Epidemiological network analysis in HIV-1 B infected patients diagnosed in Italy between 2000 and 2008

Infection, Genetics and Evolution

Volumn 11, Issue 3, 2011, Pages 624-632

  Callegaro, Annapaola ^a   Svicher, Valentina ^b   Alteri, Claudia ^b   Lo Presti, Alessandra ^c   Valenti, Daniela ^a   Goglio, Antonio ^a   Salemi, Marco ^d   Cella, Eleonora ^c   Perno, Carlo Federico ^b   Ciccozzi, Massimo ^c   Maggiolo, Franco ^a  

^a OSPEDALI RIUNITI   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

^c Department of Infectious Diseases Istituto Superiore di Sanità ^*  (Italy)

^d UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

Epidemiological network; HIV 1 subtype B epidemic; Phylogenetic analysis; Time scaled phylogenies; Transmitted drug resistance (TDR)

Indexed keywords

NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; PROTEINASE INHIBITOR; RNA DIRECTED DNA POLYMERASE INHIBITOR; THYMIDINE DERIVATIVE;

ADULT; ANTIVIRAL RESISTANCE; ARTICLE; CLADISTICS; CONTROLLED STUDY; FEMALE; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; HUMAN IMMUNODEFICIENCY VIRUS PREVALENCE; ITALY; MALE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEROTYPE; STRUCTURAL GENE; VIRUS CARRIER; VIRUS MUTATION; VIRUS STRAIN; VIRUS TRANSMISSION;

ADULT; AMINO ACID SUBSTITUTION; BAYES THEOREM; DRUG RESISTANCE, VIRAL; FEMALE; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; ITALY; MALE; MIDDLE AGED; PHYLOGENY; SEQUENCE ANALYSIS, RNA;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 79953121289     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2011.01.019     Document Type: Article

References (38)

1. Alteri C., Svicher V., Gori C., D'Arrigo R., Ciccozzi M., Ceccherini-Silberstein F., Selleri M., Bardacci S.A., Giuliani M., Elia P., Scognamiglio P., Orchi N., Giradi E., Perno C.F. Characterization of the pattern of drug-resistance mutations in newly diagnosed HIV-1 infected patients naïve to the antiretroviral drugs. BMC Infect. Dis. 2009, 16:9-111. SENDIH Study Group.
2. Baldanti F., Paolucci S., Ravasi G., Maccabruni A., Moriggia A., Barbarini G., Maserati R. Changes in circulation of B and non-B HIV strains: spotlight on a reference centre for infectious disease in Northern Italy. J. Med. Virol. 2008, 80:947-952.
3. Balotta C., Facchi G., Violin M., van Dooren S., Cozzi-Lepri A., Forbici F., Bertoli A., Riva C., Senese D., Caramello P., Carnevale G., Rizzardini G., Cremonini L., Monno L., Rezza G., Perno C.F., Ippolito G., d'Arminio-Monforte A., Vandamme A.M., Moroni M. Increasing prevalence of non-clade B HIV-1 strains men and women as monitored by analysis of reverse transcriptase and protease sequences. J. AIDS 2001, 27:499-505. ICONA Study Group.
4. Bennett D.E., Camacho R.J., Otelea D., Kurizkes D.R., Fleury H., Kiuchi M., Heneine W., Kantor R., Schapiro J.M., Vandamme A.M., Sandstrom P., Boucher C.A., van de Vijver D., Rhee S.Y., Liu T.F., Pillay D., Shafer R.W. Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One 2009, 4:1-8.
5. Brenner B.G., Roger M., Moisi D.D., Oliveira M., Hardy I., Turgel R., Charest H., Routy J.P., Wainberg M.A. Transmission networks of drug resistance acquired in primary/early stage HIV infection. AIDS 2008, 22:2509-2515. Montreal PHI Cohort, HIV Prevention Study Group.
6. Brenner B.G., Roger M., Routy J.P., Moisi D., Ntemgwa M., Matte C., Baril J.C., Thomas R., Rouleau D., Bruneau J., Leblanc R., Legault M., Tremblay C., Charest H., Waimberg M.A. High rates of forward transmission events after acute/early HIV-1 infection. J. Infect. Dis. 2007, 195:951-959. Quebec Primary HIV Infection Study Group.
7. Buonaguro L., Petrizzo A., Tagliamonte M., Vitone F., Re M.C., Pilotti E., Casoli C., Sbreglia C., Perrella O., Tornesello M.L., Buonaguro F.M. Molecular and phylogenetic analysis of HIV-1 variants circulating in Italy. Infect. Agents Cancer 2008, 10:3-13.
8. Castelnuovo B., Chiesa E., Rusconi S., Adorni F., Bongiovanni M., Melzi S., Cicconi P., Tordato F., Meroni L., Bini T., d'Arminio-Monforte A. Declining incidence of AIDS and increasing prevalence of AIDS presenters among AIDS patients in Italy. Eur. J. Clin. Microbiol. Infect. Dis. 2003, 22:663-669.
9. Ciccozzi M., Montieri S., Salemi M., De Oliveira T., Dorrucci M., Sinicco A., De Luca A., Giuliani M., Balotta C., Rezza G. An outbreak of HIV-1 subtype G among Italian injecting drug users. AIDS 2007, 21:1213-1215.
10. Cong M.E., Heneine W., Garcia-Lerma J.C. The fitness cost of mutations associated with human immunodeficiency virus type 1 drug resistance is modulated by mutational interactions. J. Virol. 2007, 81:3037-3041.
11. Costagliola D., Descamps D., Assoumou L., Morand-Joubert L., Marcelin A.G., Brodard V., Delaugerre C., Mackiewicz V., Ruffault A., Izopet J., Plantier J.C., Tamalet C., Yerly S., Saidi S., Brun-Vezinet S., Masquelier B. Prevalence of HIV- drug resistance in treated patients: a French nationwide study. J AIDS 2007, 46:12-28. Agence Nationale de Recherches sur le SIDA et les Hepatites Virales (ANRS) AC11 Resistance Study Group.
12. De Ronde A., van Dooren M., van Der Hoek L., Bouwhuis D., de Rooij E., van Gemen B., de Boer R., Goudsmit J. Establishment of new transmissible and drug-sensitive human immunodeficiency virus type 1 wild types due to transmission of nucleoside analogue-resistant virus. J Virol. 2001, 75:595-602.
13. Domaoal R.A., Bambara R.A., Demeter L.M. HIV-1 reverse transcriptase mutants resistant to non-nucleoside reverse transcriptase inhibitors do not adversely affect DNA synthesis: pre-steady-state and steady-state kinetic studies. J. AIDS 2006, 42:405-411.
14. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
15. Grant R.M., Hecht F.M., Warmerdam M., Liu L., Liegler T., Petropoulos C.J., Hellmann N.S., Chesney M., Busch M.P., Kahn J.O. Time trends in primary HIV-1 drug resistance among recently infected persons. JAMA 2002, 288:181-188.
16. Hall T.A. Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98 NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
17. Hue S., Gifford R.J., Dunn D., Fernhill E., Pillay D. Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naïve individuals. J. Virol. 2009, 83:2645-2654. UK Collaborative Group on HIV Drug Resistance.
18. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17(8):754-755.
19. Kass R.E., Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 1995, 90:773-795.
20. Keele B.F., Giorgi E.E., Salazar-Gonzalez J.F. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:7552-7557.
21. Lapadula G., Izzo I., Gargiulo F., Paraninfo G., Castelnuovo F., Quiros-Roldan E., Cologni G., Ceresoli F., Manca N., Carosi G., Torti G. Updated prevalence of genotypic resistance among HIV-1 positive patients naïve to antiretroviral therapy: a single center analysis. J. Med. Virol. 2008, 80:747-753.
22. Martinez-Picado J., Savara A.V., Sutton L., D'Aquila R.T. Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1. J. Virol. 1999, 73:3744-3752.
23. Pillay D., Taylor S., Richman D.D. Incidence and impact of resistance against approved antiretroviral drugs. Rev. Med. Virol. 2000, 10:231-253.
24. Schmidt H.A., Strimmer K., Vingron M., von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
25. Suligoi B., Boros S., Camoni L., Lepore D. Aggiornamento delle nuove diagnosi di infezione da HIV al 31 dicembre 2007 e dei casi di AIDS in Italia al 31 dicembre 2008. Notiziario dell' Istituto Superiore di Sanità 2009, 22(1):3-27.
26. Suchard M.A., Weiss R.E., Sinsheimer J.S. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 2001, 18:1001-1013.
27. The SPREAD Programme Transmission of drug-resistant HIV-1 in Europe remains limited to single classes. AIDS 2008, 22:625-635.
28. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Symp. Ser. 1994, 25:4876-4882.
29. Tozzi V., Zaccarelli M., Bonfigli S., Lorenzini P., Liuzzi G., Trotta M.P., Forbici F., Gori C., Bertoli A., Bellagamba R., Narciso P., Perno C.F., Antinori A. Drug-class-wide resistance to antiretrovirals in HIV-infected patients failing therapy: prevalence, risk factors and virological outcome. Antivir. Ther. 2006, 11:553-560. Collaborative Group for Clinical Use of HIV Genotype Resistance Test.
30. Turner D., Brenner B., Routy J.P., Moisi D., Rosberger Z., Roger M., Wainberg M.A. Diminished representation of HIV-1 variants containing select drug resistance-conferring mutations in reverse transcriptase in primary HIV infection. J. AIDS 2004, 37:1627-1631.
31. UK Collaborative Group on HIV Drug Resistance, UK Collaborative HIV Cohort Study, UK Register of HIV Seroconverters Evidence of a decline in transmitted HIV-1 drug-resistance in the United Kingdom. AIDS 2007, 21:1035-1039.
32. Violin M., Cozzi-Lepri A., Velleca R., Vincenti A., D'Elia S., Chiodo F., Ghinelli F., Bertoli A., d'Arminio Monforte A., Perno C.F., Moroni M., Balotta C. Risk of failure in patients with 215 HIV-1 revertants starting their first thymidine analog-containing highly active antiretroviral therapy. AIDS 2004, 18:227-235.
33. Violin M., Velleca R., Cozzi-Lepri A., Riva C., Grossi P.A., Carnevale g., Rizzardini G., Petrelli E., Perno C.F., Monforte A., Balotta C. Prevalence of HIV-1 Primary Drug Resistance in Seroconverters of the ICoNA Cohort Over the Period 1996-2001. J. AIDS 2004, 36:761-764. ICONA Study Group.
34. Walker P.R., Pybus O.G., Rambaut A., Holmes E.C. Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth. Infect. Genet. Evol. 2005, 5:199-208.
35. Wensing A.M., van de Vijver D.A., Angarano G., Asjo B., Balotta C., Boeri E., Camacho R., Chaix M.L., Costagliola D., De Luca A., Derdelinckx I., Grossman Z., Hamouda O., Hatzakis A., Hemmer R., Hoepelman A., Horban A., Korn K., Kucherer C., Leitner T., Loveday C., MacRae E., Malikovic I., de Mendoza C., Meyer L., Nielsen C., Op de Coul E.L., Ormaasen V., Paraskevis D., Perrin L., Puchhammer-Stockl E., Ruiz L., Salminen M., Schmit J.C., Schneider F., Schuurman R., Soriano V., Stanczak G., Stanojevic M., Vandamme A.M., Van Laethem K., Violin M., Yerly S., Zazzi M., Boucher C.A. SPREAD Programme Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management. J. Infect. Dis. 2005, 192:958-966.
36. Yerly S., Junier T., Gayet-Ageron A., Amari E.B., von Wyl V., Günthard H.F., Hirschel B., Zdobnov E., Kaiser L. Swiss HIV Cohort Study The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection. AIDS 2009, 23:1415-1423.
37. Yerly S., von Wyl V., Ledergerber B., Boni J., Schupbach J., Burgisser P., Klimkait T., Rickenbach M., Kaiser L., Gunthard H.F., Perrin L. Transmission of HIV-1 drug-resistance in Switzerland: a 10-year molecular epidemiology survey. Antivir. Ther. 2007, 21:2223-2229. Swiss HIV Cohort Study.
38. Yerly S., Vora S., Rizzardi P., Chave J.P., Vernazza P.L., Flepp M., Telenti A., Battegay M., Veuthey A.L., Bru J.P., Rickenbach M., Hirschel B., Perrin L. Acute HIV infection: impact on the spread of HIV and transmission of drug resistance. AIDS 2001, 15(17 (November)):2287-2292. Swiss HIV Cohort Study.