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Benoit P, Jolicoeur G, Point F, Soucy C, Normand K, Morency-Potvin P, Gagnon S, Kaufmann DE, Tremblay C, Coutlée F, Harrigan PR, Hardy I, Smith M, Savard P, Grandjean Lapierre S. On-demand, hospital-based, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic epidemiology to support nosocomial outbreak investigations: A prospective molecular epidemiology study. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e45. [PMID: 36960087 PMCID: PMC10028942 DOI: 10.1017/ash.2023.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 03/10/2023]
Abstract
Objectives We evaluated the added value of infection control-guided, on demand, and locally performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic sequencing to support outbreak investigation and control in acute-care settings. Design and setting This 18-month prospective molecular epidemiology study was conducted at a tertiary-care hospital in Montreal, Canada. When nosocomial transmission was suspected by local infection control, viral genomic sequencing was performed locally for all putative outbreak cases. Molecular and conventional epidemiology data were correlated on a just-in-time basis to improve understanding of coronavirus disease 2019 (COVID-19) transmission and reinforce or adapt control measures. Results Between April 2020 and October 2021, 6 outbreaks including 59 nosocomial infections (per the epidemiological definition) were investigated. Genomic data supported 7 distinct transmission clusters involving 6 patients and 26 healthcare workers. We identified multiple distinct modes of transmission, which led to reinforcement and adaptation of infection control measures. Molecular epidemiology data also refuted (n = 14) suspected transmission events in favor of community acquired but institutionally clustered cases. Conclusion SARS-CoV-2 genomic sequencing can refute or strengthen transmission hypotheses from conventional nosocomial epidemiological investigations, and guide implementation of setting-specific control strategies. Our study represents a template for prospective, on site, outbreak-focused SARS-CoV-2 sequencing. This approach may become increasingly relevant in a COVID-19 endemic state where systematic sequencing within centralized surveillance programs is not available. Trial registration clinicaltrials.gov identifier: NCT05411562.
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Affiliation(s)
- Patrick Benoit
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
| | - Gisèle Jolicoeur
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Floriane Point
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Chantal Soucy
- Infection Prevention and Control Service, Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Karine Normand
- Infection Prevention and Control Service, Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Philippe Morency-Potvin
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
- Infectious Diseases Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
| | - Simon Gagnon
- Molecular Biology Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
| | - Daniel E. Kaufmann
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
- Infectious Diseases Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
| | - Cécile Tremblay
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
- Infectious Diseases Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
| | - François Coutlée
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
- Infectious Diseases Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
- Molecular Biology Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
| | - P. Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Isabelle Hardy
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
- Molecular Biology Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
| | - Martin Smith
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Patrice Savard
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
- Infection Prevention and Control Service, Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
- Infectious Diseases Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
| | - Simon Grandjean Lapierre
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
- Infectious Diseases Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
- Molecular Biology Service, Centre Hospitalier de l’Université de Montréal, Saint-Denis, Montréal, Québec, Canada
- Author for correspondence: Simon Grandjean Lapierre, MD, MSc, FRCPC, Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, Québec, H3T 1J4, Canada. E-mail:
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Rosca EC, Heneghan C, Spencer EA, Brassey J, Plüddemann A, Onakpoya IJ, Evans D, Conly JM, Jefferson T. Transmission of SARS-CoV-2 Associated with Cruise Ship Travel: A Systematic Review. Trop Med Infect Dis 2022; 7:290. [PMID: 36288031 PMCID: PMC9610645 DOI: 10.3390/tropicalmed7100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Maritime and river travel may be associated with respiratory viral spread via infected passengers and/or crew and potentially through other transmission routes. The transmission models of SARS-CoV-2 associated with cruise ship travel are based on transmission dynamics of other respiratory viruses. We aimed to provide a summary and evaluation of relevant data on SARS-CoV-2 transmission aboard cruise ships, report policy implications, and highlight research gaps. Methods: We searched four electronic databases (up to 26 May 2022) and included studies on SARS-CoV-2 transmission aboard cruise ships. The quality of the studies was assessed based on five criteria, and relevant findings were reported. Results: We included 23 papers on onboard SARS-CoV-2 transmission (with 15 reports on different aspects of the outbreak on Diamond Princess and nine reports on other international cruises), 2 environmental studies, and 1 systematic review. Three articles presented data on both international cruises and the Diamond Princess. The quality of evidence from most studies was low to very low. Index case definitions were heterogeneous. The proportion of traced contacts ranged from 0.19 to 100%. Studies that followed up >80% of passengers and crew reported attack rates (AR) up to 59%. The presence of a distinct dose−response relationship was demonstrated by findings of increased ARs in multi-person cabins. Two studies performed viral cultures with eight positive results. Genomic sequencing and phylogenetic analyses were performed in individuals from three cruises. Two environmental studies reported PCR-positive samples (cycle threshold range 26.21−39.00). In one study, no infectious virus was isolated from any of the 76 environmental samples. Conclusion: Our review suggests that crowding and multiple persons per cabin were associated with an increased risk of transmission on cruise ships. Variations in design, methodology, and case ascertainment limit comparisons across studies and quantification of transmission risk. Standardized guidelines for conducting and reporting studies on cruise ships of acute respiratory infection transmission should be developed.
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Affiliation(s)
- Elena Cecilia Rosca
- Department of Neurology, Victor Babes University of Medicine and Pharmacy, Piata Eftimie Murgu 2, 300041 Timisoara, Romania
| | - Carl Heneghan
- Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Oxford OX2 6GG, UK
| | - Elizabeth A. Spencer
- Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Oxford OX2 6GG, UK
| | - Jon Brassey
- Trip Database Ltd., Glasllwch Lane, Newport NP20 3PS, UK
| | - Annette Plüddemann
- Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Oxford OX2 6GG, UK
| | - Igho J. Onakpoya
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK
| | - David Evans
- Li Ka Shing Institute of Virology, and Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - John M. Conly
- Departments of Medicine, Microbiology, Immunology & Infectious Diseases, and Pathology & Laboratory Medicine, Synder Institute for Chronic Diseases and O’Brien Institute for Public Health, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
| | - Tom Jefferson
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK
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Andréoletti J, Zwaans A, Warnock RCM, Aguirre-Fernández G, Barido-Sottani J, Gupta A, Stadler T, Manceau M. The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology. Syst Biol 2022; 71:1440-1452. [PMID: 35608305 PMCID: PMC9558841 DOI: 10.1093/sysbio/syac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution, these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, that is, lacking morphological and molecular data, which we call occurrences, provide invaluable information to estimate the past number of lineages. Here, we present new methodological developments around the fossilized birth–death process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death, and sampling rates; and (iii) estimate the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical data sets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the coronavirus disease 2019 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics. [Birth–death model; epidemiology; fossils; macroevolution; occurrences; phylogenetics; skyline.]
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Affiliation(s)
- Jérémy Andréoletti
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Antoine Zwaans
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Rachel C M Warnock
- GeoZentrum Nordbayern,Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | | | - Joëlle Barido-Sottani
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, USA
| | - Ankit Gupta
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Marc Manceau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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Kim J, Cheon S, Ahn I. NGS data vectorization, clustering, and finding key codons in SARS-CoV-2 variations. BMC Bioinformatics 2022; 23:187. [PMID: 35581558 PMCID: PMC9113074 DOI: 10.1186/s12859-022-04718-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 05/06/2022] [Indexed: 11/10/2022] Open
Abstract
The rapid global spread and dissemination of SARS-CoV-2 has provided the virus with numerous opportunities to develop several variants. Thus, it is critical to determine the degree of the variations and in which part of the virus those variations occurred. Therefore, in this study, methods that could be used to vectorize the sequence data, perform clustering analysis, and visualize the results were proposed using machine learning methods. To conduct this study, a total of 224,073 cases of SARS-CoV-2 sequence data were collected through NCBI and GISAID, and the data were visualized using dimensionality reduction and clustering analysis models such as T-SNE and DBSCAN. The SARS-CoV-2 virus, which was first detected, was distinguished from different variations, including Omicron and Delta, in the cluster results. Furthermore, it was possible to examine which codon changes in the spike protein caused the variants to be distinguished using feature importance extraction models such as Random Forest or Shapely Value. The proposed method has the advantage of being able to analyse and visualize a large amount of data at once compared to the existing tree-based sequence data analysis. The proposed method was able to identify and visualize significant changes between the SARS-CoV-2 virus, which was first detected in Wuhan, China, in December 2019, and the newly formed mutant virus group. As a result of clustering analysis using sequence data, it was possible to confirm the formation of clusters among various variants in a two-dimensional graph, and by extracting the importance of variables, it was possible to confirm which codon changes played a major role in distinguishing variants. Furthermore, since the proposed method can handle a variety of data sequences, it can be used for all kinds of diseases, including influenza and SARS-CoV-2. Therefore, the proposed method has the potential to become widely used for the effective analysis of disease variations.
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Affiliation(s)
- Juhyeon Kim
- Department of Data-Centric Problem Solving Research, Korea Institute of Science and Technology Information, Yuseong-gu, Daejeon, Korea.,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, Korea.,Department of Industrial Engineering, Ajou University, Suwon, South Korea
| | - Saeyeon Cheon
- Applied Artificial Intelligence Major, University of Science & Technology, Yuseong-gu, Daejeon, Korea
| | - Insung Ahn
- Department of Data-Centric Problem Solving Research, Korea Institute of Science and Technology Information, Yuseong-gu, Daejeon, Korea. .,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, Korea. .,Applied Artificial Intelligence Major, University of Science & Technology, Yuseong-gu, Daejeon, Korea.
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