Publications

Turk, T., Bachmann, N., Kadelka, C., Böni, J., Yerly, S., Aubert, V., Klimkait, T., Battegay, M., Bernasconi, E., Calmy, A., Cavassini, M., Furrer, H., Hoffmann, M., Günthard, H. F., Kouyos, R. D., Swiss HIV Cohort Study, Aubert, V., Battegay, M., Bernasconi, E., Böni, J., Braun, D. L., Bucher, H. C., Calmy, A., Cavassini, M., Ciuffi, A., Dollenmaier, G., Egger, M., Elzi, L., Fehr, J., Fellay, J., Furrer, H., Fux, C. A., Günthard, H. F., Haerry, D., Hasse, B., Hirsch, H. H., Hoffmann, M., Hösli, I., Kahlert, C., Kaiser, L., Keiser, O., Klimkait, T., Kouyos, R. D., Kovari, H., Ledergerber, B., Martinetti, G., Martinez de Tejada, B., Marzolini, C., Metzner, K. J., Müller, N., Nicca, D., Pantaleo, G., Paioni, P., Rauch, A., Rudin, C., Scherrer, A. U., Schmid, P., Speck, R., Stöckle, M., Tarr, P., Trkola, A., Vernazza, P., Wandeler, G., Weber, R. and Yerly, S. (2017) ‘Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis’, eLife, 6, p. e28721. doi: 10.7554/eLife.28721.   
Puga, D., Cerutti, B., Molisana, C., Bader, J., Faturiyele, O., Ringera, I., Lejone, T., Pfeiffer, K., Klimkait, T. and Labhardt, N. D. (2016) ‘Still far from 90-90-90 : virologic outcomes of children on antiretroviral therapy in nurse-led clinics in rural Lesotho’, Pediatric infectious disease journal. Lippincott Williams & Wilkins, 35(1), pp. 78-80. doi: 10.1097/INF.0000000000000929.   edoc
Bader, J., Schoni-Affolter, F., Boni, J., Gorgievski-Hrisoho, M., Martinetti, G., Battegay, M., Klimkait, T. and Swiss, H. I. V. C. S. (2016) ‘Correlating HIV tropism with immunological response under combination antiretroviral therapy’, HIV Med. Wiley-Blackwell, 17(8), pp. 615-622. doi: 10.1111/hiv.12365.   edoc | Open Access
Cerutti, B., Bader, J., Ehmer, J., Pfeiffer, K., Klimkait, T. and Labhardt, N. D. (2016) ‘Performance of risk-charts to guide targeted HIV viral load monitoring of ART : applying the method on the data from a multi-centre-study in rural Lesotho’, Journal of acquired immune deficiency syndromes and human retrovirology. Lippincott Williams & Wilkins, pp. e22-e25. doi: 10.1097/QAI.0000000000000961.   edoc | Open Access
Montazeri, H., Kuipers, J., Kouyos, R., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Gunthard, H. F., Beerenwinkel, N. and Swiss, H. I. V. C. S. (2016) ‘Large-scale inference of conjunctive Bayesian networks’, Bioinformatics, 32(17), pp. i727-i735. doi: 10.1093/bioinformatics/btw459.   
Rusert, P., Kouyos, R. D., Kadelka, C., Ebner, H., Schanz, M., Huber, M., Braun, D. L., Hoze, N., Scherrer, A., Magnus, C., Weber, J., Uhr, T., Cippa, V., Thorball, C. W., Kuster, H., Cavassini, M., Bernasconi, E., Hoffmann, M., Calmy, A., Battegay, M., Rauch, A., Yerly, S., Aubert, V., Klimkait, T., Boni, J., Fellay, J., Regoes, R. R., Gunthard, H. F., Trkola, A. and Swiss, H. I. V. C. S. (2016) ‘Determinants of HIV-1 broadly neutralizing antibody induction’, Nat Med, 22(11), pp. 1260-1267. doi: 10.1038/nm.4187.   
Scherrer, A. U., von Wyl, V., Yang, W. L., Kouyos, R. D., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Cavassini, M., Battegay, M., Furrer, H., Calmy, A., Vernazza, P., Bernasconi, E., Gunthard, H. F., the Swiss, H. I. V. C. S., Aubert, V., Battegay, M., Bernasconi, E., Boni, J., Braun, D. L., Bucher, H. C., Burton-Jeangros, C., Calmy, A., Cavassini, M., Dollenmaier, G., Egger, M., Elzi, L., Fehr, J., Fellay, J., Furrer, H., Fux, C. A., Gorgievski, M., Gunthard, H., Haerry, D., Hasse, B., Hirsch, H. H., Hoffmann, M., Hosli, I., Kahlert, C., Kaiser, L., Keiser, O., Klimkait, T., Kouyos, R., Kovari, H., Ledergerber, B., Martinetti, G., Martinez de Tejada, B., Marzolini, C., Metzner, K., Muller, N., Nadal, D., Nicca, D., Pantaleo, G., Rauch, A., Regenass, S., Rudin, C., Schoni-Affolter, F., Schmid, P., Speck, R., Stockle, M., Tarr, P., Trkola, A., Vernazza, P., Weber, R. and Yerly, S. (2016) ‘Emergence of Acquired HIV-1 Drug Resistance Almost Stopped in Switzerland: A 15-Year Prospective Cohort Analysis’, Clin Infect Dis, 62(10), pp. 1310-1317. doi: 10.1093/cid/ciw128.   
Ragonnet-Cronin, M. L., Shilaih, M., Gunthard, H. F., Hodcroft, E. B., Boni, J., Fearnhill, E., Dunn, D., Yerly, S., Klimkait, T., Aubert, V., Yang, W. L., Brown, A. E., Lycett, S. J., Kouyos, R. and Brown, A. J. (2016) ‘A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland’, Sci Rep, 6, p. 32251. doi: 10.1038/srep32251.   
Scherrer, A. U., Yang, W. L., Kouyos, R. D., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Cavassini, M., Battegay, M., Hauser, C., Calmy, A., Schmid, P., Bernasconi, E., Gunthard, H. F. and Swiss, H. I. V. C. S. (2016) ‘Successful Prevention of Transmission of Integrase Resistance in the Swiss HIV Cohort Study’, J Infect Dis, 214(3), pp. 399-402. doi: 10.1093/infdis/jiw165.   
Ngo-Giang-Huong, N., Wittkop, L., Judd, A., Reiss, P., Goetghebuer, T., Duiculescu, D., Noguera-Julian, A., Marczynska, M., Giacquinto, C., Ene, L., Ramos, J. T., Cellerai, C., Klimkait, T., Brichard, B., Valerius, N., Sabin, C., Teira, R., Obel, N., Stephan, C., de Wit, S., Thorne, C., Gibb, D., Schwimmer, C., Campbell, M. A., Pillay, D., Lallemant, M. and EuroCoord, C.-E. joint project study group (2016) ‘Prevalence and effect of pre-treatment drug resistance on the virological response to antiretroviral treatment initiated in HIV-infected children - a EuroCoord-CHAIN-EPPICC joint project’, BMC Infect Dis, 16(1), p. 654. doi: 10.1186/s12879-016-1968-2.   
Oberle, C. S., Joos, B., Rusert, P., Campbell, N. K., Beauparlant, D., Kuster, H., Weber, J., Schenkel, C. D., Scherrer, A. U., Magnus, C., Kouyos, R., Rieder, P., Niederost, B., Braun, D. L., Pavlovic, J., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Trkola, A., Metzner, K. J., Gunthard, H. F. and Swiss, H. I. V. C. S. (2016) ‘Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs’, Retrovirology, 13(1), p. 62. doi: 10.1186/s12977-016-0299-0.   
Marzel, A., Shilaih, M., Yang, W. L., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Braun, D. L., Calmy, A., Furrer, H., Cavassini, M., Battegay, M., Vernazza, P. L., Bernasconi, E., Gunthard, H. F., Kouyos, R. D., Swiss, H. I. V. C. S., Aubert, V., Battegay, M., Bernasconi, E., Boni, J., Bucher, H. C., Burton-Jeangros, C., Calmy, A., Cavassini, M., Dollenmaier, G., Egger, M., Elzi, L., Fehr, J., Fellay, J., Furrer, H., Fux, C. A., Gorgievski, M., Gunthard, H. F., Haerry, D., Hasse, B., Hirsch, H. H., Hoffmann, M., Hosli, I., Kahlert, C., Kaiser, L., Keiser, O., Klimkait, T., Kouyos, R. D., Kovari, H., Ledergerber, B., Martinetti, G., de Tejada, B. M., Metzner, K., Muller, N., Nadal, D., Nicca, D., Pantaleo, G., Rauch, A., Regenass, S., Rickenbach, M., Rudin, C., Schoni-Affolter, F., Schmid, P., Schupbach, J., Speck, R., Tarr, P., Trkola, A., Vernazza, P. L., Weber, R. and Yerly, S. (2016) ‘HIV-1 Transmission During Recent Infection and During Treatment Interruptions as Major Drivers of New Infections in the Swiss HIV Cohort Study’, Clin Infect Dis, 62(1), pp. 115-122. doi: 10.1093/cid/civ732.   
Edwards, S., Stucki, H., Bader, J., Vidal, V., Kaiser, R., Battegay, M., Klimkait, T. and Swiss, H. I. V. C. S. (2015) ‘A diagnostic HIV-1 tropism system based on sequence relatedness’, Journal of Clinical Microbiology, 53(2), pp. 597-610. doi: 10.1128/JCM.02762-14.   edoc
Heyman, H. M., Senejoux, F., Seibert, I., Klimkait, T., Maharaj, V. J. and Meyer, J. J. (2015) ‘Identification of anti-HIV active dicaffeoylquinic- and tricaffeoylquinic acids in Helichrysum populifolium by NMR-based metabolomic guided fractionation’, Fitoterapia, 103, pp. 155-164. doi: 10.1016/j.fitote.2015.03.024.   edoc
Schupbach, J., Niederhauser, C., Yerly, S., Regenass, S., Gorgievski, M., Aubert, V., Ciardo, D., Klimkait, T., Dollenmaier, G., Andreutti, C., Martinetti, G., Brandenberger, M. and Gebhardt, M. D. (2015) ‘Decreasing Proportion of Recent Infections among Newly Diagnosed HIV-1 Cases in Switzerland, 2008 to 2013 Based on Line-Immunoassay-Based Algorithms’, PLoS One, 10(7), p. e0131828. doi: 10.1371/journal.pone.0131828.   edoc
Hasse, B., Tarr, P. E., Marques-Vidal, P., Waeber, G., Preisig, M., Mooser, V., Valeri, F., Djalali, S., Andri, R., Bernasconi, E., Calmy, A., Cavassini, M., Vernazza, P., Battegay, M., Weber, R., Senn, O., Vollenweider, P., Ledergerber, B., CoLaus Cohort, F., the Swiss, H. I. V. C. S., Aubert, V., Barth, J., Battegay, M., Bernasconi, E., Boni, J., Bucher, H. C., Burton-Jeangros, C., Calmy, A., Cavassini, M., Egger, M., Elzi, L., Fehr, J., Fellay, J., Furrer, H., Fux, C. A., Gorgievski, M., Gunthard, H., Haerry, D., Hasse, B., Hirsch, H. H., Hosli, I., Kahlert, C., Kaiser, L., Keiser, O., Klimkait, T., Kouyos, R., Kovari, H., Ledergerber, B., Martinetti, G., Martinez de Tejada, B., Metzner, K., Muller, N., Nadal, D., Pantaleo, G., Rauch, A., Regenass, S., Rickenbach, M., Rudin, C., Schoni-Affolter, F., Schmid, P., Schultze, D., Schupbach, J., Speck, R., Staehelin, C., Tarr, P., Telenti, A., Trkola, A., Vernazza, P., Weber, R., Yerly, S., Jean-Michel, A., Murielle, B., Jean Michel, G., Christoph, H., Thomas, L., Pedro, M. V., Vincent, M., Fred, P., Martin, P., Peter, V., Roland, V. K., Aidacic, V., Gerard, W., Jurg, B., Markus, B., Heinz, B., Martin, B., Hans-Ulrich, B., Ivo, B., Reto, C., Isabelle, C., Corinne, C., Sima, D., Peter, D., Simone, E., Andrea, F., Markus, F., Claudius, F., Jakob, F., Ali, G. M., Matthias, G., Denis, H., Marcel, H., Walter, H., Simon, H., Felix, H., Paul, H., Eva, K., Vladimir, K., Daniel, K., Stephan, K., Beat, K., Benedict, K., Heidi, K., Vesna, L., Giovanni, L., Werner, L. H., Phillippe, L., Severin, L., Christoph, M., Jurgen, M., Damian, M., Werner, M., Titus, M., Valentina, N., Jakob, R., Thomas, R., Hana, S., Frank, S., Georg, S., Oliver, S., Pietro, S., Jacques, S., Alfred, S., Alois, S., Claudia, S., Othmar, S., Phuoc, T. T., Marco, V., Alessandro, V., Rene, V. A., Hans, W., Fritz, W., Johanna, W. S., Joseph, W. and Marco, Z. (2015) ‘Strong Impact of Smoking on Multimorbidity and Cardiovascular Risk Among Human Immunodeficiency Virus-Infected Individuals in Comparison With the General Population’, Open Forum Infectious Diseases. Oxford University Press, 2(3), p. ofv108. doi: 10.1093/ofid/ofv108.   edoc | Open Access
Wagner, S., Kurz, M., Klimkait, T. and Swiss, H. I. V. C. S. (2015) ‘Algorithm evolution for drug resistance prediction: comparison of systems for HIV-1 genotyping’, Antiviral Therapy, 20(6), pp. 661-665. doi: 10.3851/IMP2947.   edoc
Yang, W.-L., Kouyos, R., Scherrer, A. U., Boni, J., Shah, C., Yerly, S., Klimkait, T., Aubert, V., Furrer, H., Battegay, M., Cavassini, M., Bernasconi, E., Vernazza, P., Held, L., Ledergerber, B., Gunthard, H. F. and Swiss, H. I. V. C. S. (2015) ‘Assessing the Paradox Between Transmitted and Acquired HIV Type 1 Drug Resistance Mutations in the Swiss HIV Cohort Study From 1998 to 2012’, The Journal of Infectious Diseases, 212(1), pp. 28-38. doi: 10.1093/infdis/jiv012.   edoc
Yang, W.-L., Kouyos, R. D., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Scherrer, A. U., Shilaih, M., Hinkley, T., Petropoulos, C., Bonhoeffer, S., Gunthard, H. F. and Swiss, H. I. V. C. S. (2015) ‘Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds’, PLoS Pathogens, 11(3), p. e1004722. doi: 10.1371/journal.ppat.1004722.   edoc
Yang, W.-L., Kouyos, R. D., Scherrer, A. U., Boni, J., Shah, C., Yerly, S., Klimkait, T., Aubert, V., Hirzel, C., Battegay, M., Cavassini, M., Bernasconi, E., Vernazza, P., Held, L., Ledergerber, B., Günthard, H. F., Swiss, H. I. V. C. S. and Swiss, H. I. V. C. S. S. (2015) ‘Assessing efficacy of different nucleos(t)ide backbones in NNRTI-containing regimens in the Swiss HIV Cohort Study’, Journal of Antimicrobial Chemotherapy, 70(12), pp. 3323-3331. doi: 10.1093/jac/dkv257.   edoc
Kouyos, R. D., Hasse, B., Calmy, A., Cavassini, M., Furrer, H., Stockle, M., Vernazza, P. L., Bernasconi, E., Weber, R., Gunthard, H. F., Swiss, H. I. V. C. S., Aubert, V., Battegay, M., Bernasconi, E., Boni, J., Bucher, H. C., Burton-Jeangros, C., Calmy, A., Cavassini, M., Dollenmaier, G., Egger, M., Elzi, L., Fehr, J., Fellay, J., Furrer, H., Fux, C. A., Gorgievski, M., Gunthard, H., Haerry, D., Hasse, B., Hirsch, H. H., Hoffmann, M., Hosli, I., Kahlert, C., Kaiser, L., Keiser, O., Klimkait, T., Kouyos, R., Kovari, H., Ledergerber, B., Martinetti, G., de Tejada, B. M., Metzner, K., Muller, N., Nadal, D., Nicca, D., Pantaleo, G., Rauch, A., Regenass, S., Rickenbach, M., Rudin, C., Schoni-Affolter, F., Schmid, P., Schupbach, J., Speck, R., Tarr, P., Trkola, A., Vernazza, P., Weber, R. and Yerly, S. (2015) ‘Increases in Condomless Sex in the Swiss HIV Cohort Study’, Open Forum Infectious Diseases, 2(2), p. ofv077. doi: 10.1093/ofid/ofv077.   edoc | Open Access
Labhardt, N. D., Bader, J., Ramoeletsi, M., Kamele, M., Lejone, T. I., Cheleboi, M., Motlatsi, M. M., Ehmer, J., Faturyiele, O., Puga, D. and Klimkait, T. (2014) ‘Clinical and socio-demographic predictors for virologic failure in rural Southern Africa: preliminary findings from CART-1’, J Int AIDS Soc, 17(4 Suppl 3), p. 19666. doi: 10.7448/IAS.17.4.19666.   
Kouyos, R. D., Rauch, A., Braun, D. L., Yang, W. L., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Shah, C., Kovari, H., Calmy, A., Cavassini, M., Battegay, M., Vernazza, P. L., Bernasconi, E., Ledergerber, B., Gunthard, H. F. and Swiss, H. I. V. C. S. (2014) ‘Higher risk of incident hepatitis C virus coinfection among men who have sex with men, in whom the HIV genetic bottleneck at transmission was wide’, J Infect Dis, 210(10), pp. 1555-1561. doi: 10.1093/infdis/jiu315.   
Drescher, S. M., von Wyl, V., Yang, W. L., Boni, J., Yerly, S., Shah, C., Aubert, V., Klimkait, T., Taffe, P., Furrer, H., Battegay, M., Ambrosioni, J., Cavassini, M., Bernasconi, E., Vernazza, P. L., Ledergerber, B., Gunthard, H. F., Kouyos, R. D. and Swiss, H. I. V. C. S. (2014) ‘Treatment-naive individuals are the major source of transmitted HIV-1 drug resistance in men who have sex with men in the Swiss HIV Cohort Study’, Clin Infect Dis, 58(2), pp. 285-294. doi: 10.1093/cid/cit694.   
Vetter, B. N., Orlowski, V., Fransen, K., Niederhauser, C., Aubert, V., Brandenberger, M., Ciardo, D., Dollenmaier, G., Klimkait, T., Regenass, S., Schmid, P., Schottstedt, V., Suter-Riniker, F., Yerly, S., Shah, C., Boni, J. and Schupbach, J. (2014) ‘Generation of a recombinant Gag virus-like-particle panel for the evaluation of p24 antigen detection by diagnostic HIV tests’, PLoS One, 9(10), p. e111552. doi: 10.1371/journal.pone.0111552.   
Hasse, B., Iff, M., Ledergerber, B., Calmy, A., Schmid, P., Hauser, C., Cavassini, M., Bernasconi, E., Marzolini, C., Tarr, P. E., Swiss HIV Cohort Study, Aubert, V., Barth, J., Battegay, M., Bernasconi, E., Böni, J., Bucher, H. C., Burton-Jeangros, C., Calmy, A., Cavassini, M., Egger, M., Elzi, L., Fehr, J., Fellay, J., Furrer, H., Fux, C. A., Gorgievski, M., Günthard, H., Haerry, D., Hasse, B., Hirsch, H. H., Hösli, I., Kahlert, C., Kaiser, L., Keiser, O., Klimkait, T., Kouyos, R., Kovari, H., Ledergerber, B., Martinetti, G., Martinez de Tejada, B., Metzner, K., Müller, N., Nadal, D., Pantaleo, G., Rauch, A., Regenass, S., Rickenbach, M., Rudin, C., Schöni-Affolter, F., Schmid, P., Schultze, D., Schüpbach, J., Speck, R., Staehelin, C., Tarr, P., Telenti, A., Trkola, A., Vernazza, P., Weber, R. and Yerly, S. (2014) ‘Obesity Trends and Body Mass Index Changes After Starting Antiretroviral Treatment: The Swiss HIV Cohort Study’, Open forum infectious diseases, 1(2), p. ofu040. doi: 10.1093/ofid/ofu040.   
Kouyos, R. D., Rauch, A., Boni, J., Yerly, S., Shah, C., Aubert, V., Klimkait, T., Kovari, H., Calmy, A., Cavassini, M., Battegay, M., Vernazza, P. L., Bernasconi, E., Ledergerber, B., Gunthard, H. F. and Swiss, H. I. V. C. S. (2014) ‘Clustering of HCV coinfections on HIV phylogeny indicates domestic and sexual transmission of HCV’, Int J Epidemiol, 43(3), pp. 887-896. doi: 10.1093/ije/dyt276.   
Metzner, K. J., Scherrer, A. U., von Wyl, V., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Furrer, H., Hirsch, H. H., Vernazza, P. L., Cavassini, M., Calmy, A., Bernasconi, E., Weber, R., Gunthard, H. F. and Swiss, H. I. V. C. S. (2014) ‘Limited clinical benefit of minority K103N and Y181C-variant detection in addition to routine genotypic resistance testing in antiretroviral therapy-naive patients’, AIDS, 28(15), pp. 2231-2239. doi: 10.1097/QAD.0000000000000397.   
Avila, D., Keiser, O., Egger, M., Kouyos, R., Boni, J., Yerly, S., Klimkait, T., Vernazza, P. L., Aubert, V., Rauch, A., Bonhoeffer, S., Gunthard, H. F., Stadler, T., Spycher, B. D. and Swiss, H. I. V. C. S. (2014) ‘Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland’, Am J Epidemiol, 179(12), pp. 1514-1525. doi: 10.1093/aje/kwu076.   
Mehling, M., Fritz, S., Hafner, P., Eichin, D., Yonekawa, T., Klimkait, T., Lindberg, R. L., Kappos, L. and Hess, C. (2013) ‘Preserved Antigen-Specific Immune Response in Patients with Multiple Sclerosis Responding to IFNbeta-Therapy’, PLoS ONE. Public Library of Science, 8(11), p. e78532. doi: 10.1371/journal.pone.0078532.   edoc
Beerenwinkel, N., Montazeri, H., Schuhmacher, H., Knupfer, P., von Wyl, V., Furrer, H., Battegay, M., Hirschel, B., Cavassini, M., Vernazza, P., Bernasconi, E., Yerly, S., Boni, J., Klimkait, T., Cellerai, C., Gunthard, H. F. and Swiss HIV Cohort Study (2013) ‘The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients’, PLoS Computational Biology. Library of Science, 9(8). doi: 10.1371/journal.pcbi.1003203.   edoc
Cusini, A., Vernazza, P. L., Yerly, S., Decosterd, L. A., Ledergerber, B., Fux, C. A., Rohrbach, J., Widmer, N., Hirschel, B., Gaudenz, R., Cavassini, M., Klimkait, T., Zenger, F., Gutmann, C., Opravil, M., Gunthard, H. F. and Swiss HIV Cohort Study (2013) ‘Higher CNS Penetration-Effectiveness of Long-term Combination Antiretroviral Therapy Is Associated With Better HIV-1 Viral Suppression in Cerebrospinal Fluid’, JAIDS: journal of acquired immune deficiency syndromes. Lippincott Williams & Wilkins, 62(1), pp. 28-35. doi: 10.1097/Qai.0b013e318274e2b0.   edoc
Schupbach, J., Gebhardt, M. D., Scherrer, A. U., Bisset, L. R., Niederhauser, C., Regenass, S., Yerly, S., Aubert, V., Suter, F., Pfister, S., Martinetti, G., Andreutti, C., Klimkait, T., Brandenberger, M., Gunthard, H. F. and Swiss HIV Cohort Study (2013) ‘Simple Estimation of Incident HIV Infection Rates in Notification Cohorts Based on Window Periods of Algorithms for Evaluation of Line-Immunoassay Result Patterns’, PLoS ONE. Public Library of Science, Vol. 8, H. 8 , e71662. doi: 10.1371/journal.pone.0071662.   edoc
Louvel, S., Moodley, N., Seibert, I., Steenkamp, P., Nthambeleni, R., Vidal, V., Maharaj, V. and Klimkait, T. (2013) ‘Identification of compounds from the plant species Alepidea amatymbica active against HIV’, South African journal of botany. Elsevier, Vol. 86, pp. 9-14. doi: 10.1016/J.Sajb.2013.01.009.   edoc
Masimba, P., Kituma, E., Klimkait, T., Horvath, E., Stoeckle, M., Hatz, C., Mossdorf, E., Mwaigomole, E., Khamis, S., Jullu, B., Abdulla, S., Tanner, M. and Felger, I. (2013) ‘Prevalence of drug resistance mutations and HIV type 1 subtypes in an HIV type 1-infected cohort in rural Tanzania’, AIDS research and human retroviruses. Mary Ann Liebert, 29(9), pp. 1229-1236. doi: 10.1089/AID.2011.0367.   edoc
Omolo, J. J., Maharaj, V., Naidoo, D., Klimkait, T., Malebo, H. M., Mtullu, S., Lyaruu, H. V. M. and de Koning, C. B. (2012) ‘Bioassay-guided investigation of the Tanzanian plant Pyrenacantha kaurabassana for potential anti-HIV-active compounds’, Journal of natural products. American Society of Pharmacognosy, 75(10), pp. 1712-1716. doi: 10.1021/Np300255r.   edoc
Lubbe, A., Seibert, I., Klimkait, T. and van der Kooy, F. (2012) ‘Ethnopharmacology in overdrive : the remarkable anti-HIV activity of Artemisia annua’, Journal of ethnopharmacology. Elsevier Scientific Publishers, 141(3), pp. 854-859. doi: 10.1016/J.Jep.2012.03.024.   edoc
Stadler, T., Kouyos, R., von Wyl, V., Yerly, S., Boni, J., Burgisser, P., Klimkait, T., Joos, B., Rieder, P., Xie, D., Gunthard, H. F., Drummond, A. J., Bonhoeffer, S. and Swiss HIV Cohort Study (2012) ‘Estimating the basic reproductive number from viral sequence data’, Molecular biology and evolution. Oxford University Press, 29(1), pp. 347-357. doi: 10.1093/Molbev/Msr217.   edoc
Scherrer, A. U., Ledergerber, B., von Wyl, V., Boni, J., Yerly, S., Klimkait, T., Cellerai, C., Furrer, H., Calmy, A., Cavassini, M., Elzi, L., Vernazza, P. L., Bernasconi, E., Gunthard, H. F. and Swiss HIV Cohort Study Shcs (2012) ‘Minor protease inhibitor mutations at baseline do not increase the risk for a virological failure in HIV-1 subtype B infected patients’, PLoS ONE. Public Library of Science, 7(6), p. e37983. doi: 10.1371/journal.pone.0037983.   edoc
Scherrer, A. U., von Wyl, V., Gotte, M., Klimkait, T., Cellerai, C., Yerly, S., Boni, J., Held, L., Ledergerber, B., Gunthard, H. F. and Swiss HIV Cohort Study (2012) ‘Polymorphic mutations associated with the emergence of the multinucleoside/tide resistance mutations 69 insertion and Q151M’, Journal of acquired immune deficiency syndromes and human retrovirology. Lippincott Williams & Wilkins, 59(2), pp. 105-112. doi: 10.1097/Qai.0b013e31823c8b69.   edoc
Scherrer, A. U., Boni, J., Yerly, S., Klimkait, T., Aubert, V., Furrer, H., Calmy, A., Cavassini, M., Elzi, L., Vernazza, P. L., Bernasconi, E., Ledergerber, B., Gunthard, H. F. and Swiss HIV Cohort Study Shcs (2012) ‘Long-lasting protection of activity of nucleoside reverse transcriptase inhibitors and protease inhibitors (PIs) by boosted PI containing regimens’, PLoS ONE. Public Library of Science, 7(11), p. e50307. doi: 10.1371/journal.pone.0050307.   edoc
Schupbach, J., Bisset, L. R., Gebhardt, M. D., Regenass, S., Burgisser, P., Gorgievski, M., Klimkait, T., Andreutti, C., Martinetti, G., Niederhauser, C., Yerly, S., Pfister, S., Schultze, D., Brandenberger, M., Schoni-Affolter, F., Scherrer, A. U., Gunthard, H. F. and Swiss HIV Cohort Study (2012) ‘Diagnostic performance of line-immunoassay based algorithms for incident HIV-1 infection’, BMC infectious diseases. BioMed Central, Vol. 12 , 88. doi: 10.1186/1471-2334-12-88.   edoc
Kemal, K. S., Ramirez, C. M., Burger, H., Foley, B., Mayers, D., Klimkait, T., Hamy, F., Anastos, K., Petrovic, K., Minin, V. N., Suchard, M. A. and Weiser, B. (2012) ‘Recombination between variants from genital tract and plasma : evolution of multidrug-resistant HIV type 1’, Aids research and human retroviruses. Mary Ann Liebert, 28(12), pp. 1766-1774. doi: 10.1089/Aid.2011.0383.   edoc
Leventhal, G. E., Kouyos, R., Stadler, T., von Wyl, V., Yerly, S., Boni, J., Cellerai, C., Klimkait, T., Gunthard, H. F. and Bonhoeffer, S. (2012) ‘Inferring epidemic contact structure from phylogenetic trees’, PLoS Computational Biology. Library of Science, 8(3), p. e1002413. doi: 10.1371/journal.pcbi.1002413.   edoc
Klimkait, T. (2012) ‘The XTrack system: application and advantage’, Intervirology. Karger, 55(2), pp. 118-122. doi: 10.1159/000332003.   edoc | Open Access
von Wyl, V., Yerly, S., Böni, J., Shah, C., Cellerai, C., Klimkait, T., Battegay, M., Bernasconi, E., Cavassini, M., Furrer, H., Hirschel, B., Vernazza, P. L., Ledergerber, B., Günthard, H. F. and Swiss HIV Cohort Study (2012) ‘Incidence of HIV-1 drug resistance among antiretroviral treatment-naive individuals starting modern therapy combinations’, Clinical infectious diseases. Oxford University Press, 54(1), pp. 131-140. doi: 10.1093/Cid/Cir728.   edoc
Vidal, V., Potterat, O., Louvel, S., Hamy, F., Mojarrab, M., Sanglier, J. J., Klimkait, T. and Hamburger, M. (2012) ‘Library-based discovery and characterization of Daphnane diterpenes as potent and selective HIV inhibitors in Daphne gnidium’, Journal of natural products. American Society of Pharmacognosy, 75(3), pp. 414-419. doi: 10.1021/Np200855d.   edoc
Stadler, T., Kouyos, R., von Wyl, V., Yerly, S., Böni, J., Bürgisser, P., Klimkait, T., Joos, B., Rieder, P., Xie, D., Günthard, H. F., Drummond, A. J., Bonhoeffer, S. and the Swiss HIV Cohort Study (2012) ‘Estimating the Basic Reproductive Number from Viral Sequence Data’, MOL BIOL EVOL, 29, pp. 347-357. doi: 10.1093/molbev/msr217.   
Scherrer, A. U., von Wyl, V., Götte, M., Klimkait, T., Cellerai, C., Yerly, S., Böni, J., Held, L., Ledergerber, B., Günthard, H. F. and The Swiss HIV Cohort Study (2012) ‘Polymorphic Mutations Associated With the Emergence of the Multinucleoside/Tide Resistance Mutations 69 Insertion and Q151M.’, JAIDS-J ACQ IMM DEF, 59, pp. 105-112.   
Fehr, J., Glass, T. R., Louvel, S., Hamy, F., Hirsch, H. H., von Wyl, V., Boni, J., Yerly, S., Burgisser, P., Cavassini, M., Fux, C. A., Hirschel, B., Vernazza, P., Martinetti, G., Bernasconi, E., Gunthard, H. F., Battegay, M., Bucher, H. C. and Klimkait, T. (2011) ‘Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals - the Swiss HIV Cohort Study’, Journal of translational medicine. BioMed Central, Vol. 9 , 14, p. 14. doi: 10.1186/1479-5876-9-14.   edoc
Kouyos, R. D., von Wyl, V., Hinkley, T., Petropoulos, C. J., Haddad, M., Whitcomb, J. M., Boni, J., Yerly, S., Cellerai, C., Klimkait, T., Gunthard, H. F., Bonhoeffer, S. and Swiss HIV Cohort Study (2011) ‘Assessing predicted HIV-1 replicative capacity in a clinical setting’, PLoS Pathogens. Public Library of Science, 7(11), p. e1002321. doi: 10.1371/journal.ppat.1002321.   edoc
Schüpbach, J., Bisset, L. R., Regenass, S., Bürgisser, P., Gorgievski, M., Steffen, I., Andreutti, C., Martinetti, G., Shah, C., Yerly, S., Klimkait, T., Gebhardt, M., Schöni-Affolter, F., Rickenbach, M., Swiss HIV Cohort Study, Barth, J., Battegay, M., Bernascon, E., Böni, J., Bucher, H. C., Bürgisser, P., Burton-Jeangros, C., Calmy, A., Cavassini, M., Dubs, R., Egger, M., Elzi, L., Fehr, J., Fischer, M., Flepp, M., Francioli, P., Furrer, H., Fux, C. A., Gorgievski, M., Günthard, H., Hasse, B., Hirsch, H. H., Hirschel, B., Hösli, I., Kahlert, C., Kaiser, L., Keiser, O., Kind, C., Klimkait, T., Kovari, H., Ledergerber, B., Martinetti, G., Martinez de Tejada, B., Müller, N., Nadal, D., Pantaleo, G., Rauch, A., Regenass, S., Rickenbach, M., Rudin, C., Schmid, P., Schultze, D., Schöni-Affolter, F., Schüpbach, J., Speck, R., Taffé, P., Telenti, A., Trkola, A., Vernazza, P., von Wyl, V., Weber, R. and Yerly, S. (2011) ‘High specificity of line-immunoassay based algorithms for recent HIV-1 infection independent of viral subtype and stage of disease’, BMC infectious diseases. BioMed Central, Vol. 11 , 254, p. 254. doi: 10.1186/1471-2334-11-254.   edoc
Mehling, M., Hilbert, P., Fritz, S., Durovic, B., Eichin, D., Gasser, O., Kuhle, J., Klimkait, T., Lindberg, R. L. P., Kappos, L. and Hess, C. (2011) ‘Antigen-specific adaptive immune responses in fingolimod-treated multiple sclerosis patients’, Annals of neurology. Wiley-Liss, 69(2), pp. 408-413. doi: 10.1002/ana.22352.   edoc
Miazga, A., Hamy, F., Louvel, S., Klimkait, T., Pietrusiewicz, Z., Kurzy?ska-Kokorniak, A., Figlerowicz, M., Wi?ska, P. and Kulikowski, T. (2011) ‘Thiated derivatives of 2’,3’-dideoxy-3’-fluorothymidine : synthesis, in vitro anti-HIV-1 activity and interaction with recombinant drug resistant HIV-1 reverse transcriptase forms’, Antiviral research. Elsevier, 92(1), pp. 57-63. doi: 10.1016/J.Antiviral.2011.05.012.   edoc
Scherrer, A. U., von Wyl, V., Joos, B., Klimkait, T., Burgisser, P., Yerly, S., Boni, J., Ledergerber, B., Gunthard, H. F. and Swiss HIV Cohort Study (2011) ‘Predictors for the emergence of the 2 multi-nucleoside/nucleotide resistance mutations 69 insertion and Q151M and their impact on clinical outcome in the Swiss HIV cohort study’, Journal of infectious diseases. Oxford University Press, 203(6), pp. 791-797. doi: 10.1093/infdis/jiq130.   edoc
Scherrer, A. U., Ledergerber, B., von Wyl, V., Böni, J., Yerly, S., Klimkait, T., Bürgisser, P., Rauch, A., Hirschel, B., Cavassini, M., Elzi, L., Vernazza, P. L., Bernasconi, E., Held, L., Günthard, H. F. and Swiss HIV Cohort Study (2011) ‘Improved virological outcome in White patients infected with HIV-1 non-B subtypes compared to subtype B’, Clinical infectious diseases. Oxford University Press, 53(11), pp. 1143-1152. doi: 10.1093/cid/cir669.   edoc
Daikeler, T., Hoenger, G., Oehri, I., Tyndall, A., Gratwohl, A., Brander, C., Klimkait, T., Gasser, O. and Hess, C. (2011) ‘Dominant Epstein-Barr virus-specific T-cell responses are maintained during moderate and intense immunosuppressive treatment’, Annals of the rheumatic diseases. British Medical Association, 70(2), pp. 395-396. doi: 10.1136/ard.2010.129734.   edoc
Kouyos, R. D., von Wyl, V., Yerly, S., Boni, J., Rieder, P., Joos, B., Taffe, P., Shah, C., Burgisser, P., Klimkait, T., Weber, R., Hirschel, B., Cavassini, M., Rauch, A., Battegay, M., Vernazza, P. L., Bernasconi, E., Ledergerber, B., Bonhoeffer, S., Gunthard, H. F. and Swiss HIV Cohort Study (2011) ‘Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection’, Clinical infectious diseases. Oxford University Press, 52(4), pp. 532-539. doi: 10.1093/cid/ciq164.   edoc
Scherrer, A. U., von Wyl, V., Boni, J., Yerly, S., Klimkait, T., Burgisser, P., Garzoni, C., Hirschel, B., Cavassini, M., Battegay, M., Vernazza, P. L., Bernasconi, E., Ledergerber, B., Gunthard, H. F. and Swiss HIV Cohort Study Shcs (2011) ‘Viral suppression rates in salvage treatment with raltegravir improved with the administration of genotypic partially active or inactive nucleoside/tide reverse transcriptase inhibitors’, JAIDS. Lippincott Williams & Wilkins, 57(1), pp. 24-31. doi: 10.1097/QAI.0b013e318211925e.   edoc
von Wyl, V., Kouyos, R. D., Yerly, S., Böni, J., Shah, C., Bürgisser, P., Klimkait, T., Weber, R., Hirschel, B., Cavassini, M., Staehelin, C., Battegay, M., Vernazza, P. L., Bernasconi, E., Ledergerber, B., Bonhoeffer, S., Günthard, H. F. and Swiss HIV Cohort Study (2011) ‘The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland’, Journal of infectious diseases. Oxford University Press, 204(7), pp. 1095-1103. doi: 10.1093/infdis/jir491.   edoc
Vandekerckhove, L. P. R., Wensing, A. M. J., Kaiser, R., Brun-Vezinet, F., Clotet, B., De Luca, A., Dressler, S., Garcia, F., Geretti, A. M., Klimkait, T., Korn, K., Masquelier, B., Perno, C. F., Schapiro, J. M., Soriano, V., Sonnerborg, A., Vandamme, A. M., Verhofstede, C., Walter, H., Zazzi, M., Boucher, C. A. B. and European Consensus Grp Clinical (2011) ‘European guidelines on the clinical management of HIV-1 tropism testing’, The Lancet infectious diseases. Elsevier, 11(5), pp. 394-407. doi: 10.1016/S1473-3099(10)70319-4.   edoc
Fehr, J., Glass, T. R., Louvel, S., Hamy, F., Hirsch, H. H., von Wyl, V., Boni, J., Yerly, S., Burgisser, P., Cavassini, M., Fux, C. A., Hirschel, B., Vernazza, P., Martinetti, G., Bernasconi, E., Gunthard, H. F., Battegay, M., Bucher, H. C., Klimkait, T. and Hiv Cohort Study, A. T. S. (2011) ‘Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals - the Swiss HIV Cohort Study’, J TRANSL MED, 9, p. 14. doi: 10.1186/1479-5876-9-14.   
Kouyos, R. D., von Wyl, V., Yerly, S., Boni, J., Rieder, P., Joos, B., Taffe, P., Shah, C., Burgisser, P., Klimkait, T., Weber, R., Hirschel, B., Cavassini, M., Rauch, A., Battegay, M., Vernazza, P. L., Bernasconi, E., Ledergerber, B., Bonhoeffer, S., Gunthard, H. F. and Swiss HIV Cohort Study (2010) ‘Ambiguity in population-based sequencing of HIV-1 as a marker for the age of HIV infection’, Antiviral therapy. International Medical Press, Vol. 15 , A158-A158.   edoc
Scherrer, A. U., von Wyl, V., Fux, C. A., Opravil, M., Bucher, H. C., Fayet, A., Decosterd, L. A., Hirschel, B., Khanlari, B., Yerly, S., Klimkait, T., Furrer, H., Ledergerber, B. and Günthard, H. F. (2010) ‘Implementation of raltegravir in routine clinical practice : selection criteria for choosing this drug, virologic response rates, and characteristics of failures’, JAIDS: journal of acquired immune deficiency syndromes. Lippincott Williams & Wilkins, 53(4), pp. 464-471. doi: 10.1097/QAI.0b013e3181bca4ec.   edoc
von Wyl, V., Ehteshami, M., Symons, J., Bürgisser, P., Nijhuis, M., Demeter, L. M., Yerly, S., Böni, J., Klimkait, T., Schuurman, R., Ledergerber, B., Götte, M., Günthard Huldrych, F. and Swiss HIV Cohort Study (2010) ‘Epidemiological and biological evidence for a compensatory effect of connection domain mutation N348I on M184V in HIV-1 reverse transcriptase’, Journal of infectious diseases. Oxford University Press, 201(7), pp. 1054-1062. doi: 10.1086/651168.   edoc
von Wyl, V., Ehteshami, M., Demeter, L. M., Bürgisser, P., Nijhuis, M., Symons, J., Yerly, S., Böni, J., Klimkait, T., Schuurman, R., Ledergerber, B., Götte, M., Günthard Huldrych, F. and Swiss HIV Cohort Study (2010) ‘HIV-1 reverse transcriptase connection domain mutations : dynamics of emergence and implications for success of combination antiretroviral therapy’, Clinical infectious diseases. Oxford University Press, 51(5), pp. 620-628.   edoc
Rieder, P., Joos, B., von Wyl, V., Kuster, H., Grube, C., Leemann, C., Böni, J., Yerly, S., Klimkait, T., Bürgisser, P., Weber, R., Fischer, M., Günthard Huldrych, F. and Swiss HIV Cohort Study (2010) ‘HIV-1 transmission after cessation of early antiretroviral therapy among men having sex with men’, AIDS. Current Science, 24(8), pp. 1177-1183. doi: 10.1097/QAD.0b013e328338e4de.   edoc
Kouyos, R. D., 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, P. L., Bernasconi, E., Rickenbach, M., Ledergerber, B., Bonhoeffer, S. and Günthard, H. F. (2010) ‘Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland’, Journal of infectious diseases. Oxford University Press, 201(10), pp. 1488-1497.   edoc
Opravil, M., Klimkait, T., Louvel, S., Wolf, E., Battegay, M., Fux, C. A., Bernasconi, E., Vogel, M., Speck, R., Weber, R. and Swiss HIV Cohort Study (2010) ‘Prior therapy influences the efficacy of lamivudine monotherapy in patients with lamivudine-resistant HIV-1 infection’, JAIDS: journal of acquired immune deficiency syndromes. Lippincott Williams & Wilkins, 54(1), pp. 51-58.   edoc
Müller, V., von Wyl, V., Yerly, S., Böni, J., Klimkait, T., Bürgisser, P., Ledergerber, B., Günthard, H. F. and Bonhoeffer, S. (2009) ‘African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study’, AIDS : official journal of the International AIDS Society. Current Science, 23(10), pp. 1269-1276.   edoc
von Wyl, V., Yerly, S., Bürgisser, P., Klimkait, T., Battegay, M., Bernasconi, E., Cavassini, M., Furrer, H., Hirschel, B., Vernazza, P. L., Francioli, P., Bonhoeffer, S., Ledergerber, B., Günthard Huldrych, F. and Swiss HIV Cohort Study (2009) ‘Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland’, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. Oxford University Press, 48(7), pp. 979-987.   edoc
Scherrer, A. U., Hasse, B., von Wyl, V., Yerly, S., Böni, J., Bürgisser, P., Klimkait, T., Bucher, H. C., Ledergerber, B. and Günthard, H. F. (2009) ‘Prevalence of etravirine mutations and impact on response to treatment in routine clinical care : the Swiss HIV Cohort Study (SHCS)’, HIV medicine : the official journal of the British HIV Association (BHIVA) and the European AIDS Clinical Society (EACS). Blackwell, Vol. 10, pp. 647-656.   edoc
Tschudin, S., Steimann, S., Bitzer, J., Hösli, I., Holzgreve, W., Elzi, L., Klimkait, T., Rudin, C., Battegay, M. and De Geyter, C. (2008) ‘Round-table multidisciplinary counselling of couples with HIV prior to assisted reproduction’, Reproductive biomedicine online. Elsevier, 17(2), pp. 167-174. doi: 10.1016/S1472-6483(10)60191-5.   edoc
Louvel, S., Battegay, M., Vernazza, P., Bregenzer, T., Klimkait, T., Hamy, F. and Swiss, H. C. S. (2008) ‘Detection of drug-resistant HIV minorities in clinical specimens and therapy failure’, HIV medicine. Blackwell, 9(3), pp. 133-141.   edoc
Weiser, B., Philpott, S., Klimkait, T., Burger, H., Kitchen, C., Bürgisser, P., Gorgievski, M., Perrin, L., Piffaretti, J. C., Ledergerber, B. and Swiss, H. C. S. (2008) ‘HIV-1 coreceptor usage and CXCR4-specific viral load predict clinical disease progression during combination antiretroviral therapy’, AIDS. Current Science, 22(4), pp. 469-479.   edoc
von Wyl, V., Yerly, S., Böni, J., Bürgisser, P., Klimkait, T., Battegay, M., Bernasconi, E., Cavassini, M., Furrer, H., Hirschel, B., Vernazza, P. L., Rickenbach, M., Ledergerber, B., Günthard, H. F. and Swiss, H. C. S. (2008) ‘Factors associated with the emergence of K65R in patients with HIV-1 infection treated with combination antiretroviral therapy containing tenofovir’, Clinical infectious diseases. Oxford University Press, 46(8), pp. 1299-1309.   edoc