AG with emerging recombinants in south-eastern Nigeria

Udeze

Olaleye

Odaibo

2020

Heliyon

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Human Immunodeficiency Virus is characterized by high degree of genetic diversity with marked differences in its geographic distribution even within a country. This study was designed to identify the strains of HIV-1 circulating among infected individuals in southeastern parts of Nigeria. Genomic DNA was extracted from blood samples of 30 HIV-1 infected individuals from Anambra, Delta and Imo states of southeastern Nigeria. Portions of the genome corresponding to entire p24 gag , entire protease and C2–V3 env genes were amplified by nested PCR, sequenced using Sanger's method and phylogenetically analysed. Out of the 30 samples sequenced, 17, 28 and 14 readable sequences were obtained for gag , pol and env regions respectively. The most prevalent subtypes were CRF02_AG (41.2% in gag , 57.1% in pol protease and 50.0% in env ) and G (29.4% in gag , 35.7% in pol protease and 35.7% in env ). Other subtypes identified include A (17.7% in gag , 7.1% in env ) and J (7.1% in env ). Also 2 sequences each in gag (11.8%) and pol protease (7.1%) regions were unclassified but preliminary analysis showed they are recombinants. Furthermore, 71.4% of the isolates with sequences in the 3 regions and 26.7% of those with sequences in 2 genomic regions were recombinant forms. CRF02_AG and subtype G are the predominant HIV-1 strains circulating among infected individuals in southeastern Nigeria. Preliminary analysis results of unclassified sequences suggest that they are new recombinants.

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“…[2][3][4] In 1995-1996 HIV-1 infections began to increase dramatically concomitantly with the expansion of a subtype A variant of Central African ancestry 5 that originated in Southern Ukraine 6,7 and spread to all countries of the former Soviet Union (FSU), in most of which it is the predominant HIV-1 genetic form 8,9 ; for this reason it is frequently designated A FSU variant. In addition to A FSU , other HIV-1 genetic forms circulating in FSU countries at lower prevalences include subtype B, predominant in men who have sex with men, [8][9][10] CRF03_AB, predominant in the Russian cities of Kaliningrad 11 and Cherepovets, 12 subtype F, circulating as a minor variant in St. Petersburg, Russia, 13 and a CRF02_AG variant (CRF02_AG FSU ), 14,15 which was first detected among injecting drug users (IDUs) in Tashkent, Uzbekistan, in 1999-2000, 14 and has subsequently been reported in Kazakhstan, new near full-length genome sequences of CRF63_02A1, reanalyzing its mosaic structure, and we estimate its epidemic history. For this study, 26 serum samples from HIV-1-infected individuals were collected in May and June 2013 at the Center for Prevention and Control of AIDS and Infectious Diseases, Koltsovo, Novosibirsk region, which is located 5 km from the city of Novosibirsk and attends all HIV-infected people of the Novosibirsk region.…”

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confidence: 99%

Short Communication: Molecular Epidemiology, Phylogeny, and Phylodynamics of CRF63_02A1, a Recently Originated HIV-1 Circulating Recombinant Form Spreading in Siberia

Shcherbakova

Shalamova²,

Delgado³

et al. 2014

AIDS Research and Human Retroviruses

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The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A FSU ) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A FSU , which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.

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Near Full-Length Genome Characterization of a Newly Identified HIV Type 1 Subtype F Variant Circulating in St. Petersburg, Russia

Cited by 9 publications

References 17 publications

Development of a contemporary globally diverse HIV viral panel by the EQAPOL program

Development of a contemporary globally diverse HIV viral panel by the EQAPOL program

Phylogeny of partial gag, pol and env genes show predominance of HIV-1G and CRF02_AG with emerging recombinants in south-eastern Nigeria

Short Communication: Molecular Epidemiology, Phylogeny, and Phylodynamics of CRF63_02A1, a Recently Originated HIV-1 Circulating Recombinant Form Spreading in Siberia

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