{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T08:44:22Z","timestamp":1768553062427,"version":"3.49.0"},"reference-count":52,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2017,10,9]],"date-time":"2017-10-09T00:00:00Z","timestamp":1507507200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006595","name":"Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii","doi-asserted-by":"publisher","award":["BEST-HOPE project 4-003\/2012"],"award-info":[{"award-number":["BEST-HOPE project 4-003\/2012"]}],"id":[{"id":"10.13039\/501100006595","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006595","name":"Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii","doi-asserted-by":"publisher","award":["HIV-ID 260\/2015"],"award-info":[{"award-number":["HIV-ID 260\/2015"]}],"id":[{"id":"10.13039\/501100006595","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005802","name":"Autoritatea National\u0103 pentru Cercetare Stiintific\u0103","doi-asserted-by":"publisher","award":["GreenVac project, 5SEE\/2014"],"award-info":[{"award-number":["GreenVac project, 5SEE\/2014"]}],"id":[{"id":"10.13039\/501100005802","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005802","name":"Autoritatea National\u0103 pentru Cercetare Stiintific\u0103","doi-asserted-by":"publisher","award":["CRCBABI project (642\/2014)"],"award-info":[{"award-number":["CRCBABI project (642\/2014)"]}],"id":[{"id":"10.13039\/501100005802","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005802","name":"Autoritatea National\u0103 pentru Cercetare Stiintific\u0103","doi-asserted-by":"publisher","award":["POSDRU\/1591\/1.5\/S\/135760-CERO"],"award-info":[{"award-number":["POSDRU\/1591\/1.5\/S\/135760-CERO"]}],"id":[{"id":"10.13039\/501100005802","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek \u2013 Vlaanderen","doi-asserted-by":"crossref","award":["PhD grant"],"award-info":[{"award-number":["PhD grant"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0185866","type":"journal-article","created":{"date-parts":[[2017,10,9]],"date-time":"2017-10-09T13:38:42Z","timestamp":1507556322000},"page":"e0185866","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["Epidemic dispersion of HIV and HCV in a population of co-infected Romanian injecting drug users"],"prefix":"10.1371","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6707-3720","authenticated-orcid":true,"given":"Simona","family":"Paraschiv","sequence":"first","affiliation":[]},{"given":"Leontina","family":"Banica","sequence":"additional","affiliation":[]},{"given":"Ionelia","family":"Nicolae","sequence":"additional","affiliation":[]},{"given":"Iulia","family":"Niculescu","sequence":"additional","affiliation":[]},{"given":"Adrian","family":"Abagiu","sequence":"additional","affiliation":[]},{"given":"Raluca","family":"Jipa","sequence":"additional","affiliation":[]},{"given":"Andrea-Clemencia","family":"Pineda-Pe\u00f1a","sequence":"additional","affiliation":[]},{"given":"Marta","family":"Pingarilho","sequence":"additional","affiliation":[]},{"given":"Emil","family":"Neaga","sequence":"additional","affiliation":[]},{"given":"Kristof","family":"Theys","sequence":"additional","affiliation":[]},{"given":"Pieter","family":"Libin","sequence":"additional","affiliation":[]},{"given":"Dan","family":"Otelea","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Abecasis","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2017,10,9]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1016\/S0140-6736(08)61311-2","article-title":"Global epidemiology of injecting drug use and HIV among people who inject drugs: a systematic review","volume":"372","author":"BM Mathers","year":"2008","journal-title":"Lancet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"S17","DOI":"10.1097\/QAI.0b013e3181f9c04c","article-title":"HIV among people who use drugs: a global perspective of populations at risk","volume":"55","author":"JK Stockman","year":"2010","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1097\/COH.0b013e328354131e","article-title":"HIV and viral hepatitis C coinfection in people who inject drugs: implications of new direct acting antivirals for hepatitis C virus treatment","volume":"7","author":"N Walsh","year":"2012","journal-title":"Curr Opin HIV AIDS"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1111\/j.1753-6405.2007.00007.x","article-title":"High hepatitis C incidence in new injecting drug users: a policy failure?","volume":"31","author":"L Maher","year":"2007","journal-title":"Aust N Z J Public Health"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1258\/095646207779949907","article-title":"High prevalence of blood-borne virus infections and high-risk behaviour among injecting drug users in Tallinn, Estonia","volume":"18","author":"A Uusk\u00fcla","year":"2007","journal-title":"Int J STD AIDS"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/nrgastro.2014.17","article-title":"HCV and HIV co-infection: mechanisms and management","volume":"11","author":"JY Chen","year":"2014","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"23","DOI":"10.2174\/157016207779316297","article-title":"HIV genetic diversity: biological and public health consequences","volume":"5","author":"IF Butler","year":"2007","journal-title":"Curr HIV Res"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1002\/hep.26744","article-title":"Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource","volume":"59","author":"DB Smith","year":"2014","journal-title":"Hepatology"},{"key":"ref9","unstructured":"Romanian HIV\/AIDS National Committee Report. 2014; 20\u201321, available from <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.cnlas.ro\/images\/doc\/31122014_eng.pdf\" xlink:type=\"simple\">http:\/\/www.cnlas.ro\/images\/doc\/31122014_eng.pdf<\/ext-link>, accessed 7 March 2017"},{"key":"ref10","unstructured":"Abagiu A and Botescu A. Update on country situation: Romania; 2nd meeting on detecting and responding to outbreaks of HIV among IDUs. 2012; 11, available from <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.emcdda.europa.eu\/attachements.cfm\/att_195213_EN_02%20Romania.pdf\" xlink:type=\"simple\">www.emcdda.europa.eu\/attachements.cfm\/att_195213_EN_02%20Romania.pdf<\/ext-link>"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1089\/aid.2014.0189","article-title":"Recent HIV-1 outbreak among Intravenous Drug Users in Romania: Evidence for cocirculation of CRF14_BG and subtype F1 strains","volume":"31","author":"I Niculescu","year":"2015","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.meegid.2015.08.004","article-title":"Enhanced HIV-1 surveillance using molecular epidemiology to study and monitor HIV-1 outbreaks among intravenous drug users (IDUs) in Athens and Bucharest","volume":"35","author":"D Paraskevis","year":"2015","journal-title":"Infect Genet Evol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1086\/380821","article-title":"Spread of hepatitis C virus among European injection drug users infected with HIV: a phylogenetic analysis","volume":"189","author":"L van Asten","year":"2004","journal-title":"J Infect Dis"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1093\/cid\/ciq200","article-title":"Patterns and characteristics of hepatitis C transmission clusters among HIV-positive and HIV-negative individuals in the Australian trial in acute hepatitis C","volume":"52","author":"GV Matthews","year":"2011","journal-title":"Clin Infect Dis"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.meegid.2013.04.032","article-title":"Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools","volume":"19","author":"AC Pineda-Pe\u00f1a","year":"2013","journal-title":"Infect Genet Evol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1093\/bioinformatics\/16.4.400","article-title":"Detecting hypermutations in viral sequences with an emphasis on G\u2014&gt; A hypermutation","volume":"16","author":"PP Rose","year":"2000","journal-title":"Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/S0166-0934(03)00070-3","article-title":"Determining hepatitis C genotype by analyzing the sequence of the NS5b region","volume":"109","author":"K Sandres-Saun\u00e9","year":"2003","journal-title":"J Virol Methods"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.3851\/IMP1900","article-title":"NS3 protease polymorphism and natural resistance to protease inhibitors in French patients infected with HCV genotypes 1\u20135","volume":"16","author":"S Vallet","year":"2011","journal-title":"Antivir Ther"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1093\/nar\/gkp455","article-title":"A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences","volume":"37","author":"LCJ Alcantara","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"ref20","unstructured":"Available from <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.hiv.lanl.gov\/\" xlink:type=\"simple\">http:\/\/www.hiv.lanl.gov\/<\/ext-link>"},{"key":"ref21","unstructured":"Available from <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.ncbi.nlm.nih.gov\/nucleotide\/\" xlink:type=\"simple\">http:\/\/www.ncbi.nlm.nih.gov\/nucleotide\/<\/ext-link>"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1742-4690-6-39","article-title":"Close phylogenetic relationship between Angolan and Romanian HIV-1 subtype F1 isolates","volume":"6","author":"ML Guimar\u00e3es","year":"2009","journal-title":"Retrovirology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1016\/j.meegid.2012.03.014","article-title":"Phylodynamics of HIV-1 subtype F1 in Angola, Brazil and Romania","volume":"12","author":"G Bello","year":"2012","journal-title":"Infect Genet Evol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"RC Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PLoS One"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"AJ Drummond","year":"2012","journal-title":"Mol Biol Evol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"AJ Drummond","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed phylogenetics and dating with confidence","volume":"4","author":"AJ Drummond","year":"2006","journal-title":"PLoS Biol"},{"key":"ref29","unstructured":"Rambaut A, Suchard M, Drummond A. Tracer. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/tree.bio.ed.ac.uk\/software\/tracer\/\" xlink:type=\"simple\">http:\/\/tree.bio.ed.ac.uk\/software\/tracer\/<\/ext-link>"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"AJ Drummond","year":"2007","journal-title":"BMC Evol Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1097\/QAI.0b013e3181eb3002","article-title":"Population dynamics of HIV-1 subtype B in a cohort of men-having-sex-with-men in Rome, Italy","volume":"55","author":"G Zehender","year":"2010","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1097\/QAI.0b013e318276becc","article-title":"Phylogenetics of the Danish HIV epidemic: the role of very late presenters in sustaining the epidemic","volume":"62","author":"AM Audelin","year":"2013","journal-title":"J Acquir Immune Defic Syndr"},{"issue":"1","key":"ref33","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"A Rambaut","year":"2016","journal-title":"Virus Evol"},{"key":"ref34","unstructured":"Guide for HIV\/AIDS clinical care, HIV classification: CDC and WHO staging systems. 2014; available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/aidsetc.org\/guide\/hiv-classification-cdc-and-who-staging-systems\" xlink:type=\"simple\">http:\/\/aidsetc.org\/guide\/hiv-classification-cdc-and-who-staging-systems<\/ext-link>"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"15198","DOI":"10.1038\/srep15198","article-title":"Co-infections and transmission networks of HCV, HIV-1 and HPgV among people who inject drugs","volume":"5","author":"KT Ng","year":"2015","journal-title":"Sci Rep"},{"key":"ref36","unstructured":"UNAIDS 2013 Global report, The Epidemic\u2019s Enduring Impact On People Who Inject Drugs. 2013; 30\u201331, available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.unaids.org\/sites\/default\/files\/media_asset\/UNAIDS_Global_Report_2013_en_1.pdf\" xlink:type=\"simple\">http:\/\/www.unaids.org\/sites\/default\/files\/media_asset\/UNAIDS_Global_Report_2013_en_1.pdf<\/ext-link>."},{"key":"ref37","unstructured":"United Nations Office on Drugs and Crime, World Drug Report 2015 available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.unodc.org\/documents\/wdr2015\/WDR15_Chapter_1.pdf\" xlink:type=\"simple\">https:\/\/www.unodc.org\/documents\/wdr2015\/WDR15_Chapter_1.pdf<\/ext-link>, pag 6,"},{"key":"ref38","unstructured":"Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/files.unaids.org\/en\/dataanalysis\/knowyourresponse\/countryprogressreports\/2014countries\/ROU_narrative_report_2014.pdf\" xlink:type=\"simple\">http:\/\/files.unaids.org\/en\/dataanalysis\/knowyourresponse\/countryprogressreports\/2014countries\/ROU_narrative_report_2014.pdf<\/ext-link>"},{"key":"ref39","unstructured":"Botescu A, Abagiu A, Mardarescu M, Ursan M. HIV\/AIDS among injecting drug users in Romania. Report of a recent outbreak and initial response policies. 2012; 5\u201314 available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.emcdda.europa.eu\/attachements.cfm\/att_192024_EN_HIV_outbreak_Romania_2012.pdf\" xlink:type=\"simple\">http:\/\/www.emcdda.europa.eu\/attachements.cfm\/att_192024_EN_HIV_outbreak_Romania_2012.pdf<\/ext-link>"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e24130","DOI":"10.1371\/journal.pone.0024130","article-title":"Origin and epidemiological history of HIV-1 CRF14_BG","volume":"6","author":"I B\u00e1rtolo","year":"2011","journal-title":"PLoS One"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1093\/infdis\/jis926","article-title":"Pathogenesis of accelerated fibrosis in HIV\/HCV co-infection","volume":"207","author":"W Lin","year":"2013","journal-title":"J Infect Dis"},{"issue":"7121","key":"ref42","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/444836a","article-title":"Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak","volume":"444","author":"T de Oliveira","year":"2006","journal-title":"Nature"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1126\/science.1256739","article-title":"HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations","volume":"346","author":"NR Faria","year":"2014","journal-title":"Science"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1093\/jac\/dkt305","article-title":"Predominance of CXCR4 tropism in HIV-1 CRF14_BG strains from newly diagnosed infections","volume":"69","author":"L P\u00e9rez-\u00c1lvarez","year":"2014","journal-title":"J Antimicrob Chemother"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.jhep.2007.07.033","article-title":"The changing epidemiology of hepatitis C virus infection in Europe","volume":"48","author":"JI Esteban","year":"2008","journal-title":"J Hepatol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1111\/j.1365-2893.2005.00649.x","article-title":"Molecular epidemiology of hepatitis C virus (HCV) in Greece: temporal trends in HCV genotype-specific incidence and molecular characterization of genotype 4 isolates","volume":"13","author":"A Katsoulidou","year":"2006","journal-title":"J Viral Hepat"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1002\/jmv.23384","article-title":"Hepatitis C virus genotype 4d in Southern Italy: reconstruction of its origin and spread by a phylodynamic analysis","volume":"84","author":"M Ciccozzi","year":"2012","journal-title":"J Med Virol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1002\/jmv.20706","article-title":"High prevalence of hepatitis C virus subtypes 4c and 4d in Malaga (Spain): phylogenetic and epidemiological analyses","volume":"78","author":"N Fern\u00e1ndez-Arc\u00e1s","year":"2006","journal-title":"J Med Virol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"3832","DOI":"10.1128\/JCM.01146-09","article-title":"Emergence of hepatitis C virus genotype 4: phylogenetic analysis reveals three distinct epidemiological profiles","volume":"47","author":"J de Bruijne","year":"2009","journal-title":"J Clin Microbiol"},{"key":"ref50","first-page":"45","article-title":"HCV genotype 1 is almost exclusively present in Romanian patients with chronic hepatitis C","volume":"18","author":"M Grigorescu","year":"2009","journal-title":"J Gastrointestin Liver Dis"},{"key":"ref51","first-page":"373","article-title":"The prevalence and risk factors of hepatitis C virus infection in adult population in Romania: a nationwide survey 2006\u20132008","volume":"19","author":"L Gheorghe","year":"2010","journal-title":"J Gastrointestin Liver Dis"},{"key":"ref52","first-page":"672","article-title":"Hepatitis C Virus Genotypes in Injecting Drug Users from Romania","volume":"6","author":"C Sultana","year":"2011","journal-title":"Cent Eur J Med"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0185866","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T21:33:18Z","timestamp":1540243998000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0185866"}},"subtitle":[],"editor":[{"given":"Zhefeng","family":"Meng","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,10,9]]},"references-count":52,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2017,10,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0185866","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10,9]]}}}