Zurich Primary HIV Infection Study

Publication List Clinical Research Priority Program University of Zurich (CRPP): Viral Infectious Diseases – Zurich Primary Infection Study (www.clinicaltrials.gov)

A) Original articles in peer reviewed journals

  1. Schüpbach J, Gebhardt MD, Scherrer AU, Bisset LR, Niederhauser C, Regenass S, Yerly S, Aubert V, Suter F, Pfister S, Martinetti G, Andreutti C, Klimkait T, Brandenberger M, Günthard HF, and the Swiss HIV Cohort Study. 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. 2013;8(8):e71662. (IF 3.7 / cited by 1)
     
  2. Metzner KJ, Scherrer AU, Preiswerk B, Joos B, von Wyl V, Leemann C, Rieder P, Braun D, Grube C, Kuster H, Böni J, Yerly S, Klimkait T, Aubert V, Furrer H, Battegay M, Vernazza PL, Cavassini M, Calmy A, Bernasconi E, Weber R, Günthard HF, and the Swiss HIV Cohort Study. Origin of minority drug-resistant HIV-1 variants in primary HIV-1 infection. The Journal of Infectious Diseases. 2013;208(7):1102-1112. (IF 5.8 / cited by 4)
     
  3. 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, Böni J, Klimkait T, Cellerai C, Günthard HF, and the Swiss HIV Cohort Study. The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients. PLOS Computational Biology. 2013;9(8):e1003203. (IF 4.9 / cited by 1)
     
  4. Shirreff G, Alizon S, Cori A, Günthard HF, Laeyendecker O, van Sighem A, Bezemer D, Fraser C. How effectively can HIV phylogenies be used to measure heritability? Evolution, Medicine, and Public Health. 2013; doi:10.1093/emph/eot019:209-224. (IF not defined)
     
  5. Drescher SM, von Wyl V, Yang WL, Böni J, Yerly S, Shah C , Aubert V, Klimkait T, Taffé P, Furrer H, Battegay M, Ambrosioni J, Cavassini M, Bernasconi E, Vernazza PL, Ledergerber B , Günthard HF, Kouyos RD, and the Swiss HIV Cohort Study (SHCS). 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. Clinical Infectious Diseases. 2014;58(2):285-294. (IF 9.4 / cited by 3)
     
  6. Leventhal GE, Günthard HF, Bonhoeffer S, Stadler T. Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Molecular Biology and Evolution. 2014;31(1):6–17. (IF 10.4 / cited by 3)
     
  7. Bastidas S, Graw F, Smith MZ, Kuster H, Günthard HF, Oxenius A. CD8+ T cells are activated in an antigen-independent manner in HIV-infected individuals. Journal of Immunology. 2014;192(4):1732-1744. (IF 5.5 / cited by 1)
     
  8. Kouyos RD, Rauch A, Böni J, Yerly S, Shah C, Aubert V, Klimkait T, Kovari H, Calmy A, Cavassini M, Battegay M, Vernazza PL, Bernasconi E, Ledergerber B, Günthard HF, and the Swiss HIV Cohort Study. Clustering of HCV coinfections on HIV phylogeny indicates domestic and sexual transmission of HCV. International Journal of Epidemiology. 2014; doi: 10.1093/ije/dyt276. (IF 10.0 / cited by 1)
     
  9. Avila D, Keiser O, Egger M, Kouyos R, Boni J, Yerly S, Klimkait T, Vernazza PL, Aubert V, Rauch A, Bonhoeffer S, Gunthard HF, Stadler T, Spycher BD, and the Swiss HIV Cohort Study. Social Meets Molecular: Combining Phylogenetic and Latent Class Analyses to Understand HIV-1 Transmission in Switzerland. American Journal of Epidemiology. 2014;179(12):1514-1525. (IF 5.0 / cited by 0)
     
  10. Metzner K, Scherrer AU, von Wyl V, Böni J, Yerly S, Klimkait T, Aubert V, Furrer H, Hirsch HH, Vernazza PL, Cavassini M, Calmy A, Bernasconi E, Weber R, Günthard HF, and the Swiss HIV Cohort Study. Limited clinical benefit of minority K103N and Y181C-variant detection in addition to routine genotypic resistance testing in antiretroviral therapy-naive patients. AIDS. 2014;28(15):2231-2239. (IF 6.5 / cited by 0)
     
  11. Kouyos RD, Rauch A, Braun DL, Yang WL, Böni J, Yerly S, Klimkait T, Aubert V, Shah C, Kovari H, Calmy A, Cavassini M, Battegay M, Vernazza PL, Bernasconi E, Ledergerber B, Günthard HF, and the Swiss HIV Cohort Study. 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. The Journal of Infectious Diseases. 2014;210:1555-61. (IF 5.8 / cited by 0)
     
  12. Di Giallonardo F, Töpfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, Patrignani A, Däumer M, Beisel C, Rusert P, Trkola A, Günthard HF, Roth V, Beerenwinkel N, Metzner KJ. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Research. 2014; 42(14):e e115 (IF 8.8 / cited by 0)
     
  13. Althaus CL, Joos B, Perelson AS, Günthard HF. Quantifying the turnover of transcriptional subclasses of HIV-1-infected cells. PLoS Computational Biology. 2014; 10(10):e1003871. (IF 4.8 / cited by 0)
     
  14. Schanz M, Liechti T, Zagordi O, Miho E, Reddy ST, Günthard HF, Trkola A, Huber M. High-Throughput Sequencing of Human Immunoglobulin Variable Regions with Subtype Identification. PLoS One. 2014;9(11):e111726 (IF 3.7 / cited by 0)
     
  15. Brandenberg OF, Rusert P, Magnus C, Weber J, Böni J, Günthard HF, Regoes RR, Trkola A. Partial rescue of V1V2 mutant infectivity by HIV-1 cell-cell transmission supports the domain’s exceptional capacity for sequence variation. Retrovirology. 2014;11:75:2-22. (IF 4.8 / cited by 0)
     
  16. Braun DL, Kouyos R, Oberle C, Grube C, Beda J, Fellay J, McLaren PJ, Kuster H, Günthard HF. A novel acute retroviral syndrome severity score predicts the key surrogate markers for HIV-1 disease progression. PLoS One. 2014;9(12):e114111 (IF 3.7 / cited by 0)
     
  17. Zimmermann K, Liechti T, Haas A, Rehr M, Trkola A, Günthard HF, Oxenius A. HIV-1 gp120-anti-gp120 immune complexes are efficiently captured by CD4+ T cells which renders them unresponsive to TCR-induced activation. Journal of Immunology. 2015;194(2):637-49 (IF not defined)
     
  18. Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard H, Suchard MA. Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution. Methods in Ecology and Evolution. 2015; in press
     
  19. Seifert D, Di Giallonardo F, Metzner KJ, Günthard HF, Beerenwinkel N. Bayesian inference of viral fitness landscapes in the quasispecies model. Genetics. 2015; in press.
     
  20. Yang WL, Kouyos R, Scherrer AU, Böni J, Shah C, Yerly S, Klimkait T, Aubert V, Furrer H, Battegay M, Cavassini M, Bernasconi E, Vernazza P, Held L, Ledergerber B, Günthard HF, and the Swiss HIV Cohort Study. Assessing the paradox between transmitted and acquired HIV-1 drug resistance in the Swiss HIV Cohort Study from 1998 to 2012. Journal of Infectious Diseases. 2015; in press
     
  21. Yang WL, Kouyos RD, Böni J, Yerly S, Klimkait T, Aubert V, Scherrer AU, Shilaih M, Hinkley T, Petropoulos C, Bonhoeffer S, Günthard HF, and the Swiss HIV Cohort Study. Persistence of Transmitted HIV-1 Drug Resistance Mutations Associated with Fitness Costs and Viral Genetic Backgrounds. PLoS Pathogens. 2015; 11(3): e1004722.
     
  22. Kohler I, Kouyos R, Bianchi M, Grube C, Wyrzucki A, Günthard HF, Hangartner L. The impact of vaccination on the breadth and magnitude of the antibody response to influenza A viruses in HIV-infected individuals. AIDS, 2015; 29/14:1803-10.
     
  23. Braun DL, MD; Kouyos RD, Balmer B, Grube C, Weber R, Günthard HF. Frequency and spectrum of unexpected clinical manifestations of primary HIV-1 infection. Clinical Infectious Diseases, 2015;61(6):1013–21.
     
  24. Vongrad V, Imig J, Mohammadi P, Kishore S, Jaskiewicz L, Hall J, Günthard HF, Beerenwinkel N, and J Metzner KJ. HIV-1 RNAs are not part of the Argonaute 2 associated RNA interference pathway in macrophages. PLoS One. 2015; 10(7):e0132127.
     
  25. Montazeri H, Günthard HF, Wan-Lin Yang WL, Kouyos R, Beerenwinkel N, and the Swiss HIV Cohort Study. Estimating the dynamics and dependencies of accumulating mutations. Biostatistics. 2015;16(4):713-26.
     
  26. Zimmermann K, Bastidas S, Knecht L, Kuster H, Vavricka SR, Günthard HF, Oxenius A. Gut commensal microbes do not represent a dominant antigenic source for continuous CD4+ T-cell activation during HIV-1 infection. European Journal of Immunology, 2015; 45: 3107–3113.
     
  27. Yang WL, Kouyos RD, Scherrer AU, Böni J, Shah C, Yerly S, Klimkait T, Aubert V, Hirzel C, Battegay M, Cavassini M, Bernasconi E, Vernazza P, Held L, Ledergerber B, and Günthard HF, on behalf of the SHCS. Assessing efficacy of different nucleos(t)ide backbones in NNRTI-containing regimens in the Swiss HIV Cohort Study. Journal of Antimicrobial Chemotherapy. 2015;70(12):3323-31.
     
  28. Marzel A, Shilaih M, Yang WL, Böni J, Yerly S, Klimkait T, Aubert V, Braun DL, Calmy A, Furrer H, Cavassini M, Battegay M, Vernazza PL, Bernasconi E, Günthard HF, Kouyos RD, and the SHCS. HIV-1 transmission during recent infection and during treatment interruptions as major drivers of new infections in the Swiss HIV Cohort Study. Clinical Infectious Diseases. 2016;62(1):115–22.
     
  29. Seifert D, Di Giallonardo F, Töpfer A, Singer J, Schmutz S, Günthard HF, Beerenwinkel N, Metzner KJ. A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations. Journal of Molecular Biology 2016;428(1):238-50.

  30. Scherrer AU , von Wyl V, Yang WL, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Cavassini M, Battegay M, Furrer H, Calmy A, Vernazza P, Bernasconi E, Günthard HF, and the SHCS. Emergence of acquired HIV-1 drug resistance has almost been stopped in Switzerland - a 15 year prospective cohort analysis. Clinical Infectious Diseases. 2016; in press.
     
  31. Kok YL, Vongrad V, Shilaih M, Di Giallonardo F, Kuster H, Kouyos R, Günthard HF, Metzner KJ. Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4+ T cells. Scientific Reports. 2016; 12;6:24157. doi: 10.1038/srep24157.
     
  32. Scherrer AU , von Wyl V, Yang WL, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Cavassini M, Battegay M, Furrer H, Calmy A, Vernazza P, Bernasconi E, Günthard HF, and the SHCS. Emergence of acquired HIV-1 drug resistance has almost been stopped in Switzerland - a 15 year prospective cohort analysis. Clinical Infectious Diseases. 2016;62:1310-1317.
     
  33. Shilaih M, Marzel A, Scherrer AU, Braun DL, Kovari H, Rougemont M, Darling K, Battegay M, Hoffmann M, Bernasconi E, Hirzel C, Günthard HF, Kouyos R, and SHCS. Dually Active HIV/HBV Antiretrovirals Protect Against Incident Hepatitis B Infections: Potential for Prophylaxis. Journal of Infectious Diseases. 2016;214:599–606.
     
  34. Shilaih M, Marzel A, Yang WL, Scherrer AU, Schüpbach J, Böni J, Yerly S, Hirsch HH, Aubert V, Cavassini M, Klimkait T, Vernazza PL, Bernasconi E, Furrer H, Günthard HF, Kouyos R, and the SHCS. Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland. Scientific Reports. 2016;6:27580 | DOI: 10.1038/srep27580.
     
  35. Scherrer AU, Yang WL, Kouyos RD, Böni J, Yerly S, Klimkait T, Aubert V, Cavassini M, Battegay M, Hauser C, Calmy A, Schmid P, Bernasconi E,. Günthard HF, and the SHCS. Successful prevention of transmission of integrase resistance in the Swiss HIV Cohort Study. Journal of Infectious Diseases. 2016;214:399–402.
     
  36. Montazeri H, Kuipers J, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Günthard HF, Beerenwinkel N, and the SHCS. Large-scale inference of Conjunctive Bayesian Networks. Bioinformatics. 2016;32(17):i727-i735.
     
  37. Oberle CS, Joos B, Rusert P, Campbell NK, Beauparlant D, Kuster H, Weber J, Schenkel CD, Scherrer AU, Magnus C, Kouyos R, Rieder P, Niederöst B, Braun DL, Pavlovic J, Böni J, Yerly S, Klimkait T, Aubert V, Trkola A, Metzner KJ, Günthard HF, and the SHCS. Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs. Retrovirology. 2016;13(1):62.
     
  38. Ragonnet-Cronin ML, Shilaih M, Günthard HF, Hodcroft EB, Böni J, Fearnhill E, Dunn D, Yerly S, Klimkait T, Aubert V, Yang WL, Brown AE, Lycett S, Kouyos R, Andrew, Brown AJL. A direct comparison of two densely sampled HIV epidemics: The UK and Switzerland. Scientific Reports. 2016;6:32251.
     
  39. Rusert P*, Kouyos RD*, Kadelka C, Ebner H, Schanz M, Huber M, Braun DL, Hozé N, Scherrer A, Magnus C, Weber J, Uhr T, Cippa V, Thorball CW, Kuster H, Cavassini M, Bernasconi E, Hoffmann M, Calmy A, Battegay M, Rauch A, Yerly S, Aubert V, Klimkait T, Böni J, Fellay J, Regoes RR, Günthard HF*, Trkola A*, and the SHCS. Determinants of HIV-1 broadly neutralizing antibody induction. Nature Medicine. 2016;22(11):1260-1267 [*shared first and last author].
     
  40. Shilaih M, Marzel A, Braun DL, Scherrer AU, Kovari H, Young J, Calmy A, Darling K, Battegay M, Hoffmann M, Bernasconi E, Thurnheer MC, Günthard HF, Kouyos R, and the SHCS. Factors associated with syphilis incidence in the HIV infected in the era of highly active antiretrovirals. Medicine. 2017; 2017;96(2):e5849.
     
  41. Brandenberg OF, Magnus C, Rusert P, Günthard HF, Regoes RR, Trkola A. Predicting HIV-1 transmission and antibody neutralization efficacy in vivo from stoichiometric parameters. PLoS Pathogens. 2017;13(5):e1006313.
     
  42. Bachmann N, Turk T, Kadelka C, Marzel A, Shilaih M, Böni J, Aubert V, Klimkait T, Leventhal GE, Günthard HF, Kouyos R, and SHCS. Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup. Retrovirology. 2017;14(1):33 (IF 3.9 / cited by 0).
     
  43. Nemeth J, Vongrad V, Metzner KJ, Strouvelle V, Weber R, Pedrioli P, Aebersold R, Günthard HF*,  Collins BC*. In vivo and in vitro proteome analysis of HIV-1 infected, human CD4+ T cells. Molecular and Cellular Proteomics. 2017; 16:4:S108-S123  [*shared last author].
     
  44. Beauparlant D, Rusert P, Magnus C, Kadelka C, Weber J, Uhr T, Zagordi O, Oberle C, Duenas-Decamp MJ, Clapham PR, Metzner KJ, Günthard HF, Alexandra Trkola A. Delineating CD4 dependency of HIV-1: Adaptation to infect low level CD4 expressing target cells widens cellular tropism but severely impacts on envelope functionality. PLoS Pathogens. 2017; 13(3):e1006255.
     
  45. Rasmussen DA , Kouyos R, Günthard HF, Stadler T. Phylodynamics on local sexual contact networks. PLoS Computational Biology. 2017; 13(3):e1005448.
     
  46. Marzel A, Shilaih M, Turk T, Campbell NK, Yang WL, Böni J, Yerly S, Klimkait T, Aubert V, Furrer H, Calmy A, Battegay M, Cavassini M, Bernasconi E, Schmid P, Metzner KJ, Günthard HF, Kouyos RD, and the SHCS. Mining for pairs: Shared clinic visit dates identify steady HIV positive partnerships. HIV Medicine. 2017; 18(9):667-676.
     
  47. 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 HF*, Roger D Kouyos RD*. Assessing the danger of self-sustained HIV epidemics from phylogenetic cluster analysis. eLife. 2017; in press [*shared last author].
     
  48. Braun Dominique L, Marzel Alex, Steffen Daniela, Schreiber Peter W, Grube Christina, Scherrer Alexandra U, Kouyos Roger D*, Günthard HF*, and the Swiss HIV Cohort Study. High rates of subsequent asymptomatic STIs and risky sexual behavior in patients initially presenting with primary HIV-1 infection. Clinical Infection Diseases. 2017; in press [*shared last author].

B) case reports

  1. Von Braun A, Braun DL, Kamarachev J, Günthard HF. New onset of Kaposi sarcoma in an HIV-1-infected homosexual man, despite early antiretroviral treatment, sustained viral suppression, and immune restoration. Open Forum Infectious Diseases. 2014;in press. (IF not defined)
     
  2. Schreiber PW, Aceto L, Korach R, Marreros N, Ryser-Degiorgis MP, Günthard HF. Cluster of leptospirosis acquired through river surfing in Switzerland. Open Forum Infectious Diseases. 2015; doi:10.1093

C) reviews / letters (peer reviewed)

  1. Braun DL, Nemeth J, Günthard HF. Die akute HIV-Infektion darf nicht verpasst werden. Therapeutische Umschau. 2014; 71(8):469-474 (IF not defined).
     
  2. Hoenigl M, Braun DL, Kouyos R, Günthard HF, Little SJ. Evaluation of the predictive potential of the short acute retroviral syndrome severity score for HIV-1 disease progression in individuals with acute HIV infection. Journal of Acquired Immune Deficiency Syndromes. 2017;1;74(4):e114-e117 (IF 3.6 / cited by 0).
     
  3. Oberle CS, Magnus C, Joos B, Rusert P, Beauparlant D, Kouyos R, Trkola A, Metzner KJ and Günthard HF. Reply to correspondence ‘Conserved signatures indicate HIV‑1 transmission is under strong selection and thus is not a “stochastic” process’ by Gonzalez et al., Retrovirology 2017. Retrovirology. 2017;1186/s12977-017-0332-y (IF 3.9 / cited by 0).