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Schlösser M, Kartashev VV, Mikkola VH, Shemshura A, Saukhat S, Kolpakov D, Suladze A, Tverdokhlebova T, Hutt K, Heger E, Knops E, Böhm M, Di Cristanziano V, Kaiser R, Sönnerborg A, Zazzi M, Bobkova M, Sierra S. HIV-1 Sub-Subtype A6: Settings for Normalised Identification and Molecular Epidemiology in the Southern Federal District, Russia. Viruses 2020; 12:v12040475. [PMID: 32331438 PMCID: PMC7232409 DOI: 10.3390/v12040475] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 01/08/2023] Open
Abstract
Russia has one of the largest and fastest growing HIV epidemics. However, epidemiological data are scarce. Sub-subtype A6 is most prevalent in Russia but its identification is challenging. We analysed protease/reverse transcriptase-, integrase-sequences, and epidemiological data from 303 patients to develop a methodology for the systematisation of A6 identification and to describe the HIV epidemiology in the Russian Southern Federal District. Drug consumption (32.0%) and heterosexual contact (27.1%) were the major reported transmission risks. This study successfully established the settings for systematic identification of A6 samples. Low frequency of subtype B (3.3%) and large prevalence of sub-subtype A6 (69.6%) and subtype G (23.4%) were detected. Transmitted PI- (8.8%) and NRTI-resistance (6.4%) were detected in therapy-naive patients. In therapy-experienced patients, 17.3% of the isolates showed resistance to PIs, 50.0% to NRTI, 39.2% to NNRTIs, and 9.5% to INSTIs. Multiresistance was identified in 52 isolates, 40 corresponding to two-class resistance and seven to three-class resistance. Two resistance-associated-mutations significantly associated to sub-subtype A6 samples: A62VRT and G190SRT. This study establishes the conditions for a systematic annotation of sub-subtype A6 to normalise epidemiological studies. Accurate knowledge on South Russian epidemiology will allow for the development of efficient regional frameworks for HIV-1 infection management.
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Affiliation(s)
- Madita Schlösser
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Vladimir V. Kartashev
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
- Department of Infectious Diseases, Rostov State Medical University, 344022 Rostov-na-Donu, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Visa H. Mikkola
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS of the Ministry of Health of Krasnodar Region, 350015 Krasnodar, Russia;
| | - Sergey Saukhat
- Department of Infectious Diseases, Rostov State Medical University, 344022 Rostov-na-Donu, Russia;
| | - Dmitriy Kolpakov
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Alexandr Suladze
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Tatiana Tverdokhlebova
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Katharina Hutt
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Elena Knops
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Michael Böhm
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Rolf Kaiser
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy;
| | - Marina Bobkova
- Department of General Virology, Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia;
| | - Saleta Sierra
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
- Correspondence: ; Tel.: +49-221-4788-5807
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Murzakova A, Kireev D, Baryshev P, Lopatukhin A, Serova E, Shemshura A, Saukhat S, Kolpakov D, Matuzkova A, Suladze A, Nosik M, Eremin V, Shipulin G, Pokrovsky V. Molecular Epidemiology of HIV-1 Subtype G in the Russian Federation. Viruses 2019; 11:E348. [PMID: 30995717 PMCID: PMC6521041 DOI: 10.3390/v11040348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023] Open
Abstract
Although HIV-1 subtype A has predominated in Russia since the end of the 20th century, other viral variants also circulate in this country. The dramatic outbreak of HIV-1 subtype G in 1988-1990 represents the origin of this variant spreading in Russia. However, full genome sequencing of the nosocomial viral variant and an analysis of the current circulating variants have not been conducted. We performed near full-length genome sequencing and phylogenetic and recombination analyses of 11 samples; the samples were determined to be subtype G based on an analysis of the pol region. Three samples were reliably obtained from patients infected during the nosocomial outbreak. The other 8 samples were obtained from patients who were diagnosed in 2010-2015. Phylogenetic analysis confirmed that a man from the Democratic Republic of the Congo was the origin of the outbreak. We also found that currently circulating viral variants that were genotyped as subtype G according to their pol region are in fact unique recombinant forms. These recombinant forms are similar to the BG-recombinants from Western Europe, particularly Spain and Portugal. The limitations of subtyping based on the pol region suggest that these viral variants are more widespread in Europe than is currently supposed.
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Affiliation(s)
| | - Dmitry Kireev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
| | - Pavel Baryshev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
| | | | - Ekaterina Serova
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS of the Ministry of Health of Krasnodar Region, 350015 Krasnodar, Russia.
| | - Sergey Saukhat
- Department of Epidemiology, Rostov State Medical University, 344022 Rostov-on-Don, Russia.
| | - Dmitry Kolpakov
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Anna Matuzkova
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Alexander Suladze
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Marina Nosik
- Ilya Ilyich Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia.
| | - Vladimir Eremin
- Republican Research and Practical Center for Epidemiology and Microbiology, 220114 Minsk, Belarus.
| | - German Shipulin
- Center of Strategical Planning and Management of Biomedical Health Risks of the Ministry of Health, 119121 Moscow, Russia.
| | - Vadim Pokrovsky
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
- Department of infectious diseases with courses of epidemiology and phthisiology, RUDN University, 117198 Moscow, Russia.
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Lopatukhin A, Kireev D, Kuevda D, Pokrovskaya A, Tsyganova G, Korovina G, Pinsker A, Dementeva N, Sizova N, Peksheva O, Zaytseva N, Nosov N, Urazov N, Gerasimov V, Ermolinskaya N, Gerasimova N, Sandyreva T, Volova L, Grezina L, Kolomeets A, Sergeeva I, Neshumaev D, Boyko A, Kotova V, Balakhontseva L, Kolpakov D, Shemshura A, Saukhat S, Bukin E, Polyakov A, Kaiser R, Shipulin G, Pokrovsky V. HIV-1 genotyping tropism profile in an HIV-positive population throughout the Russian Federation. Cogent Medicine 2017. [DOI: 10.1080/2331205x.2017.1311470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Alexey Lopatukhin
- Central Research Institute for Epidemiology of Rospotrebnadzor, Novogireevskaya St. 3A, Moscow, Russian Federation
| | - Dmitry Kireev
- Central Research Institute for Epidemiology of Rospotrebnadzor, Novogireevskaya St. 3A, Moscow, Russian Federation
| | - Dmitry Kuevda
- Central Research Institute for Epidemiology of Rospotrebnadzor, Novogireevskaya St. 3A, Moscow, Russian Federation
| | - Anastasia Pokrovskaya
- Central Research Institute for Epidemiology of Rospotrebnadzor, Novogireevskaya St. 3A, Moscow, Russian Federation
| | - Galina Tsyganova
- Central Research Institute for Epidemiology of Rospotrebnadzor, Novogireevskaya St. 3A, Moscow, Russian Federation
| | - Galina Korovina
- Republican Clinical Infectious Diseases Hospital - Research Center of Prevention and Treatment of HIV Infection in Children and Pregnant Women of the Ministry of Health and Social Development of the Russian Federation, Shlisselburgsky highway 3, Saint-Petersburg, 111123, Russian Federation
| | - Alexander Pinsker
- Republican Clinical Infectious Diseases Hospital - Research Center of Prevention and Treatment of HIV Infection in Children and Pregnant Women of the Ministry of Health and Social Development of the Russian Federation, Shlisselburgsky highway 3, Saint-Petersburg, 111123, Russian Federation
| | - Natalia Dementeva
- St. Petersburg Center for Control of AIDS and Infectious Diseases, Naberezhnaya Obvodnogo Canala 179, Saint-Petersburg, 190103, Russian Federation
| | - Natalia Sizova
- St. Petersburg Center for Control of AIDS and Infectious Diseases, Naberezhnaya Obvodnogo Canala 179, Saint-Petersburg, 190103, Russian Federation
| | - Olga Peksheva
- Federal Budget Institution of Science “Nizhny Novgorod Scientific and Research Institute of Epidemiology and Microbiology Named After Academician I.N. Blokhina” of Rospotrebnadzor, Privolzhsky Okrug Centre of AIDS Prophylaxis and Control, Malaya Yamskaya St. 71, Nizhny Novgorod, 603950, Russian Federation
| | - Natalia Zaytseva
- Federal Budget Institution of Science “Nizhny Novgorod Scientific and Research Institute of Epidemiology and Microbiology Named After Academician I.N. Blokhina” of Rospotrebnadzor, Privolzhsky Okrug Centre of AIDS Prophylaxis and Control, Malaya Yamskaya St. 71, Nizhny Novgorod, 603950, Russian Federation
| | - Nikolai Nosov
- Federal Budget Institution of Science “Nizhny Novgorod Scientific and Research Institute of Epidemiology and Microbiology Named After Academician I.N. Blokhina” of Rospotrebnadzor, Privolzhsky Okrug Centre of AIDS Prophylaxis and Control, Malaya Yamskaya St. 71, Nizhny Novgorod, 603950, Russian Federation
| | - Nail Urazov
- Republican Center for Prophylaxis and Control of AIDS and Infectious Diseases, Vishnevskogo St. 2A, Kazan, 420097, Russian Federation
| | - Valery Gerasimov
- Republican Center for Prophylaxis and Control of AIDS and Infectious Diseases, Vishnevskogo St. 2A, Kazan, 420097, Russian Federation
| | - Natalia Ermolinskaya
- FSIS Yekaterinburg Research Institute of Viral Infections of Rospotrebnadzor, Letnyaya St. 23, Yekaterinburg, 620030, Russian Federation
| | - Natalia Gerasimova
- Regional Centre for AIDS Prevention, Yasnaya St. 46, Yekaterinburg, 620102, Russian Federation
| | - Tatyana Sandyreva
- Regional Centre for AIDS Prevention, Yasnaya St. 46, Yekaterinburg, 620102, Russian Federation
| | - Ludmila Volova
- Yamal-Nenets Autonomous District Center for Prevention and Control of AIDS and Infectious Diseases, Muravlenko St. 40, Noyabrsk, 629806, Russian Federation
| | - Lilia Grezina
- Yamal-Nenets Autonomous District Center for Prevention and Control of AIDS and Infectious Diseases, Muravlenko St. 40, Noyabrsk, 629806, Russian Federation
| | - Anna Kolomeets
- Omsk Research Institute of Natural Focal Infections, Siberian Federal District Center for AIDS Prevention and Fight, Prospekt Mira 7, Omsk, 644080, Russian Federation
| | - Irina Sergeeva
- Omsk Research Institute of Natural Focal Infections, Siberian Federal District Center for AIDS Prevention and Fight, Prospekt Mira 7, Omsk, 644080, Russian Federation
| | - Dmitry Neshumaev
- Krasnoyarsk Regional Centre of AIDS Prevention, Karl Marx St. 45, Krasnoyarsk, 660049, Russian Federation
| | - Anatoly Boyko
- Krasnoyarsk Regional Centre of AIDS Prevention, Karl Marx St. 45, Krasnoyarsk, 660049, Russian Federation
| | - Valeria Kotova
- Khabarovsk Research Institute of Epidemiology and Microbiology, Shevchenko St. 2, Khabarovsk, 680610, Russian Federation
| | - Ludmila Balakhontseva
- Khabarovsk Research Institute of Epidemiology and Microbiology, Shevchenko St. 2, Khabarovsk, 680610, Russian Federation
| | - Dmitry Kolpakov
- Rostov Research Institute of Microbiology and Parasitology, Gazetny Lane 119, Rostov-on-Don, 344000, Russian Federation
| | - Andrey Shemshura
- Rostov Research Institute of Microbiology and Parasitology, Gazetny Lane 119, Rostov-on-Don, 344000, Russian Federation
| | - Sergey Saukhat
- Rostov Research Institute of Microbiology and Parasitology, Gazetny Lane 119, Rostov-on-Don, 344000, Russian Federation
| | - Evgeniy Bukin
- ViiV Healthcare Russia, Bolshaya Ordynka 40, Building 4, Moscow, 119017, Russian Federation
| | - Andrey Polyakov
- ViiV Healthcare Russia, Bolshaya Ordynka 40, Building 4, Moscow, 119017, Russian Federation
| | - Rolf Kaiser
- Institute of Virology, University of Köln, Albertus-Magnus-Platz, Köln, 50923, Germany
| | - German Shipulin
- Central Research Institute for Epidemiology of Rospotrebnadzor, Novogireevskaya St. 3A, Moscow, Russian Federation
| | - Vadim Pokrovsky
- Central Research Institute for Epidemiology of Rospotrebnadzor, Novogireevskaya St. 3A, Moscow, Russian Federation
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