Infectious Disease Dynamics
Using different data sources and
mathematical methods to understand
the complex dynamics of the HIV epidemic and beyond
Our team brings together expertise from mathematics, biology, medicine, and data science
The People Who Make It Happen
Current Team
The People Who Make It Happen
Current Team
Katharina Kusejko
Group Leader
Anna Bot
PostDoc
Jessy Duran Ramirez
PhD student
Bashkim Jaha
PhD student
Nuri Han
PhD student (co-supervision)
Yuqian Wang
PhD student
The People Who Made It Happen
Past Members
The People Who Made It Happen
Past Members
Marc Weber
MD (co-supervision, MD thesis)
Caroline Lanz
MD (co-supervision, MD thesis)
Martina Reichmuth
PhD, (co-supervision, Master thesis)
Whats New
News & Stories
Insights from Our Research
Selected Publications
Inflammation and B cell activation define a plasma proteome signature predicting tuberculosis in people with HIV
Kusejko K, Arefian M, Duroux D, Zeeb M, Dollé C, Hoffmann M, Labhardt N, Wandeler G, Cavassini M, Haller S, Bernasconi E, Russenberger D, Kouyos RD, Günthard HF, Collins BC, Nemeth J; Swiss HIV Cohort Study
mBio. 2025 Aug 28
Phylogenetics and molecular evolution to understand and curb the HIV pandemic
HIV-1 Low-Level Viremia Predicts Viral Failure in Participants on Antiretroviral Therapy in the Swiss HIV Cohort Study
Lanz C, Meier J, Stöckle M, Furrer H, Calmy A, Cavassini M, Bernasconi E, Schmid P, Braun DL, Kouyos RD, Loosli T, Kusejko K*, Günthard HF*; Swiss HIV Cohort Study
Clinical Infectious Diseases, 2025 Aug 1;81(1):57-66
Machine Learning-based Prediction of Active Tuberculosis in People With Human Immunodeficiency Virus Using Clinical Data
Lena Bartl, Marius Zeeb, Marisa Kälin, Tom Loosli, Julia Notter, Hansjakob Furrer, Matthias Hoffmann, Hans H Hirsch, Robert Zangerle, Katharina Grabmeier-Pfistershammer, Michael Knappik, Alexandra Calmy, Jose Damas Fernandez, Niklaus D Labhardt, Enos Bernasconi, Huldrych F Günthard, Roger D Kouyos, Katharina Kusejko*, Johannes Nemeth*, the Swiss HIV Cohort Study
Clinical Infectious Diseases, 2025, ciaf149
Mycobacteria beyond disease
Terence K. Tutumlu, Cédric Dollé, Katharina Kusejko, Sébastien Gagneux, Silvio D. Brugger, Huldrych F. Günthard, Johannes Nemeth
Trends in Microbiology, 2025, ISSN 0966-842X
Threshold sensitivity analysis for HIV-1 transmission cluster detection using different genomic regions and subtypes
Obeng BM, Kouyos RD, Kusejko K, Salazar-Vizcaya L, Günthard HF, Kelleher AD, Di Giallonardo F; Swiss HIV Cohort Study
Virology. 2025 Jul;608:110558.
Late Re-Engagement Into HIV Care Among Adults in the Swiss HIV Cohort Study
Haas AD, Kusejko K, Cavassini M, Günthard H, Stöckle M, Calmy A, Bernasconi E, Schmid P, Egger M, Wandeler G; Swiss HIV Cohort Study
J Acquir Immune Defic Syndr. 2025 Apr 15;98(5):491-500
Time Trends in Causes of Death in People With HIV: Insights From the Swiss HIV Cohort Study
S. R. Weber, J. J. Duran Ramirez, M. Hentzien, M. Cavassini, E. Bernasconi, E. Hofmann, H. Furrer, H. Kovari, M. Stöckle, P. Schmid, D. Haerry, D. L. Braun, H. F. Günthard*, K. Kusejko*, and the Swiss HIV Cohort Study
Clinical Infectious Diseases, July 2024
Infectious disease events in people with HIV receiving kidney transplantation: Analysis of the Swiss HIV Cohort Study and the Swiss Transplant Cohort Study
Katharina Kusejko, Roger D Kouyos, Enos Bernasconi, Katia Boggian, Dominique L Braun, Alexandra Calmy, Matthias Cavassini , Christian van Delden, Hansjakob Furrer, Christian Garzoni, Hans H Hirsch, Cedric Hirzel, Oriol Manuel, Patrick Schmid, Nina Khanna, Fadi Haidar, Marco Bonani, Dela Golshayan, Michael Dickenmann, Daniel Sidler, Aurelia Schnyder, Nicolas J Mueller, Huldrych F Günthard, Peter W Schreiber; Swiss HIV Cohorts Study and the Swiss Transplant Cohort Study
BMC Infectious Diseases, October 2024
Do Infectious Diseases After Kidney Retransplantation Differ From Those After First Kidney Transplantation?
Katharina Kusejko, Dionysios Neofytos, Christian van Delden, Hans H Hirsch, Pascal Meylan, Katia Boggian, Cedric Hirzel, Christian Garzoni, Daniel Sidler, Aurelia Schnyder, Stefan Schaub, Déla Golshayan, Fadi Haidar, Marco Bonani, Roger D Kouyos, Nicolas J Mueller, Peter W Schreiber; Swiss Transplant Cohort Study
Open Forum Infectious Diseases, February 2024
Migrating a Well-Established Longitudinal Cohort Database From Oracle SQL to Research Electronic Data Entry (REDCap): Data Management Research and Design Study
Kusejko K, Smith D, Scherrer A, Paioni P, Kohns Vasconcelos M, Aebi-Popp K, Kouyos R, Günthard H, Kahlert C, Swiss HIV Cohort Study and the Swiss Mother and Child HIV Cohort Study
JMIR Form Res 2023;7:e44567
Incidence of sexually transmitted infections and association with behavioural factors: Time-to-event analysis of a large pre-exposure prophylaxis (PrEP) cohort
Hovaguimian F, Kouyos RD, Kusejko K, Schmidt AJ, Tarr PE, Bernasconi E, Braun DL, Calmy A, Notter J, Stoeckle M, Surial B, Christinet V, Darling KEA, Depmeier C, Läuchli S, Reinacher M, Rasi M, Nicca D, Bruggmann P, Haerry D, Bize R, Low N, Vock F, El Amari EB, Böni J, Bosshard PP, Fehr JS, Hampel B; SwissPrEPared Cohort Study
HIV Medicine. 2024 Jan;25(1):117-128
Understanding the Decline of Incident, Active Tuberculosis in People With Human Immunodeficiency Virus in Switzerland
Zeeb M, Tepekule B, Kusejko K, Reiber C, Kälin M, Bartl L, Notter J, Furrer H, Hoffmann M, Hirsch HH, Calmy A, Cavassini M, Labhardt ND, Bernasconi E, Braun DL, Günthard HF, Kouyos RD, Nemeth J; Swiss HIV Cohort Study
Clinical Infectious Diseases. 2023 Nov 11;77(9):1303-1311
Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics
Kusejko K, Tschumi N, Chaudron SE, Nguyen H, Battegay M, Bernasconi E, Böni J, Huber M, Calmy A, Cavassini M, Egle A, Grabmeier-Pfistershammer K, Haas B, Hirsch H, Klimkait T, Öllinger A, Perreau M, Ramette A, Flury BB, Sarcletti M, Scherrer A, Schmid P, Yerly S, Zangerle R, Günthard HF, Kouyos RD; Swiss HIV Cohort Study and the Austrian HIV Cohort Study
J Acquir Immune Defic Syndr. 2022 Aug 1;90(4):e4-e12
Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group
Nguyen H, Hampel B, Garcia Nuñez D, Battegay M, Hachfeld A, Bernasconi E, Calmy A, Cavassini M, Vernazza P, Fellay J, Rudolph H, Huber M, Leuzinger K, Perreau M, Scherrer A, Ramette AN, Yerly S, Günthard HF, Kouyos RD*, Kusejko K*; Swiss HIV Cohort Study
Clin Infect Dis. 2022 Apr 28;74(8):1468-1475
Sustained Effect on Hepatitis C Elimination Among Men Who Have Sex With Men in the Swiss HIV Cohort Study: A Systematic Re-Screening for Hepatitis C RNA Two Years Following a Nation-Wide Elimination Program
Katharina Kusejko, Luisa Salazar-Vizcaya, Cyril Shah, Marcel Stöckle, Charles Béguelin, Patrick Schmid, Marie Ongaro, Katherine Darling, Enos Bernasconi, Andri Rauch, Roger D Kouyos, Huldrych F Günthard, Jürg Böni, Jan S Fehr, Dominique L Braun, Swiss HIV Cohort Study
Clinical Infectious Diseases, Volume 75, Issue 10, 15 November 2022, Pages 1723–1731
The Interplay Between Replication Capacity of HIV-1 and Surrogate Markers of Disease
Rindler AE*, Kusejko K*, Kuster H, Neumann K, Leemann C, Zeeb M, Chaudron SE, Braun DL, Kouyos RD, Metzner KJ, Günthard HF
J Infect Dis. 2022 Sep 21;226(6):1057-1068
Developing and testing a Corona VaccinE tRiAL pLatform (COVERALL) to study Covid-19 vaccine response in immunocompromised patients
Kusejko K, Chammartin F, Smith D, Odermatt M, Schuhmacher J, Koller M, Günthard HF, Briel M, Bucher HC, Speich B; Swiss HIV Cohort Study; Swiss Transplant Cohort Study
BMC Infectious Diseases. 2022 Jul 28;22(1):654
Determinants of antibody response to severe acute respiratory syndrome coronavirus 2 mRNA vaccines in people with HIV
Chammartin F, Kusejko K, Pasin C, Trkola A, Briel M, Amico P, Stoekle MP, Eichenberger AL, Hasse B, Braun DL, Schuurmans MM, Müller TF, Tamm M, Mueller NJ, Rauch A, Koller MT, Günthard HF, Bucher HC, Speich B, Abela IA; and the Swiss HIV Cohort Study
AIDS. 2022 Aug 1;36(10):1465-1468
Collaborative Challenges of Multi-Cohort Projects in Pharmacogenetics-Why Time Is Essential for Meaningful Collaborations
Franchini F, Kusejko K, Marzolini C, Tellenbach C, Rossi S, Stampf S, Koller M, Stoyanov J, Möller B, Leichtle AB
JMIR Form Res. 2022 Sep 29;6(9):e36759
The Impact of Surgical Strategy and Rifampin on Treatment Outcome in Cutibacterium Periprosthetic Joint Infections
Katharina Kusejko, Álvaro Auñón, Bernhard Jost, Benito Natividad, Carol Strahm, Christine Thurnheer, Daniel Pablo-Marcos, Dorsaf Slama, Giulia Scanferla, Ilker Uckay, Isabelle Waldmann, Jaime Esteban, Jaime Lora-Tamayo, Martin Clauss, Marta Fernandez-Sampedro, Marjan Wouthuyzen-Bakker, Matteo Carlo Ferrari, Natalie Gassmann, Parham Sendi, Philipp Jent, Philippe C Morand, Prakhar Vijayvargiya, Rihard Trebše, Robin Patel, Roger D Kouyos, Stéphane Corvec, Tobias Siegfried Kramer, Vincent A Stadelmann, Yvonne Achermann, on behalf of the ESCMID Study Group for Implant-Associated Infections (ESGIAI)
Clinical Infectious Diseases, Volume 72, Issue 12, 15 June 2021, Pages e1064–e1073
Using longitudinally sampled viral nucleotide sequences to characterize the drivers of HIV-1 transmission
Reichmuth ML, Chaudron SE, Bachmann N, Nguyen H, Böni J, Metzner KJ, Perreau M, Klimkait T, Yerly S, Hirsch HH, Hauser C, Ramette A, Vernazza P, Cavassini M, Bernasconi E, Günthard HF, Kusejko K*, Kouyos RD*; Swiss HIV Cohort Study
HIV Med. 2021 May;22(5):346-359
Impact of an electronic alert on prescription patterns of meropenem, voriconazole and caspofungin
Chok L*, Kusejko K*, Eberhard N, Chaudron SE, Saleschus D, Kocher C, Kouyos RD, Weber R, Kuster SP
BMC Infectious Diseases 2021 Dec 20;21(1):1263
A trial platform to assess approved SARS-CoV-2 vaccines in immunocompromised patients: first sub-protocol for a pilot trial comparing the mRNA vaccines Comirnaty® and COVID-19 mRNA Vaccine Moderna®
Speich B, Chammartin F, Smith D, Stoeckle MP, Amico P, Eichenberger AL, Hasse B, Schuurmans MM, Müller T, Tamm M, Dickenmann M, Abela IA, Trkola A, Hirsch HH, Manuel O, Cavassini M, Hemkens LG, Briel M, Mueller NJ, Rauch A, Günthard HF, Koller MT, Bucher HC, Kusejko K; study groups from the Swiss HIV Cohort Study and the Swiss Transplant Cohort Study
Trials. 2021 Oct 21;22(1):724
Differences Between Infectious Disease Events in First Liver Transplant Versus Retransplantation in the Swiss Transplant Cohort Study
Kusejko K, Neofytos D, Hirsch HH, Meylan P, Boggian K, Hirzel C, Garzoni C, Kouyos RD, Mueller NJ, Schreiber PW; Swiss Transplant Cohort Study. Differences Between Infectious Disease Events in First Liver Transplant Versus Retransplantation in the Swiss Transplant Cohort Study
Liver Transplantation 2021 Sep;27(9):1283-1290
Diagnosis of latent tuberculosis infection is associated with reduced HIV viral load and lower risk for opportunistic infections in people living with HIV
Kusejko K, Günthard HF, Olson GS, Zens K, Darling K, Khanna N, Furrer H, Vetter P, Bernasconi E, Vernazza P, Hoffmann M, Kouyos RD, Nemeth J; Swiss HIV Cohort Study.
PLoS Biology, 2020 Dec 7;18(12):e300096
Chemsex drugs on the rise: a longitudinal analysis of the Swiss HIV Cohort Study from 2007 to 2017
Hampel B*, Kusejko K*, Kouyos RD, Böni J, Flepp M, Stöckle M, Conen A, Béguelin C, Künzler-Heule P, Nicca D, Schmidt AJ, Nguyen H, Delaloye J, Rougemont M, Bernasconi E, Rauch A, Günthard HF, Braun DL, Fehr J; Swiss HIV Cohort Study group
HIV Med. 2020 Apr;21(4):228-239
Differences in social and mental well-being of long-term survivors among people who inject drugs and other participants in the Swiss HIV Cohort Study: 1980-2018
Kusejko K, Marzel A, Nguyen H, Chaudron SE, Bachmann N, Weber R, Bruggmann P, Roth JA, Bernasconi E, Calmy A, Cavassini M, Bregenzer A, Böni J, Yerly S, Klimkait T, Perreau M, Walti LN, Günthard HF, Kouyos RD; Swiss HIV Cohort Study.
Antiviral Therapy 2020;25(1):43-54
Self-reported Neurocognitive Impairment in People Living With Human Immunodeficiency Virus (HIV): Characterizing Clusters of Patients With Similar Changes in Self-reported Neurocognitive Impairment, 2013-2017, in the Swiss HIV Cohort Study
Kusejko K, Salazar-Vizcaya L, Braun DL, Tarr PE, Bernasconi E, Doco-Lecompte T, Cavassini M, Schmid P, Du Pasquier R, Hauser C, Günthard HF, Kouyos RD.
Clinical Infectious Diseases 2020 Jul 27;71(3):637-644
A Systematic Phylogenetic Approach to Study the Interaction of HIV-1 With Coinfections, Noncommunicable Diseases, and Opportunistic Diseases
Kusejko K, Bachmann N, Chaudron SE, Nguyen H, Braun DL, Hampel B, Battegay M, Bernasconi E, Calmy A, Cavassini M, Hoffmann M, Böni J, Yerly S, Klimkait T, Perreau M, Rauch A, Günthard HF, Kouyos RD; Swiss HIV Cohort Study
J Infect Dis. 2019 Jun 19;220(2):244-253
Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa
Hauser A, Kusejko K, Johnson LF, Wandeler G, Riou J, Goldstein F, Egger M, Kouyos RD
PLoS Comput Biol. 2019 Jun 24;15(6):e1007083
Quantifying the drivers of HIV transmission and prevention in men who have sex with men: a population model-based analysis in Switzerland
Kusejko K, Marzel A, Hampel B, Bachmann N, Nguyen H, Fehr J, Braun DL, Battegay M, Bernasconi E, Calmy A, Cavassini M, Hoffmann M, Böni J, Yerly S, Klimkait T, Perreau M, Rauch A, Günthard HF, Kouyos RD; Swiss HIV Cohort Study
HIV Med. 2018 Nov;19(10):688-697
Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study
Kusejko K, Kadelka C, Marzel A, Battegay M, Bernasconi E, Calmy A, Cavassini M, Hoffmann M, Böni J, Yerly S, Klimkait T, Perreau M, Rauch A, Günthard HF, Kouyos RD; Swiss HIV Cohort Study
Virus Evol. 2018 Sep 18;4(2):vey024
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We are always open to enthusiastic and motivated students interested in conducting their Master’s thesis or MD thesis in our group. Please contact us if you are interested!
At the moment, there are no open PhD or PostDoc positions in our group.
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