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Reichmuth ML, Heron L, Riou J, Moser A, Hauser A, Low N, Althaus CL. Socio-demographic characteristics associated with COVID-19 vaccination uptake in Switzerland: longitudinal analysis of the CoMix study. BMC Public Health 2023; 23:1523. [PMID: 37563550 PMCID: PMC10413773 DOI: 10.1186/s12889-023-16405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Vaccination is an effective strategy to reduce morbidity and mortality from coronavirus disease 2019 (COVID-19). However, the uptake of COVID-19 vaccination has varied across and within countries. Switzerland has had lower levels of COVID-19 vaccination uptake in the general population than many other high-income countries. Understanding the socio-demographic factors associated with vaccination uptake can help to inform future vaccination strategies to increase uptake. METHODS We conducted a longitudinal online survey in the Swiss population, consisting of six survey waves from June to September 2021. Participants provided information on socio-demographic characteristics, history of testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), social contacts, willingness to be vaccinated, and vaccination status. We used a multivariable Poisson regression model to estimate the adjusted rate ratio (aRR) and 95% confidence intervals (CI) of COVID-19 vaccine uptake. RESULTS We recorded 6,758 observations from 1,884 adults. For the regression analysis, we included 3,513 observations from 1,883 participants. By September 2021, 600 (75%) of 806 study participants had received at least one vaccine dose. Participants who were older, male, and students, had a higher educational level, household income, and number of social contacts, and lived in a household with a medically vulnerable person were more likely to have received at least one vaccine dose. Female participants, those who lived in rural areas and smaller households, and people who perceived COVID-19 measures as being too strict were less likely to be vaccinated. We found no significant association between previous SARS-CoV-2 infections and vaccination uptake. CONCLUSIONS Our results suggest that socio-demographic factors as well as individual behaviours and attitudes played an important role in COVID-19 vaccination uptake in Switzerland. Therefore, appropriate communication with the public is needed to ensure that public health interventions are accepted and implemented by the population. Tailored COVID-19 vaccination strategies in Switzerland that aim to improve uptake should target specific subgroups such as women, people from rural areas or people with lower socio-demographic status.
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Affiliation(s)
- Martina L Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Leonie Heron
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - André Moser
- CTU Bern, University of Bern, Bern, Switzerland
| | - Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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Reichmuth ML, Hodcroft EB, Althaus CL. Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: Phylogenetic analysis and intervention scenarios. PLoS Pathog 2023; 19:e1011553. [PMID: 37561788 PMCID: PMC10443857 DOI: 10.1371/journal.ppat.1011553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/22/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
The SARS-CoV-2 pandemic has led to the emergence of various variants of concern (VoCs) that are associated with increased transmissibility, immune evasion, or differences in disease severity. The emergence of VoCs fueled interest in understanding the potential impact of travel restrictions and surveillance strategies to prevent or delay the early spread of VoCs. We performed phylogenetic analyses and mathematical modeling to study the importation and spread of the VoCs Alpha and Delta in Switzerland in 2020 and 2021. Using a phylogenetic approach, we estimated between 383-1,038 imports of Alpha and 455-1,347 imports of Delta into Switzerland. We then used the results from the phylogenetic analysis to parameterize a dynamic transmission model that accurately described the subsequent spread of Alpha and Delta. We modeled different counterfactual intervention scenarios to quantify the potential impact of border closures and surveillance of travelers on the spread of Alpha and Delta. We found that implementing border closures after the announcement of VoCs would have been of limited impact to mitigate the spread of VoCs. In contrast, increased surveillance of travelers could prove to be an effective measure for delaying the spread of VoCs in situations where their severity remains unclear. Our study shows how phylogenetic analysis in combination with dynamic transmission models can be used to estimate the number of imported SARS-CoV-2 variants and the potential impact of different intervention scenarios to inform the public health response during the pandemic.
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Affiliation(s)
- Martina L. Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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Riou J, Althaus CL, Allen H, Cole MJ, Grad YH, Heijne JCM, Unemo M, Low N. Projecting the development of antimicrobial resistance in Neisseria gonorrhoeae from antimicrobial surveillance data: a mathematical modelling study. BMC Infect Dis 2023; 23:252. [PMID: 37081443 PMCID: PMC10116452 DOI: 10.1186/s12879-023-08200-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND The World Health Organization recommends changing the first-line antimicrobial treatment for gonorrhoea when ≥ 5% of Neisseria gonorrhoeae cases fail treatment or are resistant. Susceptibility to ceftriaxone, the last remaining treatment option has been decreasing in many countries. We used antimicrobial resistance surveillance data and developed mathematical models to project the time to reach the 5% threshold for resistance to first-line antimicrobials used for N. gonorrhoeae. METHODS We used data from the Gonococcal Resistance to Antimicrobials Surveillance Programme (GRASP) in England and Wales from 2000-2018 about minimum inhibitory concentrations (MIC) for ciprofloxacin, azithromycin, cefixime and ceftriaxone and antimicrobial treatment in two groups, heterosexual men and women (HMW) and men who have sex with men (MSM). We developed two susceptible-infected-susceptible models to fit these data and produce projections of the proportion of resistance until 2030. The single-step model represents the situation in which a single mutation results in antimicrobial resistance. In the multi-step model, the sequential accumulation of resistance mutations is reflected by changes in the MIC distribution. RESULTS The single-step model described resistance to ciprofloxacin well. Both single-step and multi-step models could describe azithromycin and cefixime resistance, with projected resistance levels higher with the multi-step than the single step model. For ceftriaxone, with very few observed cases of full resistance, the multi-step model was needed to describe long-term dynamics of resistance. Extrapolating from the observed upward drift in MIC values, the multi-step model projected ≥ 5% resistance to ceftriaxone could be reached by 2030, based on treatment pressure alone. Ceftriaxone resistance was projected to rise to 13.2% (95% credible interval [CrI]: 0.7-44.8%) among HMW and 19.6% (95%CrI: 2.6-54.4%) among MSM by 2030. CONCLUSIONS New first-line antimicrobials for gonorrhoea treatment are needed. In the meantime, public health authorities should strengthen surveillance for AMR in N. gonorrhoeae and implement strategies for continued antimicrobial stewardship. Our models show the utility of long-term representative surveillance of gonococcal antimicrobial susceptibility data and can be adapted for use in, and for comparison with, other countries.
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Affiliation(s)
- Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | - Janneke C M Heijne
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Social Medicine, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands
| | | | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Emmenegger M, De Cecco E, Lamparter D, Jacquat RP, Riou J, Menges D, Ballouz T, Ebner D, Schneider MM, Morales IC, Doğançay B, Guo J, Wiedmer A, Domange J, Imeri M, Moos R, Zografou C, Batkitar L, Madrigal L, Schneider D, Trevisan C, Gonzalez-Guerra A, Carrella A, Dubach IL, Xu CK, Meisl G, Kosmoliaptsis V, Malinauskas T, Burgess-Brown N, Owens R, Hatch S, Mongkolsapaya J, Screaton GR, Schubert K, Huck JD, Liu F, Pojer F, Lau K, Hacker D, Probst-Müller E, Cervia C, Nilsson J, Boyman O, Saleh L, Spanaus K, von Eckardstein A, Schaer DJ, Ban N, Tsai CJ, Marino J, Schertler GF, Ebert N, Thiel V, Gottschalk J, Frey BM, Reimann RR, Hornemann S, Ring AM, Knowles TP, Puhan MA, Althaus CL, Xenarios I, Stuart DI, Aguzzi A. Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region. iScience 2023; 26:105928. [PMID: 36619367 PMCID: PMC9811913 DOI: 10.1016/j.isci.2023.105928] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/18/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Effective public health measures against SARS-CoV-2 require granular knowledge of population-level immune responses. We developed a Tripartite Automated Blood Immunoassay (TRABI) to assess the IgG response against three SARS-CoV-2 proteins. We used TRABI for continuous seromonitoring of hospital patients and blood donors (n = 72'250) in the canton of Zurich from December 2019 to December 2020 (pre-vaccine period). We found that antibodies waned with a half-life of 75 days, whereas the cumulative incidence rose from 2.3% in June 2020 to 12.2% in mid-December 2020. A follow-up health survey indicated that about 10% of patients infected with wildtype SARS-CoV-2 sustained some symptoms at least twelve months post COVID-19. Crucially, we found no evidence of a difference in long-term complications between those whose infection was symptomatic and those with asymptomatic acute infection. The cohort of asymptomatic SARS-CoV-2-infected subjects represents a resource for the study of chronic and possibly unexpected sequelae.
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Affiliation(s)
- Marc Emmenegger
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Elena De Cecco
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - David Lamparter
- Health2030 Genome Center, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Raphaël P.B. Jacquat
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
| | - Dominik Menges
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zürich, Switzerland
| | - Tala Ballouz
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zürich, Switzerland
| | - Daniel Ebner
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, England
| | - Matthias M. Schneider
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | - Berre Doğançay
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Jingjing Guo
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Anne Wiedmer
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Julie Domange
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Marigona Imeri
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Rita Moos
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Chryssa Zografou
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Leyla Batkitar
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Lidia Madrigal
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Dezirae Schneider
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Chiara Trevisan
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | | | | | - Irina L. Dubach
- Division of Internal Medicine, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Catherine K. Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Vasilis Kosmoliaptsis
- Department of Surgery, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Tomas Malinauskas
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | | | - Ray Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford OX11 0FA, UK
| | - Stephanie Hatch
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, England
| | - Juthathip Mongkolsapaya
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gavin R. Screaton
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - John D. Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Florence Pojer
- Protein Production and Structure Core Facility, EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland
| | - Kelvin Lau
- Protein Production and Structure Core Facility, EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland
| | - David Hacker
- Protein Production and Structure Core Facility, EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland
| | | | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8006 Zurich, Switzerland
| | - Lanja Saleh
- Institute of Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Katharina Spanaus
- Institute of Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | | | - Dominik J. Schaer
- Division of Internal Medicine, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Ching-Ju Tsai
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Jacopo Marino
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Gebhard F.X. Schertler
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology, 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Jochen Gottschalk
- Regional Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland
| | - Beat M. Frey
- Regional Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland
| | - Regina R. Reimann
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Simone Hornemann
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Aaron M. Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tuomas P.J. Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Milo A. Puhan
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zürich, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
| | - Ioannis Xenarios
- Health2030 Genome Center, 9 Chemin des Mines, 1202 Geneva, Switzerland
- Agora Center, University of Lausanne, 25 Avenue du Bugnon, 1005 Lausanne, Switzerland
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
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Riou J, Hauser A, Fesser A, Althaus CL, Egger M, Konstantinoudis G. Direct and indirect effects of the COVID-19 pandemic on mortality in Switzerland. Nat Commun 2023; 14:90. [PMID: 36609356 PMCID: PMC9817462 DOI: 10.1038/s41467-022-35770-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
The direct and indirect impact of the COVID-19 pandemic on population-level mortality is of concern to public health but challenging to quantify. Using data for 2011-2019, we applied Bayesian models to predict the expected number of deaths in Switzerland and compared them with laboratory-confirmed COVID-19 deaths from February 2020 to April 2022 (study period). We estimated that COVID-19-related mortality was underestimated by a factor of 0.72 (95% credible interval [CrI]: 0.46-0.78). After accounting for COVID-19 deaths, the observed mortality was -4% (95% CrI: -8 to 0) lower than expected. The deficit in mortality was concentrated in age groups 40-59 (-12%, 95%CrI: -19 to -5) and 60-69 (-8%, 95%CrI: -15 to -2). Although COVID-19 control measures may have negative effects, after subtracting COVID-19 deaths, there were fewer deaths in Switzerland during the pandemic than expected, suggesting that any negative effects of control measures were offset by the positive effects. These results have important implications for the ongoing debate about the appropriateness of COVID-19 control measures.
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Affiliation(s)
- Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,Federal Office of Public Health, Bern, Switzerland
| | - Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,Federal Office of Public Health, Bern, Switzerland
| | - Anna Fesser
- Federal Office of Public Health, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - Garyfallos Konstantinoudis
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.
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Reichmuth ML, Hodcroft EB, Riou J, Neher RA, Hens N, Althaus CL. Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021. Epidemics 2022; 41:100654. [PMID: 36444785 PMCID: PMC9671612 DOI: 10.1016/j.epidem.2022.100654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/01/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022] Open
Abstract
During the summers of 2020 and 2021, the number of confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Switzerland remained at relatively low levels, but grew steadily over time. It remains unclear to what extent epidemic growth during these periods was a result of the relaxation of local control measures or increased traveling and subsequent importation of cases. A better understanding of the role of cross-border-associated cases (imports) on the local epidemic dynamics will help to inform future surveillance strategies. We analyzed routine surveillance data of confirmed cases of SARS-CoV-2 in Switzerland from 1 June to 30 September 2020 and 2021. We used a stochastic branching process model that accounts for superspreading of SARS-CoV-2 to simulate epidemic trajectories in absence and in presence of imports during summer 2020 and 2021. The Swiss Federal Office of Public Health reported 22,919 and 145,840 confirmed cases of SARS-CoV-2 from 1 June to 30 September 2020 and 2021, respectively. Among cases with known place of exposure, 27% (3,276 of 12,088) and 25% (1,110 of 4,368) reported an exposure abroad in 2020 and 2021, respectively. Without considering the impact of imported cases, the steady growth of confirmed cases during summer periods would be consistent with a value of Re that is significantly above the critical threshold of 1. In contrast, we estimated Re at 0.84 (95% credible interval, CrI: 0.78-0.90) in 2020 and 0.82 (95% CrI: 0.74-0.90) in 2021 when imported cases were taken into account, indicating that the local Re was below the critical threshold of 1 during summer. In Switzerland, cross-border-associated SARS-CoV-2 cases had a considerable impact on the local transmission dynamics and can explain the steady growth of the epidemic during the summers of 2020 and 2021.
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Affiliation(s)
- Martina L. Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland,Correspondence to: Institute of Social and Preventive Medicine, University of Bern, Mittelstrasse 43, CH-3012 Bern, Switzerland
| | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland,Federal Office of Public Health, Liebefeld, Switzerland
| | - Richard A. Neher
- Swiss Institute of Bioinformatics, Lausanne, Switzerland,Biozentrum, University of Basel, Basel, Switzerland
| | - Niel Hens
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium,Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Gressani O, Wallinga J, Althaus CL, Hens N, Faes C. EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number. PLoS Comput Biol 2022; 18:e1010618. [PMID: 36215319 PMCID: PMC9584461 DOI: 10.1371/journal.pcbi.1010618] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 10/20/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022] Open
Abstract
In infectious disease epidemiology, the instantaneous reproduction number [Formula: see text] is a time-varying parameter defined as the average number of secondary infections generated by an infected individual at time t. It is therefore a crucial epidemiological statistic that assists public health decision makers in the management of an epidemic. We present a new Bayesian tool (EpiLPS) for robust estimation of the time-varying reproduction number. The proposed methodology smooths the epidemic curve and allows to obtain (approximate) point estimates and credible intervals of [Formula: see text] by employing the renewal equation, using Bayesian P-splines coupled with Laplace approximations of the conditional posterior of the spline vector. Two alternative approaches for inference are presented: (1) an approach based on a maximum a posteriori argument for the model hyperparameters, delivering estimates of [Formula: see text] in only a few seconds; and (2) an approach based on a Markov chain Monte Carlo (MCMC) scheme with underlying Langevin dynamics for efficient sampling of the posterior target distribution. Case counts per unit of time are assumed to follow a negative binomial distribution to account for potential overdispersion in the data that would not be captured by a classic Poisson model. Furthermore, after smoothing the epidemic curve, a "plug-in'' estimate of the reproduction number can be obtained from the renewal equation yielding a closed form expression of [Formula: see text] as a function of the spline parameters. The approach is extremely fast and free of arbitrary smoothing assumptions. EpiLPS is applied on data of SARS-CoV-1 in Hong-Kong (2003), influenza A H1N1 (2009) in the USA and on the SARS-CoV-2 pandemic (2020-2021) for Belgium, Portugal, Denmark and France.
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Affiliation(s)
- Oswaldo Gressani
- Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), Data Science Institute, Hasselt University, Hasselt, Belgium,* E-mail:
| | - Jacco Wallinga
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands,Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Niel Hens
- Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), Data Science Institute, Hasselt University, Hasselt, Belgium,Centre for Health Economics Research and Modelling Infectious Diseases, Vaxinfectio, University of Antwerp, Antwerp, Belgium
| | - Christel Faes
- Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), Data Science Institute, Hasselt University, Hasselt, Belgium
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Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Makatini Z, Moyo S, Amoako DG, Baxter C, Althaus CL, Anyaneji UJ, Kekana D, Viana R, Giandhari J, Lessells RJ, Maponga T, Maruapula D, Choga W, Matshaba M, Mbulawa MB, Msomi N, Naidoo Y, Pillay S, Sanko TJ, San JE, Scott L, Singh L, Magini NA, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht FK, Venter M, Chiloane G, McIntyre C, O'Toole A, Ruis C, Peacock TP, Roemer C, Kosakovsky Pond SL, Williamson C, Pybus OG, Bhiman JN, Glass A, Martin DP, Jackson B, Rambaut A, Laguda-Akingba O, Gaseitsiwe S, von Gottberg A, de Oliveira T. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat Med 2022; 28:1785-1790. [PMID: 35760080 PMCID: PMC9499863 DOI: 10.1038/s41591-022-01911-2] [Citation(s) in RCA: 358] [Impact Index Per Article: 179.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/21/2022] [Indexed: 11/09/2022]
Abstract
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kathleen Subramoney
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zinhle Makatini
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Daniel G Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dikeledi Kekana
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Wonderful Choga
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Mpaphi B Mbulawa
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nonkululeko A Magini
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Wendy Stevens
- Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa
| | - Graeme Dor
- National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Florette K Treurnicht
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Georginah Chiloane
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Caitlyn McIntyre
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Aine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Carolyn Williamson
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Jinal N Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Allison Glass
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Lancet Laboratories, Johannesburg, South Africa
| | - Darren P Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Oluwakemi Laguda-Akingba
- NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
- Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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9
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Giovanetti M, Fonseca V, Wilkinson E, Tegally H, San EJ, Althaus CL, Xavier J, Nanev Slavov S, Viala VL, Ranieri Jerônimo Lima A, Ribeiro G, Souza-Neto JA, Fukumasu H, Lehmann Coutinho L, Venancio da Cunha R, Freitas C, Campelo de A e Melo CF, Navegantes de Araújo W, Do Carmo Said RF, Almiron M, de Oliveira T, Coccuzzo Sampaio S, Elias MC, Covas DT, Holmes EC, Lourenço J, Kashima S, de Alcantara LCJ. Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic. Virus Evol 2022; 8:veac024. [PMID: 35371559 PMCID: PMC8971541 DOI: 10.1093/ve/veac024] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 11/14/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged variant of concern (VOC) that was first detected in early January 2021. This variant was estimated to be responsible for more than 96 per cent of cases reported between January and June 2021, being associated with increased transmissibility and disease severity, a reduction in neutralization antibodies and effectiveness of treatments or vaccines, and diagnostic detection failure. Here we show that, following several importations predominantly from the USA, the Delta variant rapidly replaced Gamma after July 2021. However, in contrast to what was seen in other countries, the rapid spread of Delta did not lead to a large increase in the number of cases and deaths reported in Brazil. We suggest that this was likely due to the relatively successful early vaccination campaign coupled with natural immunity acquired following prior infection with Gamma. Our data reinforce reports of the increased transmissibility of the Delta variant and, considering the increasing concern due to the recently identified Omicron variant, argues for the necessity to strengthen genomic monitoring on a national level to quickly detect the emergence and spread of other VOCs that might threaten global health.
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Affiliation(s)
| | | | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 238 Mazisi Kunene Rd, Glenwood, Durban 4041, South Africa,Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Banhoek Road & Joubert Street, Stellenbosch 7600, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 238 Mazisi Kunene Rd, Glenwood, Durban 4041, South Africa,Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Banhoek Road & Joubert Street, Stellenbosch 7600, South Africa
| | - Emmanuel James San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 238 Mazisi Kunene Rd, Glenwood, Durban 4041, South Africa,Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Banhoek Road & Joubert Street, Stellenbosch 7600, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Hochschulstrasse 6, Bern 3012, Switzerland
| | - Joilson Xavier
- Laboratorio de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais 31270-901, Brazil,Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Rua Conde Pereira Carneiro, 80 Gameleira, Belo Horizonte, Minas Gerais 30510-010, Brazil
| | - Svetoslav Nanev Slavov
- Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, University of São Paulo, R. Quintino Bocaiuva, nº 470 - Centro, Ribeirão Preto, SP 14015-160, Brazil
| | - Vincent Louis Viala
- Butantan Institute, Avenida Doutor Vital Brasil, 1500 - Butantã, Sao Paulo - SP, Brazil
| | | | - Gabriela Ribeiro
- Butantan Institute, Avenida Doutor Vital Brasil, 1500 - Butantã, Sao Paulo - SP, Brazil
| | - Jayme A Souza-Neto
- School of Agricultural Sciences, São Paulo State University (UNESP), R. Quintino Bocaiuva, nº 470, Botucatu 05508-900, Brazil
| | | | - Luiz Lehmann Coutinho
- Centro de Genômica Funcional da ESALQ, University of São Paulo, R. Quintino Bocaiuva, nº 470, Piracicaba, SP, Brazil
| | - Rivaldo Venancio da Cunha
- Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Carla Freitas
- Coordenacão Geral dos Laboratórios de Saúde Publica/Secretaria de Vigilância em Saúde, Ministério da Saúde (CGLAB/SVS-MS), Esplanada dos Ministérios - Bloco G - Edifício Sede - CEP, Brasília, Distrito Federal 70058-900, Brazil
| | - Carlos F Campelo de A e Melo
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Lote 19 - Avenida das Nações, SEN - Asa Norte, Brasília, Distrito Federal 70312-970, Brazil
| | - Wildo Navegantes de Araújo
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Lote 19 - Avenida das Nações, SEN - Asa Norte, Brasília, Distrito Federal 70312-970, Brazil
| | - Rodrigo Fabiano Do Carmo Said
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Lote 19 - Avenida das Nações, SEN - Asa Norte, Brasília, Distrito Federal 70312-970, Brazil
| | - Maria Almiron
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Lote 19 - Avenida das Nações, SEN - Asa Norte, Brasília, Distrito Federal 70312-970, Brazil
| | | | | | - Maria Carolina Elias
- Department of Zoology, Peter Medawar Building, University of Oxford, 1a Mansfield Rd, Oxford OX1 3SZ, UK
| | - Dimas Tadeu Covas
- Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, University of São Paulo, R. Quintino Bocaiuva, nº 470 - Centro, Ribeirão Preto, SP 14015-160, Brazil,Butantan Institute, Avenida Doutor Vital Brasil, 1500 - Butantã, Sao Paulo - SP, Brazil
| | | | - José Lourenço
- Department of Zoology, Peter Medawar Building, University of Oxford, 1a Mansfield Rd, Oxford OX1 3SZ, UK,Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, Lisbon 1749-016, Portugal
| | - Simone Kashima
- Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, University of São Paulo, R. Quintino Bocaiuva, nº 470 - Centro, Ribeirão Preto, SP 14015-160, Brazil
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10
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Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 2022; 603:679-686. [PMID: 35042229 PMCID: PMC8942855 DOI: 10.1038/s41586-022-04411-y] [Citation(s) in RCA: 918] [Impact Index Per Article: 459.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 01/02/2023]
Abstract
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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Affiliation(s)
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Daniel G Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Phillip A Bester
- Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa
- Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Michaela Davids
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Deelan Doolabh
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diana Hardie
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nei-Yuan Hsiao
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
| | - Arash Iranzadeh
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Rageema Joseph
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Legodile Koopile
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | | | - Lesego Kuate-Lere
- Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Oluwakemi Laguda-Akingba
- NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
- Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa
| | - Onalethatha Lesetedi-Mafoko
- Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Arisha Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Boitshoko Mahlangu
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Kamela Mahlakwane
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa
| | - Zinhle Makatini
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Gert Marais
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Kereng Masupu
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Mogomotsi Matshaba
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, TX, USA
| | - Simnikiwe Mayaphi
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Nokuzola Mbhele
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mpaphi B Mbulawa
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Adriano Mendes
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Koleka Mlisana
- National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Anele Mnguni
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kgomotso Moruisi
- Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Mosepele Mosepele
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Gerald Motsatsi
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Modisa S Motswaledi
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Thongbotho Mphoyakgosi
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa
| | - Peter N Mwangi
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Noxolo Ntuli
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Martin Nyaga
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Lucier Olubayo
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Botshelo Radibe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Amy Strydom
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Kathleen Subramoney
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Naume Tebeila
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Joseph Tsui
- Department of Zoology, University of Oxford, Oxford, UK
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Constantinos K Wibmer
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Boitumelo Zuze
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dominique Goedhals
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- PathCare Vermaak, Pretoria, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa
| | - Florette Treurnicht
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Marietje Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Jinal Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Allison Glass
- Lancet Laboratories, Johannesburg, South Africa
- Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Darren P Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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11
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Kostoulas P, Meletis E, Pateras K, Eusebi P, Kostoulas T, Furuya-Kanamori L, Speybroeck N, Denwood M, Doi SAR, Althaus CL, Kirkeby C, Rohani P, Dhand NK, Peñalvo JL, Thabane L, BenMiled S, Sharifi H, Walter SD. The epidemic volatility index, a novel early warning tool for identifying new waves in an epidemic. Sci Rep 2021; 11:23775. [PMID: 34893634 PMCID: PMC8664819 DOI: 10.1038/s41598-021-02622-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022] Open
Abstract
Early warning tools are crucial for the timely application of intervention strategies and the mitigation of the adverse health, social and economic effects associated with outbreaks of epidemic potential such as COVID-19. This paper introduces, the Epidemic Volatility Index (EVI), a new, conceptually simple, early warning tool for oncoming epidemic waves. EVI is based on the volatility of newly reported cases per unit of time, ideally per day, and issues an early warning when the volatility change rate exceeds a threshold. Data on the daily confirmed cases of COVID-19 are used to demonstrate the use of EVI. Results from the COVID-19 epidemic in Italy and New York State are presented here, based on the number of confirmed cases of COVID-19, from January 22, 2020, until April 13, 2021. Live daily updated predictions for all world countries and each of the United States of America are publicly available online. For Italy, the overall sensitivity for EVI was 0.82 (95% Confidence Intervals: 0.75; 0.89) and the specificity was 0.91 (0.88; 0.94). For New York, the corresponding values were 0.55 (0.47; 0.64) and 0.88 (0.84; 0.91). Consecutive issuance of early warnings is a strong indicator of main epidemic waves in any country or state. EVI’s application to data from the current COVID-19 pandemic revealed a consistent and stable performance in terms of detecting new waves. The application of EVI to other epidemics and syndromic surveillance tasks in combination with existing early warning systems will enhance our ability to act swiftly and thereby enhance containment of outbreaks.
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Affiliation(s)
| | | | | | - Paolo Eusebi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Theodoros Kostoulas
- Department of Information and Communication Systems Engineering, University of the Aegean, Aegean, Greece
| | - Luis Furuya-Kanamori
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Australia
| | - Niko Speybroeck
- Research Institute of Health and Society (IRSS), Université Catholique de Louvain, 1200, Brussels, Belgium
| | - Matthew Denwood
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Suhail A R Doi
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Carsten Kirkeby
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - Navneet K Dhand
- Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - José L Peñalvo
- Unit of Noncommunicable Diseases, Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lehana Thabane
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | | | - Hamid Sharifi
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Stephen D Walter
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
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12
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Riou J, Dupont C, Bertagnolio S, Gupta RK, Kouyos RD, Egger M, Althaus CL. Correction to: Drivers of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTIs) in nine southern African countries: a modelling study. BMC Infect Dis 2021; 21:1098. [PMID: 34696729 PMCID: PMC8543892 DOI: 10.1186/s12879-021-06791-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Julien Riou
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland.
| | - Carole Dupont
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Silvia Bertagnolio
- HIV/Hepatitis/STI Department, World Health Organization, Geneva, Switzerland
| | - Ravindra K Gupta
- Department of Infection, University College London, London, UK.,Africa Health Research Institute, Durban, South Africa
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland.,Centre for Infectious Disease Epidemiology and Research (CIDER), University of Cape Town, Cap Town, South Africa.,Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Christian L Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
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13
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Keiser O, Agoritsas T, Althaus CL, Azman AS, de Quervain D, Flahault A, Goutaki M, Merglen A, Eckerle I. A public health strategy for SARS-CoV-2, grounded in science, should guide Swiss schools through the coming winter. Swiss Med Wkly 2021; 151:w30086. [PMID: 34652090 DOI: 10.4414/smw.2021.w30086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Olivia Keiser
- Institute of Global Health, Faculty of Medicine, University of Geneva, Switzerland
| | - Thomas Agoritsas
- Department of Medicine, Geneva University Hospitals, Geneva, Switzerland; Faculty of Medicine, University of Geneva, Switzerland; Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Andrew S Azman
- Institute of Global Health, Faculty of Medicine, University of Geneva, Switzerland; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dominique de Quervain
- Transfaculty Research Platform; Division of Cognitive Neuroscience, Department of Psychology; and University Psychiatric Clinics; University of Basel, Switzerland
| | - Antoine Flahault
- Institute of Global Health, Faculty of Medicine, University of Geneva, Switzerland
| | - Myrofora Goutaki
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Arnaud Merglen
- Division of General Paediatrics, University Hospitals of Geneva and Faculty of Medicine, University of Geneva, Switzerland
| | - Isabella Eckerle
- Geneva Centre for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
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14
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Riou J, Dupont C, Bertagnolio S, Gupta RK, Kouyos RD, Egger M, L Althaus C. Drivers of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTIs) in nine southern African countries: a modelling study. BMC Infect Dis 2021; 21:1042. [PMID: 34620119 PMCID: PMC8499543 DOI: 10.1186/s12879-021-06757-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION The rise of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTI) threatens antiretroviral therapy's long-term success (ART). NNRTIs will remain an essential drug for the management of HIV-1 due to safety concerns associated with integrase inhibitors. We fitted a dynamic transmission model to historical data from 2000 to 2018 in nine countries of southern Africa to understand the mechanisms that have shaped the HIV-1 epidemic and the rise of pretreatment NNRTI resistance. METHODS We included data on HIV-1 prevalence, ART coverage, HIV-related mortality, and survey data on pretreatment NNRTI resistance from nine southern Africa countries from a systematic review, UNAIDS and World Bank. Using a Bayesian hierarchical framework, we developed a dynamic transmission model linking data on the HIV-1 epidemic to survey data on NNRTI drug resistance in each country. We estimated the proportion of resistance attributable to unregulated, off-programme use of ART. We examined each national ART programme's vulnerability to NNRTI resistance by defining a fragility index: the ratio of the rate of NNRTI resistance emergence during first-line ART over the rate of switching to second-line ART. We explored associations between fragility and characteristics of the health system of each country. RESULTS The model reliably described the dynamics of the HIV-1 epidemic and NNRTI resistance in each country. Predicted levels of resistance in 2018 ranged between 3.3% (95% credible interval 1.9-7.1) in Mozambique and 25.3% (17.9-33.8) in Eswatini. The proportion of pretreatment NNRTI resistance attributable to unregulated antiretroviral use ranged from 6% (2-14) in Eswatini to 64% (26-85) in Mozambique. The fragility index was low in Botswana (0.01; 0.0-0.11) but high in Namibia (0.48; 0.16-10.17), Eswatini (0.64; 0.23-11.8) and South Africa (1.21; 0.83-9.84). The combination of high fragility of ART programmes and high ART coverage levels was associated with a sharp increase in pretreatment NNRTI resistance. CONCLUSIONS This comparison of nine countries shows that pretreatment NNRTI resistance can be controlled despite high ART coverage levels. This was the case in Botswana, Mozambique, and Zambia, most likely because of better HIV care delivery, including rapid switching to second-line ART of patients failing first-line ART.
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Affiliation(s)
- Julien Riou
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland.
| | - Carole Dupont
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Silvia Bertagnolio
- HIV/Hepatitis/STI Department, World Health Organization, Geneva, Switzerland
| | - Ravindra K Gupta
- Department of Infection, University College London, London, UK
- Africa Health Research Institute, Durban, South Africa
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research (CIDER), University of Cape Town, Cap Town, South Africa
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christian L Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
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15
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Riou J, Panczak R, Althaus CL, Junker C, Perisa D, Schneider K, Criscuolo NG, Low N, Egger M. Socioeconomic position and the COVID-19 care cascade from testing to mortality in Switzerland: a population-based analysis. Lancet Public Health 2021; 6:e683-e691. [PMID: 34252364 PMCID: PMC8270761 DOI: 10.1016/s2468-2667(21)00160-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND The inverse care law states that disadvantaged populations need more health care than advantaged populations but receive less. Gaps in COVID-19-related health care and infection control are not well understood. We aimed to examine inequalities in health in the care cascade from testing for SARS-CoV-2 to COVID-19-related hospitalisation, intensive care unit (ICU) admission, and death in Switzerland, a wealthy country strongly affected by the pandemic. METHODS We analysed surveillance data reported to the Swiss Federal Office of Public Health from March 1, 2020, to April 16, 2021, and 2018 population data. We geocoded residential addresses of notifications to identify the Swiss neighbourhood index of socioeconomic position (Swiss-SEP). The index describes 1·27 million small neighbourhoods of approximately 50 households each on the basis of rent per m2, education and occupation of household heads, and crowding. We used negative binomial regression models to calculate incidence rate ratios (IRRs) with 95% credible intervals (CrIs) of the association between ten groups of the Swiss-SEP index defined by deciles (1=lowest, 10=highest) and outcomes. Models were adjusted for sex, age, canton, and wave of the epidemic (before or after June 8, 2020). We used three different denominators: the general population, the number of tests, and the number of positive tests. FINDINGS Analyses were based on 4 129 636 tests, 609 782 positive tests, 26 143 hospitalisations, 2432 ICU admissions, 9383 deaths, and 8 221 406 residents. Comparing the highest with the lowest Swiss-SEP group and using the general population as the denominator, more tests were done among people living in neighbourhoods of highest SEP compared with lowest SEP (adjusted IRR 1·18 [95% CrI 1·02-1·36]). Among tested people, test positivity was lower (0·75 [0·69-0·81]) in neighbourhoods of highest SEP than of lowest SEP. Among people testing positive, the adjusted IRR was 0·68 (0·62-0·74) for hospitalisation, was 0·54 (0·43-0·70) for ICU admission, and 0·86 (0·76-0·99) for death. The associations between neighbourhood SEP and outcomes were stronger in younger age groups and we found heterogeneity between areas. INTERPRETATION The inverse care law and socioeconomic inequalities were evident in Switzerland during the COVID-19 epidemic. People living in neighbourhoods of low SEP were less likely to be tested but more likely to test positive, be admitted to hospital, or die, compared with those in areas of high SEP. It is essential to continue to monitor testing for SARS-CoV-2, access and uptake of COVID-19 vaccination and outcomes of COVID-19. Governments and health-care systems should address this pandemic of inequality by taking measures to reduce health inequalities in response to the SARS-CoV-2 pandemic. FUNDING Swiss Federal Office of Public Health, Swiss National Science Foundation, EU Horizon 2020, Branco Weiss Foundation.
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Affiliation(s)
- Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Federal Office of Public Health, Liebefeld, Switzerland
| | - Radoslaw Panczak
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Damir Perisa
- Federal Office of Public Health, Liebefeld, Switzerland
| | | | - Nicola G Criscuolo
- Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa.
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16
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Chen C, Nadeau SA, Topolsky I, Manceau M, Huisman JS, Jablonski KP, Fuhrmann L, Dreifuss D, Jahn K, Beckmann C, Redondo M, Noppen C, Risch L, Risch M, Wohlwend N, Kas S, Bodmer T, Roloff T, Stange M, Egli A, Eckerle I, Kaiser L, Denes R, Feldkamp M, Nissen I, Santacroce N, Burcklen E, Aquino C, de Gouvea AC, Moccia MD, Grüter S, Sykes T, Opitz L, White G, Neff L, Popovic D, Patrignani A, Tracy J, Schlapbach R, Dermitzakis ET, Harshman K, Xenarios I, Pegeot H, Cerutti L, Penet D, Blin A, Elies M, Althaus CL, Beisel C, Beerenwinkel N, Ackermann M, Stadler T. Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland. Epidemics 2021; 37:100480. [PMID: 34488035 PMCID: PMC8452947 DOI: 10.1016/j.epidem.2021.100480] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/30/2021] [Accepted: 06/15/2021] [Indexed: 01/15/2023] Open
Abstract
Background In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a transmission fitness advantage of around 40–80 % (Volz et al., 2021; Leung et al., 2021; Davies et al., 2021). Aim This study aims to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time based on data from Switzerland. Methods We generated whole genome sequences from 11.8 % of all confirmed SARS-CoV-2 cases in Switzerland between 14 December 2020 and 11 March 2021. Based on these data, we determine the daily frequency of the B.1.1.7 variant and quantify the variant’s transmission fitness advantage on a national and a regional scale. Results We estimate B.1.1.7 had a transmission fitness advantage of 43–52 % compared to the other variants circulating in Switzerland during the study period. Further, we estimate B.1.1.7 had a reproductive number above 1 from 01 January 2021 until the end of the study period, compared to below 1 for the other variants. Specifically, we estimate the reproductive number for B.1.1.7 was 1.24 [1.07–1.41] from 01 January until 17 January 2021 and 1.18 [1.06–1.30] from 18 January until 01 March 2021 based on the whole genome sequencing data. From 10 March to 16 March 2021, once B.1.1.7 was dominant, we estimate the reproductive number was 1.14 [1.00–1.26] based on all confirmed cases. For reference, Switzerland applied more non-pharmaceutical interventions to combat SARS-CoV-2 on 18 January 2021 and lifted some measures again on 01 March 2021. Conclusion The observed increase in B.1.1.7 frequency in Switzerland during the study period is as expected based on observations in the UK. In absolute numbers, B.1.1.7 increased exponentially with an estimated doubling time of around 2–3.5 weeks. To monitor the ongoing spread of B.1.1.7, our plots are available online.
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Affiliation(s)
- Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Sarah Ann Nadeau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Marc Manceau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Jana S Huisman
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland; Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | | | | | | | - Lorenz Risch
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | - Martin Risch
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | | | - Sinem Kas
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | | | - Tim Roloff
- Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Madlen Stange
- Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Isabella Eckerle
- Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Rebecca Denes
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Mirjam Feldkamp
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ina Nissen
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Natascha Santacroce
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Elodie Burcklen
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | | | - Maria Domenica Moccia
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Simon Grüter
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Timothy Sykes
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Griffin White
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Laura Neff
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Doris Popovic
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Andrea Patrignani
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Jay Tracy
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Emmanouil T Dermitzakis
- Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
| | - Keith Harshman
- Health 2030 Genome Center, Geneva, Switzerland; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
| | - Ioannis Xenarios
- Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
| | | | | | | | | | | | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
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17
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Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, González-Candelas F, Stadler T, Neher RA. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature 2021; 595:707-712. [PMID: 34098568 DOI: 10.1038/s41586-021-03677-y] [Citation(s) in RCA: 255] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/28/2021] [Indexed: 11/09/2022]
Abstract
Following its emergence in late 2019, the spread of SARS-CoV-21,2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail3-5. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel within Europe resumed in the summer of 2020. Here we report on a SARS-CoV-2 variant, 20E (EU1), that was identified in Spain in early summer 2020 and subsequently spread across Europe. We find no evidence that this variant has increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions, we estimate that 20E (EU1) was introduced hundreds of times to European countries by summertime travellers, which is likely to have undermined local efforts to minimize infection with SARS-CoV-2. Our results illustrate how a variant can rapidly become dominant even in the absence of a substantial transmission advantage in favourable epidemiological settings. Genomic surveillance is critical for understanding how travel can affect transmission of SARS-CoV-2, and thus for informing future containment strategies as travel resumes.
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Affiliation(s)
- Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland. .,Swiss Institute of Bioinformatics, Basel, Switzerland. .,Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Moira Zuber
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Nadeau
- Swiss Institute of Bioinformatics, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Timothy G Vaughan
- Swiss Institute of Bioinformatics, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Katharine H D Crawford
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Martina L Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | - Iñaki Comas
- Tuberculosis Genomics Unit, Biomedicine Institute of Valencia (IBV-CSIC), Valencia, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando González-Candelas
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | | | - Tanja Stadler
- Swiss Institute of Bioinformatics, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland. .,Swiss Institute of Bioinformatics, Basel, Switzerland.
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18
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Menges D, Aschmann HE, Moser A, Althaus CL, von Wyl V. A Data-Driven Simulation of the Exposure Notification Cascade for Digital Contact Tracing of SARS-CoV-2 in Zurich, Switzerland. JAMA Netw Open 2021; 4:e218184. [PMID: 33929521 PMCID: PMC8087953 DOI: 10.1001/jamanetworkopen.2021.8184] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Importance Digital contact tracing (DCT) apps have been released in several countries to help interrupt SARS-CoV-2 transmission chains. However, the effect of DCT on pandemic mitigation remains to be demonstrated. Objective To estimate key populations and performance indicators along the exposure notification cascade of the SwissCovid DCT app in a clearly defined regional and temporal context. Design, Setting, and Participants This comparative effectiveness study was based on a simulation informed by measured data from issued quarantine recommendations and positive SARS-CoV-2 test results after DCT exposure notifications in the canton of Zurich. A stochastic model was developed to re-create the DCT notification cascade for Zurich. Population sizes at each cascade step were estimated using triangulation based on publicly available administrative and observational research data for the study duration from September 1 to October 31, 2020. The resultant estimates were checked for internal consistency and consistency with upstream or downstream estimates in the cascade. Stochastic sampling from data-informed parameter distributions was performed to explore the robustness of results. Subsequently, key performance indicators were evaluated to assess the potential contribution of DCT compared with manual contact tracing. Main Outcomes and Measures Receiving a voluntary quarantine recommendation and/or a positive SARS-CoV-2 test result after exposure notification. Results In September 2020, 537 app users received a positive SARS-CoV-2 test result in Zurich, 324 of whom received and entered an upload authorization code. This code triggered an app notification for an estimated 1374 (95% simulation interval [SI], 932-2586) proximity contacts and led to 722 information hotline calls, with an estimated 170 callers (95% SI, 154-186) receiving a quarantine recommendation. An estimated 939 (95% SI, 720-1127) notified app users underwent testing for SARS-CoV-2, of whom 30 (95% SI, 23-36) had positive results after an app notification. Key indicator evaluations revealed that the DCT app triggered quarantine recommendations for the equivalent of 5% of all exposed contacts placed in quarantine by manual contact tracing. For every 10.9 (95% SI, 7.6-15.6) upload authorization codes entered in the app, 1 contact had positive test results for SARS-CoV-2 after app notification. Longitudinal indicator analyses demonstrated bottlenecks in the notification cascade, because capacity limits were reached owing to an increased incidence of SARS-CoV-2 infection in October 2020. Conclusions and Relevance In this simulation study of the notification cascade of the SwissCovid DCT app, receipt of exposure notifications was associated with quarantine recommendations and identification of SARS-CoV-2-positive cases. These findings in notified proximity contacts reflect important intermediary steps toward transmission prevention.
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Affiliation(s)
- Dominik Menges
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Hélène E. Aschmann
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - André Moser
- CTU Bern, University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Viktor von Wyl
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
- Institute for Implementation Science in Health Care, University of Zurich, Zurich, Switzerland
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19
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Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, González Candelas F, Stadler T, Neher RA. Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020. medRxiv 2021:2020.10.25.20219063. [PMID: 33269368 PMCID: PMC7709189 DOI: 10.1101/2020.10.25.20219063] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Following its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic resulting in unprecedented efforts to reduce transmission and develop therapies and vaccines (WHO Emergency Committee, 2020; Zhu et al., 2020). Rapidly generated viral genome sequences have allowed the spread of the virus to be tracked via phylogenetic analysis (Worobey et al., 2020; Hadfield et al., 2018; Pybus et al., 2020). While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced, allowing continent-specific variants to emerge. However, within Europe travel resumed in the summer of 2020, and the impact of this travel on the epidemic is not well understood. Here we report on a novel SARS-CoV-2 variant, 20E (EU1), that emerged in Spain in early summer, and subsequently spread to multiple locations in Europe. We find no evidence of increased transmissibility of this variant, but instead demonstrate how rising incidence in Spain, resumption of travel across Europe, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions and quarantine requirements, we estimate 20E (EU1) was introduced hundreds of times to countries across Europe by summertime travellers, likely undermining local efforts to keep SARS-CoV-2 cases low. Our results demonstrate how a variant can rapidly become dominant even in absence of a substantial transmission advantage in favorable epidemiological settings. Genomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes.
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Affiliation(s)
- Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Moira Zuber
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Timothy G Vaughan
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Katharine H D Crawford
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Martina L Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98103, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Mateo
- Kido Dynamics SA, Avenue de Sevelin 46, 1004 Lausanne, Switzerland
| | - Alberto Hernando
- Kido Dynamics SA, Avenue de Sevelin 46, 1004 Lausanne, Switzerland
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Biomedicine Institute of Valencia (IBV-CSIC), Valencia, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- on behalf or the SeqCOVID-SPAIN consortium
| | - Fernando González Candelas
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- on behalf or the SeqCOVID-SPAIN consortium
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
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20
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Kremer C, Torneri A, Boesmans S, Meuwissen H, Verdonschot S, Driessche KV, Althaus CL, Faes C, Hens N. Quantifying superspreading for COVID-19 using Poisson mixture distributions. medRxiv 2020:2020.11.27.20239657. [PMID: 34013290 PMCID: PMC8132264 DOI: 10.1101/2020.11.27.20239657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The number of secondary cases is an important parameter for the control of infectious diseases. When individual variation in disease transmission is present, like for COVID-19, the number of secondary cases is often modelled using a negative binomial distribution. However, this may not be the best distribution to describe the underlying transmission process. We propose the use of three other offspring distributions to quantify heterogeneity in transmission, and we assess the possible bias in estimates of the offspring mean and its overdispersion when the data generating distribution is different from the one used for inference. We find that overdispersion estimates may be biased when there is a substantial amount of heterogeneity, and that the use of other distributions besides the negative binomial should be considered. We revisit three previously analysed COVID-19 datasets and quantify the proportion of cases responsible for 80% of transmission, p 80% , while acknowledging the variation arising from the assumed offspring distribution. We find that the number of secondary cases for these datasets is better described by a Poisson-lognormal distribution.
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21
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Ashcroft P, Huisman JS, Lehtinen S, Bouman JA, Althaus CL, Regoes RR, Bonhoeffer S. COVID-19 infectivity profile correction. Swiss Med Wkly 2020; 150:w20336. [PMID: 32757177 DOI: 10.4414/smw.2020.20336] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Peter Ashcroft
- Institute of Integrative Biology, ETH Zurich, Switzerland
| | - Jana S Huisman
- Institute of Integrative Biology, ETH Zurich, Switzerland
| | - Sonja Lehtinen
- Institute of Integrative Biology, ETH Zurich, Switzerland
| | | | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
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22
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Hauser A, Counotte MJ, Margossian CC, Konstantinoudis G, Low N, Althaus CL, Riou J. Estimation of SARS-CoV-2 mortality during the early stages of an epidemic: A modeling study in Hubei, China, and six regions in Europe. PLoS Med 2020; 17:e1003189. [PMID: 32722715 DOI: 10.1101/2020.08.20.20177311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/23/2020] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND As of 16 May 2020, more than 4.5 million cases and more than 300,000 deaths from disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported. Reliable estimates of mortality from SARS-CoV-2 infection are essential for understanding clinical prognosis, planning healthcare capacity, and epidemic forecasting. The case-fatality ratio (CFR), calculated from total numbers of reported cases and reported deaths, is the most commonly reported metric, but it can be a misleading measure of overall mortality. The objectives of this study were to (1) simulate the transmission dynamics of SARS-CoV-2 using publicly available surveillance data and (2) infer estimates of SARS-CoV-2 mortality adjusted for biases and examine the CFR, the symptomatic case-fatality ratio (sCFR), and the infection-fatality ratio (IFR) in different geographic locations. METHOD AND FINDINGS We developed an age-stratified susceptible-exposed-infected-removed (SEIR) compartmental model describing the dynamics of transmission and mortality during the SARS-CoV-2 epidemic. Our model accounts for two biases: preferential ascertainment of severe cases and right-censoring of mortality. We fitted the transmission model to surveillance data from Hubei Province, China, and applied the same model to six regions in Europe: Austria, Bavaria (Germany), Baden-Württemberg (Germany), Lombardy (Italy), Spain, and Switzerland. In Hubei, the baseline estimates were as follows: CFR 2.4% (95% credible interval [CrI] 2.1%-2.8%), sCFR 3.7% (3.2%-4.2%), and IFR 2.9% (2.4%-3.5%). Estimated measures of mortality changed over time. Across the six locations in Europe, estimates of CFR varied widely. Estimates of sCFR and IFR, adjusted for bias, were more similar to each other but still showed some degree of heterogeneity. Estimates of IFR ranged from 0.5% (95% CrI 0.4%-0.6%) in Switzerland to 1.4% (1.1%-1.6%) in Lombardy, Italy. In all locations, mortality increased with age. Among individuals 80 years or older, estimates of the IFR suggest that the proportion of all those infected with SARS-CoV-2 who will die ranges from 20% (95% CrI 16%-26%) in Switzerland to 34% (95% CrI 28%-40%) in Spain. A limitation of the model is that count data by date of onset are required, and these are not available in all countries. CONCLUSIONS We propose a comprehensive solution to the estimation of SARS-Cov-2 mortality from surveillance data during outbreaks. The CFR is not a good predictor of overall mortality from SARS-CoV-2 and should not be used for evaluation of policy or comparison across settings. Geographic differences in IFR suggest that a single IFR should not be applied to all settings to estimate the total size of the SARS-CoV-2 epidemic in different countries. The sCFR and IFR, adjusted for right-censoring and preferential ascertainment of severe cases, are measures that can be used to improve and monitor clinical and public health strategies to reduce the deaths from SARS-CoV-2 infection.
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Affiliation(s)
- Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Michel J Counotte
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Charles C Margossian
- Department of Statistics, Columbia University, New York, New York, United States of America
| | - Garyfallos Konstantinoudis
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Division of infectious diseases, Federal Office of Public Health, Bern, Switzerland
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23
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Hauser A, Counotte MJ, Margossian CC, Konstantinoudis G, Low N, Althaus CL, Riou J. Estimation of SARS-CoV-2 mortality during the early stages of an epidemic: A modeling study in Hubei, China, and six regions in Europe. PLoS Med 2020; 17:e1003189. [PMID: 32722715 PMCID: PMC7386608 DOI: 10.1371/journal.pmed.1003189] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND As of 16 May 2020, more than 4.5 million cases and more than 300,000 deaths from disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported. Reliable estimates of mortality from SARS-CoV-2 infection are essential for understanding clinical prognosis, planning healthcare capacity, and epidemic forecasting. The case-fatality ratio (CFR), calculated from total numbers of reported cases and reported deaths, is the most commonly reported metric, but it can be a misleading measure of overall mortality. The objectives of this study were to (1) simulate the transmission dynamics of SARS-CoV-2 using publicly available surveillance data and (2) infer estimates of SARS-CoV-2 mortality adjusted for biases and examine the CFR, the symptomatic case-fatality ratio (sCFR), and the infection-fatality ratio (IFR) in different geographic locations. METHOD AND FINDINGS We developed an age-stratified susceptible-exposed-infected-removed (SEIR) compartmental model describing the dynamics of transmission and mortality during the SARS-CoV-2 epidemic. Our model accounts for two biases: preferential ascertainment of severe cases and right-censoring of mortality. We fitted the transmission model to surveillance data from Hubei Province, China, and applied the same model to six regions in Europe: Austria, Bavaria (Germany), Baden-Württemberg (Germany), Lombardy (Italy), Spain, and Switzerland. In Hubei, the baseline estimates were as follows: CFR 2.4% (95% credible interval [CrI] 2.1%-2.8%), sCFR 3.7% (3.2%-4.2%), and IFR 2.9% (2.4%-3.5%). Estimated measures of mortality changed over time. Across the six locations in Europe, estimates of CFR varied widely. Estimates of sCFR and IFR, adjusted for bias, were more similar to each other but still showed some degree of heterogeneity. Estimates of IFR ranged from 0.5% (95% CrI 0.4%-0.6%) in Switzerland to 1.4% (1.1%-1.6%) in Lombardy, Italy. In all locations, mortality increased with age. Among individuals 80 years or older, estimates of the IFR suggest that the proportion of all those infected with SARS-CoV-2 who will die ranges from 20% (95% CrI 16%-26%) in Switzerland to 34% (95% CrI 28%-40%) in Spain. A limitation of the model is that count data by date of onset are required, and these are not available in all countries. CONCLUSIONS We propose a comprehensive solution to the estimation of SARS-Cov-2 mortality from surveillance data during outbreaks. The CFR is not a good predictor of overall mortality from SARS-CoV-2 and should not be used for evaluation of policy or comparison across settings. Geographic differences in IFR suggest that a single IFR should not be applied to all settings to estimate the total size of the SARS-CoV-2 epidemic in different countries. The sCFR and IFR, adjusted for right-censoring and preferential ascertainment of severe cases, are measures that can be used to improve and monitor clinical and public health strategies to reduce the deaths from SARS-CoV-2 infection.
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Affiliation(s)
- Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Michel J. Counotte
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Charles C. Margossian
- Department of Statistics, Columbia University, New York, New York, United States of America
| | - Garyfallos Konstantinoudis
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Division of infectious diseases, Federal Office of Public Health, Bern, Switzerland
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Chowdhury R, Heng K, Shawon MSR, Goh G, Okonofua D, Ochoa-Rosales C, Gonzalez-Jaramillo V, Bhuiya A, Reidpath D, Prathapan S, Shahzad S, Althaus CL, Gonzalez-Jaramillo N, Franco OH. Dynamic interventions to control COVID-19 pandemic: a multivariate prediction modelling study comparing 16 worldwide countries. Eur J Epidemiol 2020; 35:389-399. [PMID: 32430840 PMCID: PMC7237242 DOI: 10.1007/s10654-020-00649-w] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/09/2020] [Indexed: 12/15/2022]
Abstract
To date, non-pharmacological interventions (NPI) have been the mainstay for controlling the coronavirus disease-2019 (COVID-19) pandemic. While NPIs are effective in preventing health systems overload, these long-term measures are likely to have significant adverse economic consequences. Therefore, many countries are currently considering to lift the NPIs-increasing the likelihood of disease resurgence. In this regard, dynamic NPIs, with intervals of relaxed social distancing, may provide a more suitable alternative. However, the ideal frequency and duration of intermittent NPIs, and the ideal "break" when interventions can be temporarily relaxed, remain uncertain, especially in resource-poor settings. We employed a multivariate prediction model, based on up-to-date transmission and clinical parameters, to simulate outbreak trajectories in 16 countries, from diverse regions and economic categories. In each country, we then modelled the impacts on intensive care unit (ICU) admissions and deaths over an 18-month period for following scenarios: (1) no intervention, (2) consecutive cycles of mitigation measures followed by a relaxation period, and (3) consecutive cycles of suppression measures followed by a relaxation period. We defined these dynamic interventions based on reduction of the mean reproduction number during each cycle, assuming a basic reproduction number (R0) of 2.2 for no intervention, and subsequent effective reproduction numbers (R) of 0.8 and 0.5 for illustrative dynamic mitigation and suppression interventions, respectively. We found that dynamic cycles of 50-day mitigation followed by a 30-day relaxation reduced transmission, however, were unsuccessful in lowering ICU hospitalizations below manageable limits. By contrast, dynamic cycles of 50-day suppression followed by a 30-day relaxation kept the ICU demands below the national capacities. Additionally, we estimated that a significant number of new infections and deaths, especially in resource-poor countries, would be averted if these dynamic suppression measures were kept in place over an 18-month period. This multi-country analysis demonstrates that intermittent reductions of R below 1 through a potential combination of suppression interventions and relaxation can be an effective strategy for COVID-19 pandemic control. Such a "schedule" of social distancing might be particularly relevant to low-income countries, where a single, prolonged suppression intervention is unsustainable. Efficient implementation of dynamic suppression interventions, therefore, confers a pragmatic option to: (1) prevent critical care overload and deaths, (2) gain time to develop preventive and clinical measures, and (3) reduce economic hardship globally.
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Affiliation(s)
- Rajiv Chowdhury
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
| | - Kevin Heng
- Center for Space and Habitability, University of Bern, Bern, Switzerland
- Department of Physics, Astronomy and Astrophysics Group, University of Warwick, Coventry, UK
| | | | - Gabriel Goh
- OpenAI Artificial Intelligence Research Laboratory, San Francisco, CA, USA
| | - Daisy Okonofua
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Carolina Ochoa-Rosales
- Department of Epidemiology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
- Centro de Vida Saludable, Universidad de Concepción, Concepción, Chile
| | | | - Abbas Bhuiya
- Independent health and population researcher, Dhaka, Bangladesh
| | - Daniel Reidpath
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Shamini Prathapan
- Department of Community Medicine, University of Sri Jayewardenepura, Colombo, Sri Lanka
| | - Sara Shahzad
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Oscar H Franco
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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Cadosch D, Garcia V, Jensen JS, Low N, Althaus CL. Understanding the spread of de novo and transmitted macrolide-resistance in Mycoplasma genitalium. PeerJ 2020; 8:e8913. [PMID: 32292658 PMCID: PMC7147432 DOI: 10.7717/peerj.8913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/15/2020] [Indexed: 01/19/2023] Open
Abstract
Background The rapid spread of azithromycin resistance in sexually transmitted Mycoplasma genitalium infections is a growing concern. It is not yet clear to what degree macrolide resistance in M. genitalium results from the emergence of de novo mutations or the transmission of resistant strains. Methods We developed a compartmental transmission model to investigate the contribution of de novo macrolide resistance mutations to the spread of antimicrobial-resistant M. genitalium. We fitted the model to resistance data from France, Denmark and Sweden, estimated the time point of azithromycin introduction and the rates at which infected individuals receive treatment, and projected the future spread of resistance. Results The high probability of de novo resistance in M. genitalium accelerates the early spread of antimicrobial resistance. The relative contribution of de novo resistance subsequently decreases, and the spread of resistant infections in France, Denmark and Sweden is now mainly driven by transmitted resistance. If treatment with single-dose azithromycin continues at current rates, macrolide-resistant M. genitalium infections will reach 25% (95% confidence interval, CI [9–30]%) in France, 84% (95% CI [36–98]%) in Denmark and 62% (95% CI [48–76]%) in Sweden by 2025. Conclusions Blind treatment of urethritis with single-dose azithromycin continues to select for the spread of macrolide resistant M. genitalium. Clinical management strategies for M. genitalium should limit the unnecessary use of macrolides.
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Affiliation(s)
- Dominique Cadosch
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Victor Garcia
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,School of Life Sciences and Facility Management, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Jørgen S Jensen
- Research Unit for Reproductive Tract Microbiology, Statens Serum Institut, Copenhagen, Denmark
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Salathé M, Althaus CL, Neher R, Stringhini S, Hodcroft E, Fellay J, Zwahlen M, Senti G, Battegay M, Wilder-Smith A, Eckerle I, Egger M, Low N. COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation. Swiss Med Wkly 2020; 150:w20225. [PMID: 32191813 DOI: 10.4414/smw.2020.20225] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Switzerland is among the countries with the highest number of coronavirus disease-2019 (COVID-19) cases per capita in the world. There are likely many people with undetected SARS-CoV-2 infection because testing efforts are currently not detecting all infected people, including some with clinical disease compatible with COVID-19. Testing on its own will not stop the spread of SARS-CoV-2. Testing is part of a strategy. The World Health Organization recommends a combination of measures: rapid diagnosis and immediate isolation of cases, rigorous tracking and precautionary self-isolation of close contacts. In this article, we explain why the testing strategy in Switzerland should be strengthened urgently, as a core component of a combination approach to control COVID-19.
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Abstract
Since December 2019, China has been experiencing a large outbreak of a novel coronavirus (2019-nCoV) which can cause respiratory disease and severe pneumonia. We estimated the basic reproduction number R0 of 2019-nCoV to be around 2.2 (90% high density interval: 1.4–3.8), indicating the potential for sustained human-to-human transmission. Transmission characteristics appear to be of similar magnitude to severe acute respiratory syndrome-related coronavirus (SARS-CoV) and pandemic influenza, indicating a risk of global spread.
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Affiliation(s)
- Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Gsteiger S, Low N, Sonnenberg P, Mercer CH, Althaus CL. Gini coefficients for measuring the distribution of sexually transmitted infections among individuals with different levels of sexual activity. PeerJ 2020; 8:e8434. [PMID: 31998566 PMCID: PMC6977500 DOI: 10.7717/peerj.8434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023] Open
Abstract
Objectives Gini coefficients have been used to describe the distribution of Chlamydia trachomatis (CT) infections among individuals with different levels of sexual activity. The objectives of this study were to investigate Gini coefficients for different sexually transmitted infections (STIs), and to determine how STI control interventions might affect the Gini coefficient over time. Methods We used population-based data for sexually experienced women from two British National Surveys of Sexual Attitudes and Lifestyles (Natsal-2: 1999–2001; Natsal-3: 2010–2012) to calculate Gini coefficients for CT, Mycoplasma genitalium (MG), and human papillomavirus (HPV) types 6, 11, 16 and 18. We applied bootstrap methods to assess uncertainty and to compare Gini coefficients for different STIs. We then used a mathematical model of STI transmission to study how control interventions affect Gini coefficients. Results Gini coefficients for CT and MG were 0.33 (95% CI [0.18–0.49]) and 0.16 (95% CI [0.02–0.36]), respectively. The relatively small coefficient for MG suggests a longer infectious duration compared with CT. The coefficients for HPV types 6, 11, 16 and 18 ranged from 0.15 to 0.38. During the decade between Natsal-2 and Natsal-3, the Gini coefficient for CT did not change. The transmission model shows that higher STI treatment rates are expected to reduce prevalence and increase the Gini coefficient of STIs. In contrast, increased condom use reduces STI prevalence but does not affect the Gini coefficient. Conclusions Gini coefficients for STIs can help us to understand the distribution of STIs in the population, according to level of sexual activity, and could be used to inform STI prevention and treatment strategies.
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Affiliation(s)
- Sandro Gsteiger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Pam Sonnenberg
- Institute for Global Health, University College London, London, UK
| | | | - Christian L Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
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Counotte MJ, Althaus CL, Low N, Riou J. Impact of age-specific immunity on the timing and burden of the next Zika virus outbreak. PLoS Negl Trop Dis 2019; 13:e0007978. [PMID: 31877200 PMCID: PMC6948816 DOI: 10.1371/journal.pntd.0007978] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 01/08/2020] [Accepted: 12/08/2019] [Indexed: 01/27/2023] Open
Abstract
The 2015-2017 epidemics of Zika virus (ZIKV) in the Americas caused widespread infection, followed by protective immunity. The timing and burden of the next Zika virus outbreak remains unclear. We used an agent-based model to simulate the dynamics of age-specific immunity to ZIKV, and predict the future age-specific risk using data from Managua, Nicaragua. We also investigated the potential impact of a ZIKV vaccine. Assuming lifelong immunity, the risk of a ZIKV outbreak will remain low until 2035 and rise above 50% in 2047. The imbalance in age-specific immunity implies that people in the 15-29 age range will be at highest risk of infection during the next ZIKV outbreak, increasing the expected number of congenital abnormalities. ZIKV vaccine development and licensure are urgent to attain the maximum benefit in reducing the population-level risk of infection and the risk of adverse congenital outcomes. This urgency increases if immunity is not lifelong.
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Affiliation(s)
- Michel J. Counotte
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Brugger J, Althaus CL. Transmission of and susceptibility to seasonal influenza in Switzerland from 2003 to 2015. Epidemics 2019; 30:100373. [PMID: 31635972 DOI: 10.1016/j.epidem.2019.100373] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the seasonal patterns of influenza transmission is critical to help plan public health measures for the management and control of epidemics. Mathematical models of infectious disease transmission have been widely used to quantify the transmissibility of and susceptibility to past influenza seasons in many countries. The objective of this study was to obtain a detailed picture of the transmission dynamics of seasonal influenza in Switzerland from 2003 to 2015. To this end, we developed a compartmental influenza transmission model taking into account social mixing between different age groups and seasonal forcing. We applied a Bayesian approach using Markov chain Monte Carlo (MCMC) methods to fit the model to the reported incidence of influenza-like-illness (ILI) and virological data from Sentinella, the Swiss Sentinel Surveillance Network. The maximal basic reproduction number, R0, ranged from 1.46 to 1.81 (median). Median estimates of susceptibility to influenza ranged from 29% to 98% for different age groups, and typically decreased with age. We also found a decline in ascertainability of influenza cases with age. Our study illustrates how influenza surveillance data from Switzerland can be integrated into a Bayesian modeling framework in order to assess age-specific transmission of and susceptibility to influenza.
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Affiliation(s)
- Jon Brugger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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Smid JH, Althaus CL, Low N, Unemo M, Herrmann B. Rise and fall of the new variant of Chlamydia trachomatis in Sweden: mathematical modelling study. Sex Transm Infect 2019; 96:375-379. [PMID: 31586947 PMCID: PMC7402554 DOI: 10.1136/sextrans-2019-054057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/13/2019] [Accepted: 09/23/2019] [Indexed: 02/04/2023] Open
Abstract
Objectives A new variant of Chlamydia trachomatis (nvCT) was discovered in Sweden in 2006. The nvCT has a plasmid deletion, which escaped detection by two nucleic acid amplification tests (Abbott-Roche, AR), which were used in 14 of 21 Swedish counties. The objectives of this study were to assess when and where nvCT emerged in Sweden, the proportion of nvCT in each county and the role of a potential fitness difference between nvCT and co-circulating wild-type strains (wtCT). Methods We used a compartmental mathematical model describing the spatial and temporal spread of nvCT and wtCT. We parameterised the model using sexual behaviour data and Swedish spatial and demographic data. We used Bayesian inference to fit the model to surveillance data about reported diagnoses of chlamydia infection in each county and data from four counties that assessed the proportion of nvCT in multiple years. Results Model results indicated that nvCT emerged in central Sweden (Dalarna, Gävleborg, Västernorrland), reaching a proportion of 1% of prevalent CT infections in late 2002 or early 2003. The diagnostic selective advantage enabled rapid spread of nvCT in the presence of high treatment rates. After detection, the proportion of nvCT decreased from 30%–70% in AR counties and 5%–20% in counties that Becton Dickinson tests, to around 5% in 2015 in all counties. The decrease in nvCT was consistent with an estimated fitness cost of around 5% in transmissibility or 17% reduction in infectious duration. Conclusions We reconstructed the course of a natural experiment in which a mutant strain of C. trachomatis spread across Sweden. Our modelling study provides support, for the first time, of a reduced transmissibility or infectious duration of nvCT. This mathematical model improved our understanding of the first nvCT epidemic in Sweden and can be adapted to investigate the impact of future diagnostic escape mutants.
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Affiliation(s)
- Joost H Smid
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Magnus Unemo
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Bjőrn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Smid J, Althaus CL, Low N. Discrepancies between observed data and predictions from mathematical modelling of the impact of screening interventions on Chlamydia trachomatis prevalence. Sci Rep 2019; 9:7547. [PMID: 31101863 PMCID: PMC6525258 DOI: 10.1038/s41598-019-44003-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022] Open
Abstract
Mathematical modelling studies of C. trachomatis transmission predict that interventions to screen and treat chlamydia infection will reduce prevalence to a greater degree than that observed in empirical population-based studies. We investigated two factors that might explain this discrepancy: partial immunity after natural infection clearance and differential screening coverage according to infection risk. We used four variants of a compartmental model for heterosexual C. trachomatis transmission, parameterized using data from England about sexual behaviour, C. trachomatis testing, diagnosis and prevalence, and Markov Chain Monte Carlo methods for statistical inference. In our baseline scenario, a model in which partial immunity follows natural infection clearance and the proportion of tests done in chlamydia-infected people decreases over time fitted the data best. The model predicts that partial immunity reduced susceptibility to reinfection by 68% (95% Bayesian credible interval 46-87%). The estimated screening rate was 4.3 (2.2-6.6) times higher for infected than for uninfected women in 2000, decreasing to 2.1 (1.4-2.9) in 2011. Despite incorporation of these factors, the model still predicted a marked decline in C. trachomatis prevalence. To reduce the gap between modelling and data, advances are needed in knowledge about factors influencing the coverage of chlamydia screening, the immunology of C. trachomatis and changes in C. trachomatis prevalence at the population level.
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Affiliation(s)
- Joost Smid
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland.
| | - Nicola Low
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
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Porgo TV, Norris SL, Salanti G, Johnson LF, Simpson JA, Low N, Egger M, Althaus CL. The use of mathematical modeling studies for evidence synthesis and guideline development: A glossary. Res Synth Methods 2019; 10:125-133. [PMID: 30508309 PMCID: PMC6491984 DOI: 10.1002/jrsm.1333] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 10/12/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022]
Abstract
Mathematical modeling studies are increasingly recognised as an important tool for evidence synthesis and to inform clinical and public health decision‐making, particularly when data from systematic reviews of primary studies do not adequately answer a research question. However, systematic reviewers and guideline developers may struggle with using the results of modeling studies, because, at least in part, of the lack of a common understanding of concepts and terminology between evidence synthesis experts and mathematical modellers. The use of a common terminology for modeling studies across different clinical and epidemiological research fields that span infectious and non‐communicable diseases will help systematic reviewers and guideline developers with the understanding, characterisation, comparison, and use of mathematical modeling studies. This glossary explains key terms used in mathematical modeling studies that are particularly salient to evidence synthesis and knowledge translation in clinical medicine and public health.
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Affiliation(s)
- Teegwendé V Porgo
- Population Health and Optimal Health Practices Research Unit, Department of Social and Preventative Medicine, Faculty of Medicine, Université Laval, Quebec, Canada.,Department of Information, Evidence and Research, World Health Organization, Geneva, Switzerland
| | - Susan L Norris
- Department of Information, Evidence and Research, World Health Organization, Geneva, Switzerland
| | - Georgia Salanti
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Leigh F Johnson
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - Julie A Simpson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Omori R, Chemaitelly H, Althaus CL, Abu-Raddad LJ. Does infection with Chlamydia trachomatis induce long-lasting partial immunity? Insights from mathematical modelling. Sex Transm Infect 2018; 95:115-121. [PMID: 30181327 PMCID: PMC6580764 DOI: 10.1136/sextrans-2018-053543] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/20/2018] [Accepted: 08/07/2018] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES To explore whether existence of long-lasting partial immunity against reinfection with Chlamydia trachomatis is necessary to explain C. trachomatis prevalence patterns by age and sexual risk, and to provide a plausible estimate for the effect size, defined here as a reduction in susceptibility to reinfection. METHODS A population-based mathematical model was constructed to describe C. trachomatis natural history and transmission dynamics by age and sexual risk. The model was parameterised using natural history, and epidemiological and sexual behaviour data, and applied for UK and US data. Sensitivity analyses were conducted to assess the robustness of predictions to variations in model structure and to examine the impact of alternative assumptions for the mechanism underlying partial immunity. RESULTS Partial immunity against reinfection was found necessary to explain observed C. trachomatis prevalence patterns by age and sexual risk. The reduction in susceptibility to reinfection was estimated at 93% using UK data (95% uncertainty interval (UI)=88%-97%) and at 67% using US data (95% UI=24%-88%). The model-structure sensitivity analyses affirmed model predictions. The immunity-mechanism sensitivity analyses suggested a mechanism of susceptibility reduction against reinfection or a mechanism of infectious-period duration reduction upon reinfection. CONCLUSIONS A strong long-lasting partial immunity against C. trachomatis reinfection should be present to explain observed prevalence patterns. The mechanism of immunity could be either a reduction in susceptibility to reinfection or a reduction in duration of infection on reinfection. C. trachomatis infection appears to naturally elicit a strong long-lasting immune response, supporting the concept of vaccine development.
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Affiliation(s)
- Ryosuke Omori
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan .,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, Japan.,Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Hiam Chemaitelly
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Laith J Abu-Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar.,Department of Healthcare Policy and Research, Weill Cornell Medicine, Cornell University, New York City, New York, USA.,College of Health and Life Sciences, Hamad bin Khalifa University, Doha, Qatar
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Riesen M, Konstantinoudis G, Lang P, Low N, Hatz C, Maeusezahl M, Spaar A, Bühlmann M, Spycher BD, Althaus CL. Exploring variation in human papillomavirus vaccination uptake in Switzerland: a multilevel spatial analysis of a national vaccination coverage survey. BMJ Open 2018; 8:e021006. [PMID: 29773702 PMCID: PMC5961588 DOI: 10.1136/bmjopen-2017-021006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE Understanding the factors that influence human papillomavirus (HPV) vaccination uptake is critically important to the design of effective vaccination programmes. In Switzerland, HPV vaccination uptake (≥1 dose) by age 16 years among women ranges from 31% to 80% across 26 cantons (states). Our objective was to identify factors that are associated with the spatial variation in HPV vaccination uptake. METHODS We used cross-sectional data from the Swiss National Vaccination Coverage Survey 2009-2016 on HPV vaccination status (≥1 dose) of 14-17-year-old girls, their municipality of residence and their nationality for 21 of 26 cantons (n=8965). We examined covariates at municipality level: language, degree of urbanisation, socioeconomic position, religious denomination, results of a vote about vaccination laws as a proxy for vaccine scepticism and, at cantonal level, availability of school-based vaccination and survey period. We used a series of conditional autoregressive models to assess the effects of covariates while accounting for variability between cantons and municipal-level spatial autocorrelation. RESULTS In the best-fit model, living in cantons that have school-based vaccination (adjusted OR 2.51; 95% credible interval 1.77 to 3.56) was associated with increased uptake, while living in municipalities with lower acceptance of vaccination laws was associated with lower HPV vaccination uptake (OR 0.61; 95% credible interval 0.50 to 0.73). Overall, the covariates explained 88% of the municipal-level variation in uptake. CONCLUSIONS In Switzerland, both cantons and community opinion about vaccination play a prominent role in the variation in HPV vaccination uptake. To increase uptake, efforts should be made to mitigate vaccination scepticism and to encourage school-based vaccination.
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Affiliation(s)
- Maurane Riesen
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Garyfallos Konstantinoudis
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Graduate School for Health Sciences, University of Bern, Bern, Switzerland
| | - Phung Lang
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christoph Hatz
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Mirjam Maeusezahl
- Communicable Diseases, Swiss Federal Office of Public Health, Bern, Switzerland
| | - Anne Spaar
- Communicable Diseases, Swiss Federal Office of Public Health, Bern, Switzerland
| | - Marc Bühlmann
- Institute of Political Science, University of Bern, Bern, Switzerland
| | - Ben D Spycher
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Department of Pediatrics, Pediatric Respiratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Foerster S, Desilvestro V, Hathaway LJ, Althaus CL, Unemo M. A new rapid resazurin-based microdilution assay for antimicrobial susceptibility testing of Neisseria gonorrhoeae. J Antimicrob Chemother 2018; 72:1961-1968. [PMID: 28431096 PMCID: PMC5890744 DOI: 10.1093/jac/dkx113] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/19/2017] [Indexed: 12/27/2022] Open
Abstract
Objectives Rapid, cost-effective and objective methods for antimicrobial susceptibility testing of Neisseria gonorrhoeae would greatly enhance surveillance of antimicrobial resistance. Etest, disc diffusion and agar dilution methods are subjective, mostly laborious for large-scale testing and take ∼24 h. We aimed to develop a rapid broth microdilution assay using resazurin (blue), which is converted into resorufin (pink fluorescence) in the presence of viable bacteria. Methods The resazurin-based broth microdilution assay was established using 132 N. gonorrhoeae strains and the antimicrobials ceftriaxone, cefixime, azithromycin, spectinomycin, ciprofloxacin, tetracycline and penicillin. A regression model was used to estimate the MICs. Assay results were obtained in ∼7.5 h. Results The EC 50 of the dose-response curves correlated well with Etest MIC values (Pearson's r = 0.93). Minor errors resulting from misclassifications of intermediate strains were found for 9% of the samples. Major errors (susceptible strains misclassified as resistant) occurred for ceftriaxone (4.6%), cefixime (3.3%), azithromycin (0.6%) and tetracycline (0.2%). Only one very major error was found (a ceftriaxone-resistant strain misclassified as susceptible). Overall the sensitivity of the assay was 97.1% (95% CI 95.2-98.4) and the specificity 78.5% (95% CI 74.5-82.9). Conclusions A rapid, objective, high-throughput, quantitative and cost-effective broth microdilution assay was established for gonococci. For use in routine diagnostics without confirmatory testing, the specificity might remain suboptimal for ceftriaxone and cefixime. However, the assay is an effective low-cost method to evaluate novel antimicrobials and for high-throughput screening, and expands the currently available methodologies for surveillance of antimicrobial resistance in gonococci.
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Affiliation(s)
- Sunniva Foerster
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Lucy J Hathaway
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, Örebro University, Örebro, Sweden
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Smid JH, Garcia V, Low N, Mercer CH, Althaus CL. Age difference between heterosexual partners in Britain: Implications for the spread of Chlamydia trachomatis. Epidemics 2018; 24:60-66. [PMID: 29655934 DOI: 10.1016/j.epidem.2018.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 03/23/2018] [Accepted: 03/30/2018] [Indexed: 11/28/2022] Open
Abstract
Heterosexual partners often differ in age. Integrating realistic patterns of sexual mixing by age into dynamic transmission models has been challenging. The effects of these patterns on the transmission of sexually transmitted infections (STI) including Chlamydia trachomatis (chlamydia), the most common bacterial STI are not well understood. We describe age mixing between new heterosexual partners using age- and sex-specific data about sexual behavior reported by people aged 16-63 years in the 2000 and 2010 British National Surveys of Sexual Attitudes and Lifestyles. We incorporate mixing patterns into a compartmental transmission model fitted to age- and sex-specific, chlamydia positivity from the same surveys, to investigate C. trachomatis transmission. We show that distributions of ages of new sex partners reported by women and by men in Britain are not consistent with each other. After balancing these distributions, new heterosexual partnerships tend to involve men who are older than women (median age difference 2, IQR -1, 5 years). We identified the most likely age combinations of heterosexual partners where incident C. trachomatis infections are generated. The model results show that in >50% of chlamydia transmitting partnerships, at least one partner is ≥25 years old. This study illustrates how sexual behavior data can be used to reconstruct detailed sexual mixing patterns by age, and how these patterns can be integrated into dynamic transmission models. The proposed framework can be extended to study the effects of age-dependent transmission on incidence in any STI.
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Affiliation(s)
- Joost H Smid
- University of Bern, Institute of Social and Preventive Medicine (ISPM), Switzerland.
| | - Victor Garcia
- University of Bern, Institute of Social and Preventive Medicine (ISPM), Switzerland
| | - Nicola Low
- University of Bern, Institute of Social and Preventive Medicine (ISPM), Switzerland
| | | | - Christian L Althaus
- University of Bern, Institute of Social and Preventive Medicine (ISPM), Switzerland
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Riesen M, Garcia V, Low N, Althaus CL. Modeling the consequences of regional heterogeneity in human papillomavirus (HPV) vaccination uptake on transmission in Switzerland. Vaccine 2017; 35:7312-7321. [PMID: 29126806 DOI: 10.1016/j.vaccine.2017.10.103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/24/2017] [Accepted: 10/31/2017] [Indexed: 01/15/2023]
Abstract
BACKGROUND Completed human papillomavirus (HPV) vaccination by age 16 years among women in Switzerland ranges from 17 to 75% across 26 cantons. The consequences of regional heterogeneity in vaccination coverage on transmission and prevalence of HPV-16 are unclear. METHODS We developed a deterministic, population-based model that describes HPV-16 transmission among young adults within and between the 26 cantons of Switzerland. We parameterized the model using sexual behavior data from Switzerland and data from the Swiss National Vaccination Coverage Survey. First, we investigated the general consequences of heterogeneity in vaccination uptake between two sub-populations. We then compared the predicted prevalence of HPV-16 resulting from heterogeneous HPV vaccination uptake in all of Switzerland with homogeneous vaccination at an uptake that is identical to the national average (52%). RESULTS In our baseline scenario, HPV-16 prevalence in women is 3.34% when vaccination is introduced and begins to diverge across cantons, ranging from 0.19 to 1.20% after 15 years of vaccination. After the same time period, overall prevalence of HPV-16 in Switzerland is only marginally higher (0.63%) with heterogeneous vaccination uptake than with homogeneous uptake (0.59%). Assuming inter-cantonal sexual mixing, cantons with low vaccination uptake benefit from a reduction in prevalence at the expense of cantons with high vaccination uptake. CONCLUSIONS Regional variations in uptake diminish the overall effect of vaccination on HPV-16 prevalence in Switzerland, but the effect size is small. Cantonal efforts towards HPV-prevalence reduction by increasing vaccination uptake are impaired by cantons with low vaccination uptake. Although the expected impact on national prevalence would be relatively small, harmonization of cantonal vaccination programs would reduce inter-cantonal differences in HPV-16 prevalence.
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Affiliation(s)
- Maurane Riesen
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
| | - Victor Garcia
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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Abstract
In a Perspective on the research article by Didelot and colleagues, Magnus Unemo and Christian Althaus discuss the value of modelling studies to inform antimicrobial resistance management and the limitations of the current evidence base informing such models.
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Affiliation(s)
- Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Fingerhuth SM, Low N, Bonhoeffer S, Althaus CL. Detection of antibiotic resistance is essential for gonorrhoea point-of-care testing: a mathematical modelling study. BMC Med 2017; 15:142. [PMID: 28747205 PMCID: PMC5530576 DOI: 10.1186/s12916-017-0881-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/19/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antibiotic resistance is threatening to make gonorrhoea untreatable. Point-of-care (POC) tests that detect resistance promise individually tailored treatment, but might lead to more treatment and higher levels of resistance. We investigate the impact of POC tests on antibiotic-resistant gonorrhoea. METHODS We used data about the prevalence and incidence of gonorrhoea in men who have sex with men (MSM) and heterosexual men and women (HMW) to calibrate a mathematical gonorrhoea transmission model. With this model, we simulated four clinical pathways for the diagnosis and treatment of gonorrhoea: POC test with (POC+R) and without (POC-R) resistance detection, culture and nucleic acid amplification tests (NAATs). We calculated the proportion of resistant infections and cases averted after 5 years, and compared how fast resistant infections spread in the populations. RESULTS The proportion of resistant infections after 30 years is lowest for POC+R (median MSM: 0.18%, HMW: 0.12%), and increases for culture (MSM: 1.19%, HMW: 0.13%), NAAT (MSM: 100%, HMW: 99.27%), and POC-R (MSM: 100%, HMW: 99.73%). Per 100 000 persons, NAAT leads to 36 366 (median MSM) and 1228 (median HMW) observed cases after 5 years. Compared with NAAT, POC+R averts more cases after 5 years (median MSM: 3353, HMW: 118). POC tests that detect resistance with intermediate sensitivity slow down resistance spread more than NAAT. POC tests with very high sensitivity for the detection of resistance are needed to slow down resistance spread more than by using culture. CONCLUSIONS POC with high sensitivity to detect antibiotic resistance can keep gonorrhoea treatable longer than culture or NAAT. POC tests without reliable resistance detection should not be introduced because they can accelerate the spread of antibiotic-resistant gonorrhoea.
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Affiliation(s)
- Stephanie M Fingerhuth
- Institute of Integrative Biology, ETH Zurich, Zurich, 8092, Switzerland. .,Institute of Social and Preventive Medicine, University of Bern, Bern, 3012, Switzerland.
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, 3012, Switzerland
| | | | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, 3012, Switzerland
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Abstract
Christian Althaus and Nicola Low reflect on the contribution of sexual transmission to the spread of Zika virus.
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Affiliation(s)
- Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- * E-mail:
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Fingerhuth SM, Bonhoeffer S, Low N, Althaus CL. Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners. PLoS Pathog 2016; 12:e1005611. [PMID: 27196299 PMCID: PMC4872991 DOI: 10.1371/journal.ppat.1005611] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
The sexually transmitted bacterium Neisseria gonorrhoeae has developed resistance to all antibiotic classes that have been used for treatment and strains resistant to multiple antibiotic classes have evolved. In many countries, there is only one antibiotic remaining for empirical N. gonorrhoeae treatment, and antibiotic management to counteract resistance spread is urgently needed. Understanding dynamics and drivers of resistance spread can provide an improved rationale for antibiotic management. In our study, we first used antibiotic resistance surveillance data to estimate the rates at which antibiotic-resistant N. gonorrhoeae spread in two host populations, heterosexual men (HetM) and men who have sex with men (MSM). We found higher rates of spread for MSM (0.86 to 2.38 y−1, mean doubling time: 6 months) compared to HetM (0.24 to 0.86 y−1, mean doubling time: 16 months). We then developed a dynamic transmission model to reproduce the observed dynamics of N. gonorrhoeae transmission in populations of heterosexual men and women (HMW) and MSM. We parameterized the model using sexual behavior data and calibrated it to N. gonorrhoeae prevalence and incidence data. In the model, antibiotic-resistant N. gonorrhoeae spread with a median rate of 0.88 y−1 in HMW and 3.12 y−1 in MSM. These rates correspond to median doubling times of 9 (HMW) and 3 (MSM) months. Assuming no fitness costs, the model shows the difference in the host population’s treatment rate rather than the difference in the number of sexual partners explains the differential spread of resistance. As higher treatment rates result in faster spread of antibiotic resistance, treatment recommendations for N. gonorrhoeae should carefully balance prevention of infection and avoidance of resistance spread. More and more infectious disease treatments fail because the causative pathogens are resistant to the drugs used for treatment. For the treatment of Neisseria gonorrhoeae, a sexually transmitted bacterium, drug resistance is a particularly big problem: there is only a single antibiotic left that is recommended for treatment. We aimed to understand how antibiotic-resistant N. gonorrhoeae spread in a sexually active host population and how the spread of resistance can be slowed. From antibiotic resistance surveillance data, we first estimated the rate at which antibiotic-resistant N. gonorrhoeae spread. Second, we reproduced the observed dynamics in a mathematical model describing the transmission between hosts. We found that antibiotic-resistant N. gonorrhoeae spread faster in host populations of men who have sex with men than in host populations of heterosexuals. We could attribute the faster spread of resistant pathogens to higher treatment rates. This finding implies that promoting screening to control antibiotic-resistant N. gonorrhoeae could in fact accelerate their spread.
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Affiliation(s)
- Stephanie M. Fingerhuth
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
- * E-mail:
| | | | - Nicola Low
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
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Abbate JL, Murall CL, Richner H, Althaus CL. Potential Impact of Sexual Transmission on Ebola Virus Epidemiology: Sierra Leone as a Case Study. PLoS Negl Trop Dis 2016; 10:e0004676. [PMID: 27135922 PMCID: PMC4852896 DOI: 10.1371/journal.pntd.0004676] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/08/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Sexual transmission of Ebola virus disease (EVD) 6 months after onset of symptoms has been recently documented, and Ebola virus RNA has been detected in semen of survivors up to 9 months after onset of symptoms. As countries affected by the 2013-2015 epidemic in West Africa, by far the largest to date, are declared free of Ebola virus disease (EVD), it remains unclear what threat is posed by rare sexual transmission events that could arise from survivors. METHODOLOGY/PRINCIPAL FINDINGS We devised a compartmental mathematical model that includes sexual transmission from convalescent survivors: a SEICR (susceptible-exposed-infectious-convalescent-recovered) transmission model. We fitted the model to weekly incidence of EVD cases from the 2014-2015 epidemic in Sierra Leone. Sensitivity analyses and Monte Carlo simulations showed that a 0.1% per sex act transmission probability and a 3-month convalescent period (the two key unknown parameters of sexual transmission) create very few additional cases, but would extend the epidemic by 83 days [95% CI: 68-98 days] (p < 0.0001) on average. Strikingly, a 6-month convalescent period extended the average epidemic by 540 days (95% CI: 508-572 days), doubling the current length, despite an insignificant rise in the number of new cases generated. CONCLUSIONS/SIGNIFICANCE Our results show that reductions in the per sex act transmission probability via abstinence and condom use should reduce the number of sporadic sexual transmission events, but will not significantly reduce the epidemic size and may only minimally shorten the length of time the public health community must maintain response preparedness. While the number of infectious survivors is expected to greatly decline over the coming months, our results show that transmission events may still be expected for quite some time as each event results in a new potential cluster of non-sexual transmission. Precise measurement of the convalescent period is thus important for planning ongoing surveillance efforts.
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Affiliation(s)
- Jessica L. Abbate
- Institute for Ecology and Evolution, University of Bern, Bern, Switzerland
- UMR MIVEGEC (UMR CNRS 5290, IRD 224, UM), Institute for Research of Development (IRD), Montpellier, France
- UMR UMMISCO (UMI 209 IRD-UPMC), Bondy, France
- * E-mail:
| | - Carmen Lia Murall
- Max-Planck Institute for Dynamics and Self-Organization, Gottingen, Germany
| | - Heinz Richner
- Institute for Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
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Foerster S, Golparian D, Jacobsson S, Hathaway LJ, Low N, Shafer WM, Althaus CL, Unemo M. Genetic Resistance Determinants, In Vitro Time-Kill Curve Analysis and Pharmacodynamic Functions for the Novel Topoisomerase II Inhibitor ETX0914 (AZD0914) in Neisseria gonorrhoeae. Front Microbiol 2015; 6:1377. [PMID: 26696986 PMCID: PMC4674575 DOI: 10.3389/fmicb.2015.01377] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 11/20/2015] [Indexed: 12/02/2022] Open
Abstract
Resistance in Neisseria gonorrhoeae to all available therapeutic antimicrobials has emerged and new efficacious drugs for treatment of gonorrhea are essential. The topoisomerase II inhibitor ETX0914 (also known as AZD0914) is a new spiropyrimidinetrione antimicrobial that has different mechanisms of action from all previous and current gonorrhea treatment options. In this study, the N. gonorrhoeae resistance determinants for ETX0914 were further described and the effects of ETX0914 on the growth of N. gonorrhoeae (ETX0914 wild type, single step selected resistant mutants, and efflux pump mutants) were examined in a novel in vitro time-kill curve analysis to estimate pharmacodynamic parameters of the new antimicrobial. For comparison, ciprofloxacin, azithromycin, ceftriaxone, and tetracycline were also examined (separately and in combination with ETX0914). ETX0914 was rapidly bactericidal for all wild type strains and had similar pharmacodynamic properties to ciprofloxacin. All selected resistant mutants contained mutations in amino acid codons D429 or K450 of GyrB and inactivation of the MtrCDE efflux pump fully restored the susceptibility to ETX0914. ETX0914 alone and in combination with azithromycin and ceftriaxone was highly effective against N. gonorrhoeae and synergistic interaction with ciprofloxacin, particularly for ETX0914-resistant mutants, was found. ETX0914, monotherapy or in combination with azithromycin (to cover additional sexually transmitted infections), should be considered for phase III clinical trials and future gonorrhea treatment.
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Affiliation(s)
- Sunniva Foerster
- Institute for Infectious Diseases, University of BernBern, Switzerland
- Institute of Social and Preventive Medicine, University of BernBern, Switzerland
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for Pathogenic Neisseria, Faculty of Medicine and Health, Örebro UniversityÖrebro, Sweden
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for Pathogenic Neisseria, Faculty of Medicine and Health, Örebro UniversityÖrebro, Sweden
| | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for Pathogenic Neisseria, Faculty of Medicine and Health, Örebro UniversityÖrebro, Sweden
| | - Lucy J. Hathaway
- Institute for Infectious Diseases, University of BernBern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of BernBern, Switzerland
| | - William M. Shafer
- Department of Microbiology and Immunology, Emory University School of Medicine, AtlantaGA, USA
- Laboratories of Bacterial Pathogenesis, Veterans Affairs Medical Center, DecaturGA, USA
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of BernBern, Switzerland
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for Pathogenic Neisseria, Faculty of Medicine and Health, Örebro UniversityÖrebro, Sweden
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Althaus CL. Rapid drop in the reproduction number during the Ebola outbreak in the Democratic Republic of Congo. PeerJ 2015; 3:e1418. [PMID: 26618087 PMCID: PMC4655090 DOI: 10.7717/peerj.1418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/30/2015] [Indexed: 12/03/2022] Open
Abstract
The Democratic Republic of Congo (DRC) experienced a confined rural outbreak of Ebola virus disease (EVD) with 69 reported cases from July to October 2014. Understanding the transmission dynamics during the outbreak can provide important information for anticipating and controlling future EVD epidemics. I fitted an EVD transmission model to previously published data of this outbreak and estimated the basic reproduction number R0 = 5.2 (95% CI [4.0–6.7]). The model suggests that the net reproduction number Rt fell below unity 28 days (95% CI [25–34] days) after the onset of symptoms in the index case. This study adds to previous epidemiological descriptions of the 2014 EVD outbreak in DRC, and is consistent with the notion that a rapid implementation of control interventions helped reduce further spread.
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Affiliation(s)
- Christian L Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern , Bern , Switzerland
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Althaus CL, Choisy M, Alizon S. P08.34 Number of sex acts matters for heterosexual transmission and control of chlamydia trachomatis. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Fingerhuth SM, Bonhoeffer S, Low N, Althaus CL. 001.1 Evolution and spread of antibiotic-resistant gonorrhoea. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Foerster SF, Unemo M, Hathaway LJ, Low N, Althaus CL. 009.1 Standardised, quality assured time-kill curve analysis and pharmacodynamic functions of different antibiotics for in vitroevaluation of treatment regimens for neisseria gonorrhoeae. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
As at 15 June 2015, a large transmission cluster of Middle East respiratory syndrome coronavirus (MERSCoV)was ongoing in South Korea. To examine the potential for such events, we estimated the level of heterogeneity in MERS-CoV transmission by analyzing data on cluster size distributions. We found substantial potential for superspreading; even though it is likely that R0 < 1 overall, our analysis indicates that cluster sizes of over 150 cases are not unexpected forMERS-CoV infection.
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Affiliation(s)
- A J Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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