{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T14:23:43Z","timestamp":1790173423737,"version":"4.1.0"},"reference-count":67,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Virol J"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12985-017-0887-1","type":"journal-article","created":{"date-parts":[[2017,11,14]],"date-time":"2017-11-14T11:35:59Z","timestamp":1510659359000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Molecular evolution of HIV-1 integrase during the 20\u00a0years prior to the first approval of integrase inhibitors"],"prefix":"10.1186","volume":"14","author":[{"given":"Karolin","family":"Meixenberger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaveh Pouran","family":"Yousef","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maureen Rebecca","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sybille","family":"Somogyi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Fiedler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Bartmeyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osamah","family":"Hamouda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norbert","family":"Bannert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max","family":"von Kleist","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"K\u00fccherer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,11,14]]},"reference":[{"key":"887_CR1","first-page":"17","volume":"11","author":"F Ceccherini-Silberstein","year":"2009","unstructured":"Ceccherini-Silberstein F, Malet I, D'Arrigo R, Antinori A, Marcelin AG, Perno CF. Characterization and structural analysis of HIV-1 integrase conservation. AIDS Rev. 2009;11:17\u201329.","journal-title":"AIDS Rev"},{"key":"887_CR2","doi-asserted-by":"crossref","first-page":"3428","DOI":"10.1073\/pnas.90.8.3428","volume":"90","author":"FD Bushman","year":"1993","unstructured":"Bushman FD, Engelman A, Palmer I, Wingfield P, Craigie R. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc Natl Acad Sci U S A. 1993;90:3428\u201332.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"887_CR3","doi-asserted-by":"crossref","first-page":"8233","DOI":"10.1073\/pnas.150220297","volume":"97","author":"JC Chen","year":"2000","unstructured":"Chen JC, Krucinski J, Miercke LJ, Finer-Moore JS, Tang AH, Leavitt AD, et al. Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. Proc Natl Acad Sci U S A. 2000;97:8233\u20138.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"887_CR4","doi-asserted-by":"crossref","first-page":"7333","DOI":"10.1093\/emboj\/20.24.7333","volume":"20","author":"JY Wang","year":"2001","unstructured":"Wang JY, Ling H, Yang W, Craigie R. Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein. EMBO J. 2001;20:7333\u201343.","journal-title":"EMBO J"},{"key":"887_CR5","doi-asserted-by":"crossref","first-page":"4841","DOI":"10.1128\/JVI.72.6.4841-4848.1998","volume":"72","author":"RA Lutzke","year":"1998","unstructured":"Lutzke RA, Plasterk RH. Structure-based mutational analysis of the C-terminal DNA-binding domain of human immunodeficiency virus type 1 integrase: critical residues for protein oligomerization and DNA binding. J Virol. 1998;72:4841\u20138.","journal-title":"J Virol"},{"key":"887_CR6","doi-asserted-by":"crossref","first-page":"17308","DOI":"10.1073\/pnas.0506924102","volume":"102","author":"P Cherepanov","year":"2005","unstructured":"Cherepanov P, Ambrosio AL, Rahman S, Ellenberger T, Engelman A. Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Proc Natl Acad Sci U S A. 2005;102:17308\u201313.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"887_CR7","doi-asserted-by":"crossref","first-page":"e154","DOI":"10.1016\/S2352-3018(17)30016-4","volume":"4","author":"PE Sax","year":"2017","unstructured":"Sax PE, DeJesus E, Crofoot G, Ward D, Benson P, Dretler R, et al. Bictegravir versus dolutegravir, each with emtricitabine and tenofovir alafenamide, for initial treatment of HIV-1 infection: a randomised, double-blind, phase 2 trial. Lancet HIV. 2017;4:e154\u201360.","journal-title":"Lancet HIV."},{"key":"887_CR8","doi-asserted-by":"crossref","unstructured":"Markowitz M, Frank I, Grant RM, Mayer KH, Elion R, Goldstein D, et al. Safety and tolerability of long-acting cabotegravir injections in HIV-uninfected men (ECLAIR): a multicentre, double-blind, randomised, placebo-controlled, phase 2a trial. Lancet HIV. 2017;4(8):e331\u2013e340.","DOI":"10.1016\/S2352-3018(17)30068-1"},{"key":"887_CR9","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/1742-4690-10-57","volume":"10","author":"BA Desimmie","year":"2013","unstructured":"Desimmie BA, Schrijvers R, Demeulemeester J, Borrenberghs D, Weydert C, Thys W, et al. LEDGINs inhibit late stage HIV-1 replication by modulating integrase multimerization in the virions. Retrovirology. 2013;10:57.","journal-title":"Retrovirology"},{"key":"887_CR10","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1038\/nchembio.370","volume":"6","author":"F Christ","year":"2010","unstructured":"Christ F, Voet A, Marchand A, Nicolet S, Desimmie BA, Marchand D, et al. Rational design of small-molecule inhibitors of the LEDGF\/p75-integrase interaction and HIV replication. Nat Chem Biol. 2010;6:442\u20138.","journal-title":"Nat Chem Biol"},{"key":"887_CR11","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1016\/j.ejmech.2016.10.045","volume":"125","author":"FH Zhang","year":"2017","unstructured":"Zhang FH, Debnath B, Xu ZL, Yang LM, Song LR, Zheng YT, et al. Discovery of novel 3-hydroxypicolinamides as selective inhibitors of HIV-1 integrase-LEDGF\/p75 interaction. Eur J Med Chem. 2017;125:1051\u201363.","journal-title":"Eur J Med Chem"},{"key":"887_CR12","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1084\/jem.20041455","volume":"201","author":"A Leslie","year":"2005","unstructured":"Leslie A, Kavanagh D, Honeyborne I, Pfafferott K, Edwards C, Pillay T, et al. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J Exp Med. 2005;201:891\u2013902.","journal-title":"J Exp Med"},{"key":"887_CR13","doi-asserted-by":"crossref","first-page":"13239","DOI":"10.1128\/JVI.79.21.13239-13249.2005","volume":"79","author":"TM Allen","year":"2005","unstructured":"Allen TM, Altfeld M, Geer SC, Kalife ET, Moore C, O'Sullivan KM, et al. Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution. J Virol. 2005;79:13239\u201349.","journal-title":"J Virol"},{"key":"887_CR14","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1097\/COH.0b013e32801682f6","volume":"2","author":"M Nijhuis","year":"2007","unstructured":"Nijhuis M, van Maarseveen NM, Boucher CA. HIV protease resistance and viral fitness. Curr Opin HIV AIDS. 2007;2:108\u201315.","journal-title":"Curr Opin HIV AIDS"},{"key":"887_CR15","doi-asserted-by":"crossref","first-page":"3722","DOI":"10.1128\/JVI.78.7.3722-3732.2004","volume":"78","author":"L Chen","year":"2004","unstructured":"Chen L, Perlina A, Lee CJ. Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase. J Virol. 2004;78:3722\u201332.","journal-title":"J Virol"},{"key":"887_CR16","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.1128\/JCM.03289-13","volume":"52","author":"K Meixenberger","year":"2014","unstructured":"Meixenberger K, Hauser A, Jansen K, Yousef KP, Fiedler S, von Kleist M, et al. Assessment of ambiguous base calls in HIV-1 pol population sequences as a biomarker for identification of recent infections in HIV-1 incidence studies. J Clin Microbiol. 2014;52:2977\u201383.","journal-title":"J Clin Microbiol"},{"key":"887_CR17","doi-asserted-by":"crossref","first-page":"10313","DOI":"10.1128\/JVI.01225-12","volume":"87","author":"F Maldarelli","year":"2013","unstructured":"Maldarelli F, Kearney M, Palmer S, Stephens R, Mican J, Polis MA, et al. HIV populations are large and accumulate high genetic diversity in a nonlinear fashion. J Virol. 2013;87:10313\u201323.","journal-title":"J Virol"},{"key":"887_CR18","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/nrmicro3471","volume":"13","author":"SB Joseph","year":"2015","unstructured":"Joseph SB, Swanstrom R, Kashuba AD, Cohen MS. Bottlenecks in HIV-1 transmission: insights from the study of founder viruses. Nat Rev Microbiol. 2015;13:414\u201325.","journal-title":"Nat Rev Microbiol"},{"key":"887_CR19","doi-asserted-by":"crossref","first-page":"e1001123","DOI":"10.1371\/journal.ppat.1001123","volume":"6","author":"S Alizon","year":"2010","unstructured":"Alizon S, von Wyl V, Stadler T, Kouyos RD, Yerly S, Hirschel B, et al. Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathog. 2010;6:e1001123.","journal-title":"PLoS Pathog"},{"key":"887_CR20","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1742-4690-10-49","volume":"10","author":"S Alizon","year":"2013","unstructured":"Alizon S, Fraser C. Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology. 2013;10:49.","journal-title":"Retrovirology"},{"key":"887_CR21","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/1742-4690-9-81","volume":"9","author":"K Theys","year":"2012","unstructured":"Theys K, Deforche K, Vercauteren J, Libin P, van de Vijver DA, Albert J, et al. Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients. Retrovirology. 2012;9:81.","journal-title":"Retrovirology"},{"key":"887_CR22","doi-asserted-by":"crossref","first-page":"303","DOI":"10.2217\/fmb.13.10","volume":"8","author":"K Theys","year":"2013","unstructured":"Theys K, Abecasis AB, Vandamme AM. HIV-1 drug resistance: where do polymorphisms fit in? Future Microbiol. 2013;8:303\u20136.","journal-title":"Future Microbiol"},{"key":"887_CR23","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s12977-015-0148-6","volume":"12","author":"G Li","year":"2015","unstructured":"Li G, Piampongsant S, Faria NR, Voet A, Pineda-Pena AC, Khouri R, et al. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology. 2015;12:18.","journal-title":"Retrovirology"},{"key":"887_CR24","doi-asserted-by":"crossref","first-page":"e1003505","DOI":"10.1371\/journal.pcbi.1003505","volume":"10","author":"B Vrancken","year":"2014","unstructured":"Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, et al. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comput Biol. 2014;10:e1003505.","journal-title":"PLoS Comput Biol"},{"key":"887_CR25","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1002\/jmv.22047","volume":"83","author":"BG Brenner","year":"2011","unstructured":"Brenner BG, Lowe M, Moisi D, Hardy I, Gagnon S, Charest H, et al. Subtype diversity associated with the development of HIV-1 resistance to integrase inhibitors. J Med Virol. 2011;83:751\u20139.","journal-title":"J Med Virol"},{"key":"887_CR26","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1093\/jac\/dkp423","volume":"65","author":"C Garrido","year":"2010","unstructured":"Garrido C, Geretti AM, Zahonero N, Booth C, Strang A, Soriano V, et al. Integrase variability and susceptibility to HIV integrase inhibitors: impact of subtypes, antiretroviral experience and duration of HIV infection. J Antimicrob Chemother. 2010;65:320\u20136.","journal-title":"J Antimicrob Chemother"},{"key":"887_CR27","doi-asserted-by":"crossref","first-page":"e1002359","DOI":"10.1371\/journal.pcbi.1002359","volume":"8","author":"M von Kleist","year":"2012","unstructured":"von Kleist M, Metzner P, Marquet R, Schutte C. HIV-1 polymerase inhibition by nucleoside analogs: cellular- and kinetic parameters of efficacy, susceptibility and resistance selection. PLoS Comput Biol. 2012;8:e1002359.","journal-title":"PLoS Comput Biol"},{"key":"887_CR28","doi-asserted-by":"crossref","first-page":"e18375","DOI":"10.1371\/journal.pone.0018375","volume":"6","author":"JP Martinez","year":"2011","unstructured":"Martinez JP, Bocharov G, Ignatovich A, Reiter J, Dittmar MT, Wain-Hobson S, et al. Fitness ranking of individual mutants drives patterns of epistatic interactions in HIV-1. PLoS One. 2011;6:e18375.","journal-title":"PLoS One"},{"key":"887_CR29","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/ng.795","volume":"43","author":"T Hinkley","year":"2011","unstructured":"Hinkley T, Martins J, Chappey C, Haddad M, Stawiski E, Whitcomb JM, et al. A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat Genet. 2011;43:487\u20139.","journal-title":"Nat Genet"},{"key":"887_CR30","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1186\/1471-2105-11-409","volume":"11","author":"K Theys","year":"2010","unstructured":"Theys K, Deforche K, Beheydt G, Moreau Y, van Laethem K, Lemey P, et al. Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. BMC Bioinformatics. 2010;11:409.","journal-title":"BMC Bioinformatics"},{"key":"887_CR31","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1177\/135965350701200411","volume":"12","author":"M Lataillade","year":"2007","unstructured":"Lataillade M, Chiarella J, Kozal MJ. Natural polymorphism of the HIV-1 integrase gene and mutations associated with integrase inhibitor resistance. Antivir Ther. 2007;12:563\u201370.","journal-title":"Antivir Ther"},{"key":"887_CR32","doi-asserted-by":"crossref","first-page":"9228","DOI":"10.1128\/JVI.01535-07","volume":"82","author":"RE Myers","year":"2008","unstructured":"Myers RE, Pillay D. Analysis of natural sequence variation and covariation in human immunodeficiency virus type 1 integrase. J Virol. 2008;82:9228\u201335.","journal-title":"J Virol"},{"key":"887_CR33","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1742-4690-5-74","volume":"5","author":"SY Rhee","year":"2008","unstructured":"Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, et al. Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology. 2008;5:74.","journal-title":"Retrovirology"},{"key":"887_CR34","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1089\/aid.2010.0123","volume":"26","author":"V Varghese","year":"2010","unstructured":"Varghese V, Liu TF, Rhee SY, Libiran P, Trevino C, Fessel WJ, et al. HIV-1 integrase sequence variability in antiretroviral naive patients and in triple-class experienced patients subsequently treated with raltegravir. AIDS Res Hum Retrovir. 2010;26:1323\u20136.","journal-title":"AIDS Res Hum Retrovir"},{"key":"887_CR35","doi-asserted-by":"crossref","first-page":"6058","DOI":"10.1128\/JVI.00495-16","volume":"90","author":"SY Rhee","year":"2016","unstructured":"Rhee SY, Sankaran K, Varghese V, Winters MA, Hurt CB, Eron JJ, et al. HIV-1 protease, reverse transcriptase, and Integrase variation. J Virol. 2016;90:6058\u201370.","journal-title":"J Virol"},{"key":"887_CR36","doi-asserted-by":"crossref","first-page":"4275","DOI":"10.1128\/AAC.00397-09","volume":"53","author":"A Low","year":"2009","unstructured":"Low A, Prada N, Topper M, Vaida F, Castor D, Mohri H, et al. Natural polymorphisms of human immunodeficiency virus type 1 integrase and inherent susceptibilities to a panel of integrase inhibitors. Antimicrob Agents Chemother. 2009;53:4275\u201382.","journal-title":"Antimicrob Agents Chemother"},{"key":"887_CR37","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1093\/jac\/dkp153","volume":"64","author":"N Sichtig","year":"2009","unstructured":"Sichtig N, Sierra S, Kaiser R, Daumer M, Reuter S, Schulter E, et al. Evolution of raltegravir resistance during therapy. J Antimicrob Chemother. 2009;64:25\u201332.","journal-title":"J Antimicrob Chemother"},{"key":"887_CR38","doi-asserted-by":"crossref","first-page":"2305","DOI":"10.1093\/jac\/dkq326","volume":"65","author":"F Ceccherini-Silberstein","year":"2010","unstructured":"Ceccherini-Silberstein F, Malet I, Fabeni L, Dimonte S, Svicher V, D'Arrigo R, et al. Specific HIV-1 integrase polymorphisms change their prevalence in untreated versus antiretroviral-treated HIV-1-infected patients, all naive to integrase inhibitors. J Antimicrob Chemother. 2010;65:2305\u201318.","journal-title":"J Antimicrob Chemother"},{"key":"887_CR39","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1007\/s00430-011-0194-1","volume":"200","author":"S Sierra","year":"2011","unstructured":"Sierra S, Lubke N, Walter H, Schulter E, Reuter S, Fatkenheuer G, et al. The SnoB study: frequency of baseline raltegravir resistance mutations prevalence in different non-B subtypes. Med Microbiol Immunol. 2011;200:225\u201332.","journal-title":"Med Microbiol Immunol"},{"key":"887_CR40","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/1743-422X-8-149","volume":"8","author":"A Piralla","year":"2011","unstructured":"Piralla A, Paolucci S, Gulminetti R, Comolli G, Baldanti F. HIV integrase variability and genetic barrier in antiretroviral naive and experienced patients. Virol J. 2011;8:149.","journal-title":"Virol J"},{"key":"887_CR41","doi-asserted-by":"crossref","first-page":"19746","DOI":"10.7448\/IAS.17.4.19746","volume":"17","author":"K Meixenberger","year":"2014","unstructured":"Meixenberger K, Yousef KP, Somogyi S, Fiedler S, Bartmeyer B, von Kleist M, et al. Characterization of natural polymorphic sites of the HIV-1 integrase before the introduction of HIV-1 integrase inhibitors in Germany. J Int AIDS Soc. 2014;17:19746.","journal-title":"J Int AIDS Soc"},{"key":"887_CR42","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1097\/00126334-200103010-00010","volume":"26","author":"S Duwe","year":"2001","unstructured":"Duwe S, Brunn M, Altmann D, Hamouda O, Schmidt B, Walter H, et al. Frequency of genotypic and phenotypic drug-resistant HIV-1 among therapy-naive patients of the German Seroconverter study. J Acquir Immune Defic Syndr. 2001;26:266\u201373.","journal-title":"J Acquir Immune Defic Syndr"},{"key":"887_CR43","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1111\/j.1468-1293.2007.00504.x","volume":"8","author":"G Poggensee","year":"2007","unstructured":"Poggensee G, Kucherer C, Werning J, Somogyi S, Bieniek B, Dupke S, et al. Impact of transmission of drug-resistant HIV on the course of infection and the treatment success. Data from the German HIV-1 Seroconverter study. HIV Med. 2007;8:511\u20139.","journal-title":"HIV Med"},{"key":"887_CR44","doi-asserted-by":"crossref","first-page":"e12718","DOI":"10.1371\/journal.pone.0012718","volume":"5","author":"B Bartmeyer","year":"2010","unstructured":"Bartmeyer B, Kuecherer C, Houareau C, Werning J, Keeren K, Somogyi S, et al. Prevalence of transmitted drug resistance and impact of transmitted resistance on treatment success in the German HIV-1 Seroconverter cohort. PLoS One. 2010;5:e12718.","journal-title":"PLoS One"},{"key":"887_CR45","doi-asserted-by":"crossref","first-page":"e95956","DOI":"10.1371\/journal.pone.0095956","volume":"9","author":"F Zu Knyphausen","year":"2014","unstructured":"Zu Knyphausen F, Scheufele R, Kucherer C, Jansen K, Somogyi S, Dupke S, et al. First line treatment response in patients with transmitted HIV drug resistance and well defined time point of HIV infection: updated results from the German HIV-1 seroconverter study. PLoS One. 2014;9:e95956.","journal-title":"PLoS One"},{"key":"887_CR46","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.meegid.2013.04.032","volume":"19","author":"AC Pineda-Pena","year":"2013","unstructured":"Pineda-Pena AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, et al. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. Infect Genet Evol. 2013;19:337\u201348.","journal-title":"Infect Genet Evol."},{"key":"887_CR47","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s12977-017-0360-7","volume":"14","author":"K Anstett","year":"2017","unstructured":"Anstett K, Brenner B, Mesplede T, Wainberg MA. HIV drug resistance against strand transfer integrase inhibitors. Retrovirology. 2017;14:36.","journal-title":"Retrovirology"},{"key":"887_CR48","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1086\/503914","volume":"42","author":"TF Liu","year":"2006","unstructured":"Liu TF, Shafer RW. Web resources for HIV type 1 genotypic-resistance test interpretation. Clin Infect Dis. 2006;42:1608\u201318.","journal-title":"Clin Infect Dis."},{"key":"887_CR49","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","volume":"22","author":"A Stamatakis","year":"2006","unstructured":"Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688\u201390.","journal-title":"Bioinformatics"},{"key":"887_CR50","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1097\/QAI.0000000000001122","volume":"73","author":"K Pouran Yousef","year":"2016","unstructured":"Pouran Yousef K, Meixenberger K, Smith MR, Somogyi S, Gromoller S, Schmidt D, et al. Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses. J Acquir Immune Defic Syndr. 2016;73:356\u201363.","journal-title":"J Acquir Immune Defic Syndr"},{"key":"887_CR51","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1097\/QAD.0000000000001470","volume":"31","author":"AS Hassan","year":"2017","unstructured":"Hassan AS, Pybus OG, Sanders EJ, Albert J, Esbjornsson J. Defining HIV-1 transmission clusters based on sequence data. AIDS. 2017;31:1211\u201322.","journal-title":"AIDS"},{"key":"887_CR52","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/bioinformatics\/btp135","volume":"25","author":"CM Buslje","year":"2009","unstructured":"Buslje CM, Santos J, Delfino JM, Nielsen M. Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. Bioinformatics. 2009;25:1125\u201331.","journal-title":"Bioinformatics"},{"key":"887_CR53","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1093\/qjmed\/hcu077","volume":"107","author":"J Katchanov","year":"2014","unstructured":"Katchanov J, von Kleist M, Arasteh K, Stocker H. 'Time-to-amphotericin B' in cryptococcal meningitis in a European low-prevalence setting: analysis of diagnostic delays. QJM. 2014;107:799\u2013803.","journal-title":"QJM"},{"key":"887_CR54","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B-Methodological. 1995;57:289\u2013300.","journal-title":"Journal of the Royal Statistical Society Series B-Methodological"},{"key":"887_CR55","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/nbt.3769","volume":"35","author":"TA Hopf","year":"2017","unstructured":"Hopf TA, Ingraham JB, Poelwijk FJ, Scharfe CP, Springer M, Sander C, et al. Mutation effects predicted from sequence co-variation. Nat Biotechnol. 2017;35:128\u201335.","journal-title":"Nat Biotechnol"},{"key":"887_CR56","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1093\/bioinformatics\/btr638","volume":"28","author":"DT Jones","year":"2012","unstructured":"Jones DT, Buchan DW, Cozzetto D, Pontil M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 2012;28:184\u201390.","journal-title":"Bioinformatics"},{"key":"887_CR57","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nmeth.4210","volume":"14","author":"N Altman","year":"2017","unstructured":"Altman N, Krzywinski M. Points of significance: interpreting P values. Nat Methods. 2017;14:213\u20134.","journal-title":"Nat Methods"},{"key":"887_CR58","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1198\/000313001300339950","volume":"55","author":"T Sellke","year":"2001","unstructured":"Sellke T, Bayarri MJ, Berger JO. Calibration of p values for testing precise null hypotheses. Am Stat. 2001;55:62\u201371.","journal-title":"Am Stat"},{"key":"887_CR59","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/nmeth.3288","volume":"12","author":"LG Halsey","year":"2015","unstructured":"Halsey LG, Curran-Everett D, Vowler SL, Drummond GB. The fickle P value generates irreproducible results. Nat Methods. 2015;12:179\u201385.","journal-title":"Nat Methods"},{"key":"887_CR60","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1534\/genetics.166.3.1155","volume":"166","author":"D Shriner","year":"2004","unstructured":"Shriner D, Shankarappa R, Jensen MA, Nickle DC, Mittler JE, Margolick JB, et al. Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection. Genetics. 2004;166:1155\u201364.","journal-title":"Genetics"},{"key":"887_CR61","doi-asserted-by":"crossref","first-page":"1441","DOI":"10.1534\/genetics.105.052019","volume":"174","author":"CT Edwards","year":"2006","unstructured":"Edwards CT, Holmes EC, Pybus OG, Wilson DJ, Viscidi RP, Abrams EJ, et al. Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection. Genetics. 2006;174:1441\u201353.","journal-title":"Genetics"},{"key":"887_CR62","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1089\/aid.1998.14.869","volume":"14","author":"HF Gunthard","year":"1998","unstructured":"Gunthard HF, Wong JK, Ignacio CC, Havlir DV, Richman DD. Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples. AIDS Res Hum Retrovir. 1998;14:869\u201376.","journal-title":"AIDS Res Hum Retrovir"},{"key":"887_CR63","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1128\/JCM.43.1.406-413.2005","volume":"43","author":"S Palmer","year":"2005","unstructured":"Palmer S, Kearney M, Maldarelli F, Halvas EK, Bixby CJ, Bazmi H, et al. Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol. 2005;43:406\u201313.","journal-title":"J Clin Microbiol"},{"key":"887_CR64","doi-asserted-by":"crossref","first-page":"329","DOI":"10.3389\/fmicb.2012.00329","volume":"3","author":"N Beerenwinkel","year":"2012","unstructured":"Beerenwinkel N, Gunthard HF, Roth V, Metzner KJ. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front Microbiol. 2012;3:329.","journal-title":"Front Microbiol"},{"key":"887_CR65","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bib\/bbs081","volume":"15","author":"M Schirmer","year":"2014","unstructured":"Schirmer M, Sloan WT, Quince C. Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes. Brief Bioinform. 2014;15:431\u201342.","journal-title":"Brief Bioinform"},{"key":"887_CR66","doi-asserted-by":"crossref","first-page":"2456","DOI":"10.1093\/molbev\/msv109","volume":"32","author":"D Talavera","year":"2015","unstructured":"Talavera D, Lovell SC, Whelan S. Covariation is a poor measure of molecular Coevolution. Mol Biol Evol. 2015;32:2456\u201368.","journal-title":"Mol Biol Evol"},{"key":"887_CR67","volume-title":"The PyMOL molecular graphics system, version 1.8","author":"LLC Schrodinger","year":"2015","unstructured":"Schrodinger LLC: The PyMOL molecular graphics system, version 1.8. 2015."}],"container-title":["Virology Journal"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12985-017-0887-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T16:44:29Z","timestamp":1719593069000},"score":1,"resource":{"primary":{"URL":"https:\/\/virologyj.biomedcentral.com\/articles\/10.1186\/s12985-017-0887-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,14]]},"references-count":67,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["887"],"URL":"https:\/\/doi.org\/10.1186\/s12985-017-0887-1","relation":{},"ISSN":["1743-422X"],"issn-type":[{"value":"1743-422X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,14]]},"article-number":"223"}}