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Salazar-Vizcaya L, Kusejko K, Günthard HF, Böni J, Metzner KJ, Braun DL, Nicca D, Bernasconi E, Calmy A, Darling KEA, Wandeler G, Kouyos RD, Rauch A. An Approach to Quantifying the Interaction between Behavioral and Transmission Clusters. Viruses 2022; 14:v14040784. [PMID: 35458514 PMCID: PMC9032082 DOI: 10.3390/v14040784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/04/2023] Open
Abstract
We hypothesize that patterns of sexual behavior play a role in the conformation of transmission networks, i.e., the way you behave might influence whom you have sex with. If that was the case, behavioral grouping might in turn correlate with, and potentially predict transmission networking, e.g., proximity in a viral phylogeny. We rigorously present an intuitive approach to address this hypothesis by quantifying mapped interactions between groups defined by similarities in sexual behavior along a virus phylogeny while discussing power and sample size considerations. Data from the Swiss HIV Cohort Study on condom use and hepatitis C virus (HCV) sequences served as proof-of-concept. In this case, a strict inclusion criteria contrasting with low HCV prevalence hindered our possibilities to identify significant relationships. This manuscript serves as guide for studies aimed at characterizing interactions between behavioral patterns and transmission networks. Large transmission networks such as those of HIV or COVID-19 are prime candidates for applying this methodological approach.
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Affiliation(s)
- Luisa Salazar-Vizcaya
- Department of Infectious Diseases, Bern University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland; (G.W.); (A.R.)
- Correspondence:
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Karin J. Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Dominique L. Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Dunja Nicca
- Institute of Nursing Science, University of Basel, 4056 Basel, Switzerland;
- Department of Public Health, Epidemiology, Biostatistics and Public Health Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland;
- University of Southern Switzerland, 6928 Manno, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland;
| | - Alexandra Calmy
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland;
| | - Katharine E. A. Darling
- Infectious Diseases Service, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland;
- University of Lausanne, 1015 Lausanne, Switzerland
| | - Gilles Wandeler
- Department of Infectious Diseases, Bern University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland; (G.W.); (A.R.)
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland; (G.W.); (A.R.)
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Brenner BG, Ibanescu RI, Osman N, Cuadra-Foy E, Oliveira M, Chaillon A, Stephens D, Hardy I, Routy JP, Thomas R, Baril JG, Leblanc R, Tremblay C, Roger M. The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002-2020). Viruses 2021; 13:1643. [PMID: 34452506 PMCID: PMC8402830 DOI: 10.3390/v13081643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 01/23/2023] Open
Abstract
Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2-5 members) declined by 70% from 2006-2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.
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Affiliation(s)
- Bluma G. Brenner
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Medicine (Surgery, Infectious Disease), McGill University, Montréal, QC H3A 2M7, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Nathan Osman
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Ernesto Cuadra-Foy
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Maureen Oliveira
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Antoine Chaillon
- Department of Medicine, University of California, San Diego, CA 93903, USA;
| | - David Stephens
- Department of Mathematics and Statistics, McGill University, Montréal, QC H3A 0B9, Canada;
| | - Isabelle Hardy
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Jean-Pierre Routy
- Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC H3A 3J1, Canada;
| | - Réjean Thomas
- Clinique Médicale l’Actuel, Montréal, QC H2L 4P9, Canada;
| | - Jean-Guy Baril
- Clinique Médicale Urbaine du Quartier Latin, Montréal, QC H2L 4E9, Canada;
| | - Roger Leblanc
- Clinique Médicale OPUS, Montréal, QC H3A 1T1, Canada;
| | - Cecile Tremblay
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Michel Roger
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
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