title: Distribution and time trends of HIV-1 variants in Poland: Characteristics of non-B clades and recombinant viruses.
abstract: The spread of HIV-1 subtypes varies considerably both worldwide and within Europe, with non-B variants commonly found across various exposure groups. This study aimed to analyse the distribution and temporal trends in HIV-1 subtype variability across Poland. For analysis of the subtype distribution, 1219 partial pol sequences obtained from patients followed up in 9 of 17 Polish HIV treatment centres were used. Subtyping was inferred using the maximum likelihood method; recombination was assessed using the bootscanning and jumping profile hidden Markov model methods. Subtype B dominated in the studied group (n=1059, 86.9%); in 160 (13.1%) sequences, non-B variants were present [A1 (n=63, 5.2%), D (n=43, 3.5%), C (n=22, 1.8%), and F1 (n=2, 0.2%)]. In 25 (2.1%) cases circulating recombinant forms (CRFs) were found. Five A1 variants (0.4%) were unique AB recombinant forms (URF) not previously identified in Poland. Non-B clades were notably more common among females (n=73, 45.6%, p<0.001) and heterosexual individuals (n=103, 66.5%, p<0.001) and less frequent among men who have sex with men (MSM) (n=27, 17.42%, p<0.001). HIV-1 viral load at diagnosis was higher among non-B cases [median: 5.0 (IQR: 4.4-5.6)] vs. [median: 4.8 (IQR: 4.3-5.4) log copies/ml for subtype B (p<0.001)] with a lower CD4(+) lymphocyte count at baseline [median: 248 (IQR: 75-503) for non-B vs. median: 320 (IQR: 125-497) cells/μl for subtype B; p<0.001]. The frequency of the non-B subtypes proved stable from 2008 (11.5%) to 2014 (8.0%) [OR: 0.95 (95% CI: 0.84-1.07), p=0.4], with no temporal differences for exposure groups, gender, age and AIDS. Despite the predominance of subtype B, the variability of HIV in Poland is notable; both CRFs and URFs are present in the analysed population. Non-B variants are associated with heterosexual transmission, more advanced HIV disease and have stable temporal frequencies.
authors: Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Poland. Electronic address: mparczewski@yahoo.co.uk.
authors: Miłosz
authors: M
authors: Parczewski
authors: Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Poland.
authors: Magdalena
authors: M
authors: Leszczyszyn-Pynka
authors: Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Poland.
authors: Magdalena
authors: M
authors: Witak-Jędra
authors: Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wroclaw Medical University, Poland.
authors: Weronika
authors: W
authors: Rymer
authors: Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wroclaw Medical University, Poland.
authors: Małgorzata
authors: M
authors: Zalewska
authors: Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wroclaw Medical University, Poland.
authors: Jacek
authors: J
authors: Gąsiorowski
authors: Department of Infectious Diseases, Jagiellonian University Medical College, Kraków, Poland.
authors: Monika
authors: M
authors: Bociąga-Jasik
authors: Department of Infectious Diseases, Jagiellonian University Medical College, Kraków, Poland.
authors: Anna
authors: A
authors: Kalinowska-Nowak
authors: Department of Infectious Diseases, Jagiellonian University Medical College, Kraków, Poland.
authors: Aleksander
authors: A
authors: Garlicki
authors: Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Poland.
authors: Anna
authors: A
authors: Grzeszczuk
authors: Department of Infectious Diseases, Medical University in Gdańsk, Poland.
authors: Maria
authors: M
authors: Jankowska
authors: Department of Infectious Diseases, Medical University in Gdańsk, Poland.
authors: Małgorzata
authors: M
authors: Lemańska
authors: Department of Infectious Diseases, J. Strus Hospital, Poznan, Poland.
authors: Grażyna
authors: G
authors: Barałkiewicz
authors: Department of Infectious Diseases, Poznan University of Medical Sciences, Poland.
authors: Iwona
authors: I
authors: Mozer-Lisewska
authors: Department of Infectious Diseases, Regional Hospital in Zielona Gora, Poland.
authors: Władysław
authors: W
authors: Łojewski
authors: Department of Infectious Diseases and Hepatology, Nicolaus Copernicus University Collegium Medicum in Bydgoszcz, Poland.
authors: Edyta
authors: E
authors: Grąbczewska
authors: Department of Infectious Diseases and Hepatology, Nicolaus Copernicus University Collegium Medicum in Bydgoszcz, Poland.
authors: Anita
authors: A
authors: Olczak
authors: Department of Infectious Diseases and Hepatology, Medical University of Łódź, Poland.
authors: Elżbieta
authors: E
authors: Jabłonowska
authors: Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Poland.
authors: Anna
authors: A
authors: Urbańska
mesh_terms: D000328:Adult; D018791:CD4 Lymphocyte Count; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology* / Q000276:immunology / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D016017:Odds Ratio; D010802:Phylogeny; D011044:Poland / Q000453:epidemiology; D011995:Recombination, Genetic; D019562:Viral Load
keywords: HIV subtypes; Phylogeny; Recombination