SEQUENCE NOTES HIV-1 Genetic Diversity in Recently Diagnosed Infections in Moscow: Predominance of A FSU , Frequent Branching in Clusters, and Circulation of the Iberian Subtype G Variant Eduard Karamov, 1 Khoren Epremyan, 1 Andrei Siniavin, 1 Yury Zhernov, 1 Marı ´a Teresa Cuevas, 2 Elena Delgado, 2 Mo´ nica Sa´ nchez-Martı ´nez, 2 Cristina Carrera, 2 Galina Kornilaeva, 1 Ali Turgiev, 1,3 Joan Bacque´, 2 Lucı ´a Pe´ rez-A ´ lvarez, 2 and Michael M. Thomson 2 Abstract HIV-1 protease-reverse transcriptase sequences from 62 HIV-1-infected individuals recently diagnosed in Moscow were analyzed. Subtype A former Soviet Union (FSU) (A FSU ) variant was the predominant clade (62.9%), followed by subtype B (22.6%), unique recombinants (6.5%), subtype G (6.5%), and CRF01_AE (1.6%). A FSU predominated among people who inject drugs (88.9%) and heterosexually acquired infections (77.8%), while subtype B was the most prevalent genetic form among men who have sex with men (44%), although A FSU was also frequent in this population (36%). Forty-eight (77.4%) viruses branched within in- trasubtype clusters, three of which, of subtype B, had a majority of viruses collected outside of FSU. The four subtype G viruses identified in this study belonged to the Portuguese–Spanish (Iberian) variant and, together with three from databases, formed a Russian cluster closely related to viruses from Denmark. This is the first report of the circulation of the Iberian subtype G variant in Russia. Keywords: HIV-1, subtypes, recombinant forms, clusters, Russia R ussia is the European country with the greatest number of HIV-1-infected individuals, with around 1.16 million cumulative reported diagnoses by mid-2017. 1 In 2016, over 103,000 new HIV infections were diagnosed, with a mean annual increase of 10% in the 2011–2016 period. 1 The HIV-1 epidemic in Russia is mostly concentrated in people who inject drugs (PWID) and their heterosexual partners or casual contacts. In a 2016 survey, PWID and heterosexually acquired infections accounted for 48.8% and 48.7%, respec- tively, of new HIV-1 diagnoses. 1 Men who have sex with men (MSM) were reported to represent only 1.5% of new HIV-1 diagnoses. However, this proportion could be substantially higher, considering the large proportion of new HIV-1 diag- noses without data on transmission route and the existing laws banning the sharing of information related to homosexuality. 1 The HIV-1 epidemic in Russia is dominated by a subtype A variant 2,3 of Central African origin 4,5 which began to spread among PWID in the southern Ukrainian city of Odessa in late 1994. 5–7 This strain has propagated to all former Soviet Union (FSU) countries, in which it is the predominant HIV-1 genetic form 3 (except in Estonia), and for this reason it is often des- ignated as A FSU (although recently some authors have begun to refer to it as A6 subsubtype 8,9 ). Other HIV-1 clades circulating in Russia are CRF03_AB, predominant in the cities of Kaliningrad 10 and Cherepovets 11 ; a CRF02_AG variant, originally reported in Uzbekistan 12 but also recently detected in Moscow 13 ; CRF63_02A1, recombi- nant between the CRF02_AG, FSU strain, and A FSU , of recent origin and predominant in certain areas of Siberia 14,15 ; and subtype B, largely predominant among MSM in earlier stud- ies, 2 although more recent reports indicate that A FSU is also common in this population. 9 Within A FSU several clusters have been identified. The largest one is that bearing the characteristic V77I substitution in protease, rare in other A FSU viruses, which is widely cir- culating in Russia and other FSU countries. 16–18 In a study in St. Petersburg, 17,18 63% A FSU viruses belonged to a cluster, designated A SP1 , which also comprised viruses from the 1 Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia. 2 HIV Biology and Variability Unit, Centro Nacional de Microbiologı ´a, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain. 3 Immunomica LLC, Moscow, Russia. AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 34, Number 7, 2018 ª Mary Ann Liebert, Inc. DOI: 10.1089/aid.2018.0055 629 Downloaded by Sede De Majadahonda - Inst Salud Carlos from www.liebertpub.com at 07/22/19. For personal use only.