Molecular epidemiology of recent HIV-1 infections in southern Poland

Journal of Medical Virology

Volumn 84, Issue 12, 2012, Pages 1857-1868

  Smoleń Dzirba, Joanna ^a   Rosińska, Magdalena ^b   Kruszyński, Piotr ^a   Bratosiewicz Wasik, Jolanta ^a   Janiec, Janusz ^b   Beniowski, Marek ^c   Bociaga Jasik, Monika ^d   Jabłonowska, Elzbieta ^e   Szetela, Bartosz ^f   Porter, Kholoud ^g   Wasik, Tomasz J ^a  

^a MEDICAL UNIVERSITY OF SILESIA   (Poland)

^b NATIONAL MEDICINES INSTITUTE   (Poland)

^c Specialistic Hospital in Chorzow   (Poland)

^d JAGIELLONIAN UNIVERSITY MEDICAL COLLEGE   (Poland)

^e MEDICAL UNIVERSITY OF LODZ   (Poland)

^f WROCLAW MEDICAL UNIVERSITY   (Poland)

^g MEDICAL RESEARCH COUNCIL   (United Kingdom)

Author keywords

HIV 1; Phylogenetic analysis; Pol gene; Transmission

Indexed keywords

ADULT; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DRUG USE; FEMALE; GENE SEQUENCE; HETEROSEXUALITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MAJOR CLINICAL STUDY; MALE; MALE HOMOSEXUAL; MOLECULAR EPIDEMIOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; POLAND; STANDARD; STRUCTURAL GENE; VIRUS GENE; VIRUS TRANSMISSION;

ADULT; BASE SEQUENCE; FEMALE; GENES, VIRAL; GENETIC VARIATION; HETEROSEXUALITY; HIV INFECTIONS; HIV-1; HOMOSEXUALITY, MALE; HUMANS; MALE; PHYLOGENY; POL GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; POLAND; RNA, VIRAL; STATISTICS, NONPARAMETRIC; YOUNG ADULT;

EID: 84867691757     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.23395     Document Type: Article

References (49)

1. Balode D, Skar H, Mild M, Kolupajeva T, Ferdats A, Rozentale B, Leitner T, Albert J. 2012. Phylogenetic analysis of the Latvian HIV-1 epidemic. AIDS Res Hum Retroviruses 28:928-932.
2. Bon I, Ciccozzi M, Zehender G, Biagetti C, Verrucchi G, Lai A, Lo PrestiA, Gibellini D, Re MC. 2010. HIV-1 subtype C transmission network: The phylogenetic reconstruction strongly supports the epidemiological data. J Clin Virol 48:212-214.
3. Brenner BG, Roger M, Routy JP, Moisi D, Ntemgwa M, Matte C, Baril JG, Thomas R, Rouleau D, Bruneau J, Leblanc R, Legault M, Tremblay C, Charest H, Wainberg MA, Quebec Primary HIV Infection Study Group. High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 2007. 195:951-959.
4. Firlag-Burkacka E, Siwak E, Gizińska J, Świecki P, Cielniak I, Horban A. 2009. Changes in the trends of the HIV/AIDS epidemic, based on surveillance data of Warsaw cohort. HIV/AIDS Rev 8:12-15.
5. Fisher M, Pao D, Brown AE, Sudarshi D, Gill ON, Cane P, Buckton AJ, Parry JV, Johnson AM, Sabin C, Pillay D. 2010. Determinants of HIV-1 transmission in men who have sex with men: A combined clinical, epidemiological and phylogenetic approach. AIDS 24:1739-1747.
6. Gray RR, Tatem AJ, Lamers S, Hou W, Laeyendecker O, Serwadda D, Sewankambo N, Gray RH, Wawer M, Quinn TC, Goodenow MM, Salemi M. 2009. Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. AIDS 23:F9-F17.
7. Hall TA. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95-98.
8. Hemelaar J, Gouws E, Ghys PD, Osmanov S. 2011. WHO-UNAIDS Network for HIV Isolation and Characterisation. Global trends in molecular epidemiology of HIV-1 during 2000-2007. AIDS 25:679-689.
9. HIV sequence database. Los Alamos National Laboratory. Available at: http://www.hiv.lanl.gov.
10. Hue S, Clewley JP, Cane PA, Pillay D. 2004. HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS 18:719-728.
11. Hue S, Pillay D, Clewley JP, Pybus OG. 2005. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A 102:4425-4429.
12. Hughes G, Leigh Brown A, Rambaut A, Lycett S, Lewis S, Fearnhill E. UK Collaborative Group on HIV Drug Resistance. 2008. Recent phylodynamics of the HIV epidemic among MSM in the UK. 15th Conference on Retroviruses and Opportunistic Infections, Boston, USA, Abstract no. 13.
13. Izopet J, Salama G, Pasquier C, Sandres K, Marchou B, Massip P, Puel J. 1998. Decay of HIV-1 DNA in patients receiving suppressive antiretroviral therapy. J Acquir Immune Defic Syndr Hum Retrovirol 19:478-483.
14. Janiec J, Laskus I, Rosińska M. 2008. An attempt to evaluate point HIV prevalence for Poland in 2005. 2nd European Scientific Conference on Applied Infectious Disease Epidemiology (ESCAIDE). Berlin, Germany, Abstract no. 20080265.
15. Joint United Nations Programme on HIV/AIDS (UNAIDS). 2010. Combination HIV Prevention: Tailoring and Coordinating Biomedical, Behavioural and Structural Strategies to Reduce New HIV Infections. A UNAIDS Discussion Paper. Available at: http://www.unaids.org/en/media/unaids/contentassets/documents/unaidspublication/2011/20111110_JC2007_Combination_Prevention_paper_en.pdf.
16. Joint United Nations Programme on HIV/AIDS (UNAIDS). 2011a. Global HIV/AIDS Response. Epidemic update and health sector progress towards Universal Access. Progress Report 2011. Available at: http://www.unaids.org/en/resources/unaidspublications/2011/.
17. Joint United Nations Programme on HIV/AIDS (UNAIDS). 2011b. UNAIDS World AIDS Day Report 2011. How to get to zero: Faster. Smarter. Better. Available at: http://www.unaids.org/en/media/unaids/contentassets/documents/unaidspublication/2011/.
18. Junqueira DM, de Medeiros RM, Matte MC, Araújo LA, Chies JA, Ashton-Prolla P, Almeida SE. 2011. Reviewing the history of HIV-1: Spread of subtype B in the Americas. PLoS ONE 6:e27489.
19. Kouyos RD, von Wyl V, Yerly S, Böni J, Taffé P, Shah C, Bürgisser P, Klimkait T, Weber R, Hirschel B, Cavassini M, Furrer H, Battegay M, Vernazza PL, Bernasconi E, Rickenbach M, Ledergerber B, Bonhoeffer S, Günthard HF. 2010. Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. J Infect Dis 201:1488-1497.
20. Kramer MA, Cornelissen M, Paraskevis D, Prins M, Coutinho RA, van Sighem AI, Sabajo L, Duits AJ, Winkel CN, Prins JM, van der Ende ME, Kauffmann RH, Op de Coul EL. 2011. HIV transmission patterns among The Netherlands, Suriname, and The Netherlands Antilles: A molecular epidemiological study. AIDS Res Hum Retroviruses 27:123-130.
21. Kuiken C, Thakallapalli R, Esklid A, de Ronde A. 2000. Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus. Am J Epidemiol 152:814-822.
22. Leitner T, Escanilla D, Franzen C, Uhlén M, Albert J. 1996. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci U S A 93:10864-10869.
23. Lewis F, Hughes GJ, Rambaut A, Pozniak A, Leigh Brown AJ. 2008. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 5:e50.
24. Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, Lee HY, Bruno W, Leitner T. 2007. Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: The evolutionary rate of HIV-1 slows down when the epidemic rate increases. J Virol 81:10625-10635.
25. Marinda ET, Hargrove JW, Preiser W, Slabbert H, van Zyl G, Levin J, Moulton LH, Welte A, Humphrey J. 2010. Significantly diminished long-term specificity of the BED capture enzyme immunoassay among patients with HIV-1 with very low CD4 counts and those on antiretroviral therapy. J Acquir Immune Defic Syndr 53:496-499.
26. Openchowska M, Kuźma K. 2011. [Study on knowledge and behavior of men who have sex with men base on EMIS survey]. Study report in Polish. National AIDS Centre.
27. Pao D, Fisher M, Hue S, Dean G, Murphy G, Cane PA, Sabin CA, Pillay D. 2005. Transmission of HIV-1 during primary infection: Relationship to sexual risk and sexually transmitted infections. AIDS 19:85-90.
28. Paraskevis D, Nikolopoulos G, Tsiara C, Paraskeva D, Antoniadou A, Lazanas M, Gargalianos P, Psychogiou M, Malliori M, Kremastinou J, Hatzakis A. 2011. HIV-1 outbreak among injecting drug users in Greece, 2011: A preliminary report. Euro Surveill 16:19962.
29. Paraskevis D, Pybus O, Magiorkinis G, Hatzakis A, Wensing AM, van de Vijver DA, Albert J, Angarano G, Asjö B, Balotta C, Boeri E, Camacho R, Chaix ML, Coughlan S, Costagliola D, De Luca A, de Mendoza C, Derdelinckx I, Grossman Z, Hamouda O, Hoepelman I, Horban A, Korn K, Kücherer C, Leitner T, Loveday C, Macrae E, Maljkovic-Berry I, Meyer L, Nielsen C, Op de Coul EL, Ormaasen V, Perrin L, Puchhammer-Stöckl E, Ruiz L, Salminen MO, Schmit JC, Schuurman R, Soriano V, Stanczak J, Stanojevic M, Struck D, Van Laethem K, Violin M, Yerly S, Zazzi M, Boucher CA, Vandamme AM, SPREAD Programme. Tracing the HIV-1 subtype B mobility in Europe: A phylogeographic approach. Retrovirology 2009. 6:49-59.
30. Parczewski M, Leszczyszyn-Pynka M, Bander D, Urbańska A, Stańczak G, Boroń-Kaczmarska A. 2010. Characteristics of HIV-1 non-B subtype infections in Northwest Poland. J Med Virol 82:1306-1313.
31. Parera M, Ibanez A, Clotet B, Martinez MA. 2004. Lack of evidence for protease evolution in HIV-1 infected patients after 2 years of successful highly active antiretroviral therapy. J Infect Dis 189:1444-1451.
32. Perrin L, Kaiser L, Yerly S. 2003. Travel and the spread of HIV-1 genetic variants. Lancet Infect Dis 3:22-27.
33. Robbins KE, Lemey P, Pybus OG, Jaffe HW, Youngpairoj AS, Brown TM, Salemi M, Vandamme AM, Kalish ML. 2003. U.S. Human immunodeficiency virus type 1 epidemic: Date of origin, population history, and characterization of early strains. J Virol 77:6359-6366.
34. Robbins KE, Weidle PJ, Brown TM, Saekhou AM, Coles B, Holmberg SD, Folks TM, Kalish ML. 2002. Molecular analysis in support of an investigation of a cluster of HIV-1-infected women. AIDS Res Hum Retroviruses 18:1157-1161.
35. Rose PP, Korber BT. 2000. Detecting hypermutations in viral sequences with an emphasis on G→A hypermutation. Bioinformatics 16:400-401.
36. Rosinska M, Zielinski A. 2011. Recent increase in HIV rate by age, cohort, period analysis of surveillance data suggests changes in HIV epidemiology in Poland. Cent Eur J Public Health 19:123-127.
37. Rozanov M, Plikat U, Chappey C, Kochergin A, Tatusova T. 2004. A web-based genotyping resource for viral sequences. Nucleic Acids Res 32:654-659.
38. Salemi M, Goodenow MM, Montieri S, de Oliveira T, Santoro MM, Beshkov D, Alexiev I, Elenkov I, Elenkov I, Yakimova T, Varleva T, Rezza G, Ciccozzi M. 2008. The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries. AIDS Res Hum Retroviruses 24:771-779.
39. Skar H, Axelsson M, Berggren I, Thalme A, Gyllensten K, Liitsola K, Brummer-Korvenkontio H, Kivelä P, Spångberg E, Leitner T, Albert J. 2011. Dynamics of two separate but linked HIV-1 CRF01_AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland. J Virol 85:510-518.
40. Smolen J, Kruszynski P, Bratosiewicz-Wasik J, Witor A, Wasik TJ. 2010. HIV type 1 genetic diversity in Silesia, Poland: A retrospective analysis. AIDS Res Hum Retroviruses 26:767-776.
41. Stańczak GP, Stańczak JJ, Marczyńska M, Firlag-Burkacka E, Wiercińska-Drapało A, Leszczyszyn-Pynka M, Jabłonowska E, Małolepsza E, Dyda T, Zabek P, Horban A. 2010. Evolving patterns of HIV-1 transmitted drug resistance in Poland in the years 2000-2008. J Med Virol 82:1291-1294.
42. Stanford University: Stanford University HIV Drug Resistance Database. Available at: http://hivdb.stanford.edu/pages/WHOResistanceList.html.
43. Sullivan PS, Hamouda O, Delpech V, Geduld JE, Prejean J, Semaille C, Kaldor J, Folch C, Op de Coul E, Marcus U, Hughes G, Archibald CP, Cazein F, McDonald A, Casabona J, van Sighem A, Fenton KA. 2009. Annecy MSM epidemiology study group. Reemergence of the HIV epidemic among men who have sex with men in North America, Western Europe, and Australia, 1996-2005. Ann Epidemiol 19:423-431.
44. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739.
45. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882.
46. Viral genotyping tool. Available at: http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi.
47. von Wyl V, Kouyos RD, Yerly S, Böni J, Shah C, Bürgisser P, Klimkait T, Weber R, Hirschel B, Cavassini M, Staehelin C, Battegay M, Vernazza PL, Bernasconi E, Ledergerber B, Bonhoeffer S, Günthard HF, Swiss HIV Cohort Study. 2011. The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland. J Infect Dis 204:1095-1103.
48. Werbinska-Sienkiewicz B, Rosinska M, Furman S. 2011. HIV and AIDS in Poland in 2009. Przegl Epidemiol 65:289-295.
49. Yerly S, Jost S, Telenti A, Flepp M, Kaiser L, Chave JP, Vernazza P, Battegay M, Furrer H, Chanzy B, Burgisser P, Rickenbach M, Gebhardt M, Bernard MC, Perneger T, Hirschel B, Perrin L, Swiss HIV Cohort Study. 2004. Infrequent transmission of HIV-1 drug resistant variants. Antivir Ther 9:375-384.