Short Communication: Molecular Epidemiology of HIV Type 1 Infection in Kazakhstan: CRF02_AG Prevalence Is Increasing in the Southeastern Provinces

Lapovok, Ilya; KazennovaElena,; LagaVita,; VasilyevAlexander,; UtegenovaAliya,; AbishevAsylkhan,; DzissyukNatalya,; TukeevMarat,; Bobkova, Marina

doi:10.1089/aid.2013.0291

Cited by 16 publications

(14 citation statements)

References 13 publications

(12 reference statements)

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“…This is in agreement with recent studies reporting the identification of CRF63_02A1 in the Russian Far East 31 and Kazakhstan. 32 However, we could not find CRF63_02A1 among database viruses from Kyrgysztan, as suggested by others. (Fig.…”

Section: Crf63_02a1 Phylogeny and Phylodynamics 913mentioning

confidence: 45%

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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Section: Crf63_02a1 Phylogeny and Phylodynamics 913mentioning

confidence: 45%

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 A3, A4 and A5 subsubtypes each have few sequences described and no pure A5 strains have been identified, A5 is only found in large regions of the CRF26_A5U genomes (Meloni et al, 2004)(Vidal et al, 2006)(Vidal et al, 2009). Another group of divergent subtype A viruses, labeled as subsubtype A6 in figure 3, has spread quite widely among IDU in the regions of the former Soviet Union and surrounding areas(Bobkov et al, 1994; Lapovok et al, 2014). This group of viruses have been also named as A FSU corresponding the geographic area (former Soviet Union countries) of their endemicity.…”

Section: Hiv-1 Sivcpz Sivgormentioning

confidence: 99%

Primate immunodeficiency virus classification and nomenclature: Review

Foley

Leitner

Paraskevis

et al. 2016

Infection, Genetics and Evolution

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The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. This review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.

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“…CRF63_02A1, which is a recombination of A FSU and CRF02_AG (Baryshev et al, 2014, 2012), has also been detected in Kyrgyzstan (Laga et al, 2015a). CRF02_AG and its recombinants with A FSU have generally become prevalent in Central Asia (Uzbekistan, Kyrgyzstan, Kazakhstan) (Bobkova, 2013; Carr et al, 2005; Eyzaguirre et al, 2007; Laga et al, 2015a; Lapovok et al, 2014) and also in Asian parts of Russia as drug trafficking routes seem to be changing (Baryshev et al, 2012). It should be mentioned that A1 has been spreading in some Central and Western European countries through sexual or injecting networks (Lai et al, 2016; Parczewski et al, 2016).…”

Section: Pwid In Former Soviet Union (Fsu) States and Molecular Epmentioning

confidence: 99%

Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia

Nikolopoulos

Kostaki

Paraskevis

2016

Infection, Genetics and Evolution

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HIV strains continuously evolve, tend to recombine and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1 and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.) increasing the complexity of HIV molecular patterns.

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Short Communication: Molecular Epidemiology of HIV Type 1 Infection in Kazakhstan: CRF02_AG Prevalence Is Increasing in the Southeastern Provinces

Cited by 16 publications

References 13 publications

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

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

Primate immunodeficiency virus classification and nomenclature: Review

Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia

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