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Diarra M, Ndiaye R, Barry A, Talla C, Diagne MM, Dia N, Faye J, Sarr FD, Gaye A, Diallo A, Cisse M, Dieng I, Fall G, Tall A, Faye O, Faye O, Sall AA, Loucoubar C. Analysis of contact tracing data showed contribution of asymptomatic and non-severe infections to the maintenance of SARS-CoV-2 transmission in Senegal. Sci Rep 2023; 13:9121. [PMID: 37277417 DOI: 10.1038/s41598-023-35622-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
During the COVID-19 pandemic in Senegal, contact tracing was done to identify transmission clusters, their analysis allowed to understand their dynamics and evolution. In this study, we used information from the surveillance data and phone interviews to construct, represent and analyze COVID-19 transmission clusters from March 2, 2020, to May 31, 2021. In total, 114,040 samples were tested and 2153 transmission clusters identified. A maximum of 7 generations of secondary infections were noted. Clusters had an average of 29.58 members and 7.63 infected among them; their average duration was 27.95 days. Most of the clusters (77.3%) are concentrated in Dakar, capital city of Senegal. The 29 cases identified as super-spreaders, i.e., the indexes that had the most positive contacts, showed few symptoms or were asymptomatic. Deepest transmission clusters are those with the highest percentage of asymptomatic members. The correlation between proportion of asymptomatic and degree of transmission clusters showed that asymptomatic strongly contributed to the continuity of transmission within clusters. During this pandemic, all the efforts towards epidemiological investigations, active case-contact detection, allowed to identify in a short delay growing clusters and help response teams to mitigate the spread of the disease.
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Affiliation(s)
- Maryam Diarra
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Ramatoulaye Ndiaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Cheikh Talla
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | | | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Joseph Faye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Fatoumata Diene Sarr
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Mamadou Cisse
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Idrissa Dieng
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Gamou Fall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Adama Tall
- Scientific Direction, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou A Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal.
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2
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Increased transmission of SARS-CoV-2 in Denmark during UEFA European championships. Epidemiol Infect 2022; 150:e123. [PMID: 35317884 PMCID: PMC9254153 DOI: 10.1017/s095026882200019x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Denmark hosted four games during the 2020 UEFA European championships (EC2020). After declining positive SARS-CoV-2 test rates in Denmark, a rise occurred during and after the tournament, concomitant with the replacement of the dominant Alpha lineage (B.1.1.7) by the Delta lineage (B.1.617.2), increasing vaccination rates and cessation of several restrictions. A cohort study including 33 227 cases was conducted from 30 May to 25 July 2021, 14 days before and after the EC2020. Included was a nested cohort with event information from big-screen events and matches at the Danish national stadium, Parken (DNSP) in Copenhagen, held from 12 June to 28 June 2021. Information from whole-genome sequencing, contact tracing and Danish registries was collected. Case–case connections were used to establish transmission trees. Cases infected on match days were compared to cases not infected on match days as a reference. The crude incidence rate ratio (IRR) of transmissions was 1.55, corresponding to 584 (1.76%) cases attributable to EC2020 celebrations. The IRR adjusted for covariates was lower (IRR 1.41) but still significant, and also pointed to a reduced number of transmissions from fully vaccinated cases (IRR 0.59). These data support the hypothesis that the EC2020 celebrations contributed to the rise of cases in Denmark in the early summer of 2021.
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3
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de la Rosa-Zamboni D, Ortega-Riosvelasco F, González-García N, Gamiño-Arroyo AE, Espinosa-González GA, Valladares-Wagner JM, Saldívar-Flores A, Aguilar-Guzmán O, Sanchez-Pujol JC, López-Martínez B, Villa-Guillén M, Parra-Ortega I, Jamaica-Balderas LMDC, Sienra-Monge JJL, Guerrero-Díaz AC. Tracing COVID-19 Source of Infection Among Health Personnel in a Pediatric Hospital. Front Pediatr 2022; 10:897113. [PMID: 35757120 PMCID: PMC9218243 DOI: 10.3389/fped.2022.897113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/02/2022] [Indexed: 12/24/2022] Open
Abstract
Health personnel (HP) have been universally recognized as especially susceptible to COVID-19. In Mexico, our home country, HP has one of the highest death rates from the disease. From the beginning of the SARS-CoV-2 pandemic, an office for initial attention for HP and a call center were established at a COVID-19 national reference pediatric hospital, aimed at early detection of COVID-19 cases and stopping local transmission. The detection and call center implementation and operation, and tracing methodology are described here. A total of 1,042 HP were evaluated, with 221 positive cases identified (7.7% of all HP currently working and 26% of the HP tested). Community contagion was most prevalent (46%), followed by other HP (27%), household (14%), and hospitalized patients (13%). Clusters and contact network analysis are discussed. This is one of the first reports that address the details of the implementation process of contact tracing in a pediatric hospital from the perspective of a hybrid hospital with COVID-19 and non-COVID-19 areas.
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Affiliation(s)
- Daniela de la Rosa-Zamboni
- Department of Comprehensive Patient Care, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Nadia González-García
- Department of Research, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | | | | | | | - Olivia Aguilar-Guzmán
- Department of Nursing, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | | | - Mónica Villa-Guillén
- Department of Medical Management, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Israel Parra-Ortega
- Department of Clinical Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Ahmadi M, Sharifi A, Khalili S. Presentation of a developed sub-epidemic model for estimation of the COVID-19 pandemic and assessment of travel-related risks in Iran. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:14521-14529. [PMID: 33215282 PMCID: PMC7676861 DOI: 10.1007/s11356-020-11644-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/11/2020] [Indexed: 05/05/2023]
Abstract
The COVID-19 pandemic is one of the contagious diseases involving all the world in 2019-2020. Also, all people are concerned about the future of this catastrophe and how the continuous outbreak can be prevented. Some countries are not successful in controlling the outbreak; therefore, the incidence is observed in several peaks. In this paper, firstly single-peak SIR models are used for historical data. Regarding the SIR model, the termination time of the outbreak should have been in early June 2020. However, several peaks invalidate the results of single-peak models. Therefore, we should present a model to support pandemics with several extrema. In this paper, we presented the generalized logistic growth model (GLM) to estimate sub-epidemic waves of the COVID-19 outbreak in Iran. Therefore, the presented model simulated scenarios of two, three, and four waves in the observed incidence. In the second part of the paper, we assessed travel-related risk in inter-provincial travels in Iran. Moreover, the results of travel-related risk show that typical travel between Tehran and other sites exposed Isfahan, Gilan, Mazandaran, and West Azerbaijan in the higher risk of infection greater than 100 people per day. Therefore, controlling this movement can prevent great numbers of infection, remarkably.
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Affiliation(s)
- Mohsen Ahmadi
- Department of Industrial Engineering, Urmia University of Technology (UUT), P.O. Box 57166-419, Urmia, Iran
| | - Abbas Sharifi
- Department of Mechanical Engineering, Urmia University of Technology (UUT), P.O. Box 57166-419, Urmia, Iran.
| | - Sarv Khalili
- Department of Medicine, Islamic Azad University Tehran Medical Sciences, P.O. Box 19395-1495, Tehran, Iran
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5
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Gaythorpe K, Morris A, Imai N, Stewart M, Freeman J, Choi M. Chainchecker: An application to visualise and explore transmission chains for Ebola virus disease. PLoS One 2021; 16:e0247002. [PMID: 33606709 PMCID: PMC7894960 DOI: 10.1371/journal.pone.0247002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 01/31/2021] [Indexed: 11/18/2022] Open
Abstract
2020 saw the continuation of the second largest outbreak of Ebola virus disease (EVD) in history. Determining epidemiological links between cases is a key part of outbreak control. However, due to the large quantity of data and subsequent data entry errors, inconsistencies in potential epidemiological links are difficult to identify. We present chainchecker, an online and offline shiny application which visualises, curates and verifies transmission chain data. The application includes the calculation of exposure windows for individual cases of EVD based on user defined incubation periods and user specified symptom profiles. It has an upload function for viral hemorrhagic fever data and utility for additional entries. This data may then be visualised as a transmission tree with inconsistent links highlighted. Finally, there is utility for cluster analysis and the ability to highlight nosocomial transmission. chainchecker is a R shiny application which has an offline version for use with VHF (viral hemorrhagic fever) databases or linelists. The software is available at https://shiny.dide.imperial.ac.uk/chainchecker which is a web-based application that links to the desktop application available for download and the github repository, https://github.com/imperialebola2018/chainchecker.
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Affiliation(s)
- Katy Gaythorpe
- Imperial College London, London, United Kingdom
- * E-mail:
| | - Aaron Morris
- University of Cambridge, Cambridge, United Kingdom
| | | | - Miles Stewart
- Applied Physic Laboratory, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeffrey Freeman
- Applied Physic Laboratory, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Mary Choi
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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6
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Al Wahaibi A, Al Manji A, Al Maani A, Al Rawahi B, Al Harthy K, Alyaquobi F, Al-Jardani A, Petersen E, Al Abri S. COVID-19 epidemic monitoring after non-pharmaceutical interventions: The use of time-varying reproduction number in a country with a large migrant population. Int J Infect Dis 2020; 99:466-472. [PMID: 32829052 PMCID: PMC7439014 DOI: 10.1016/j.ijid.2020.08.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/12/2020] [Accepted: 08/16/2020] [Indexed: 02/07/2023] Open
Abstract
Rt can be used to closely monitor the non-pharmaceutical interventions (NPI) of the COVID-19 epidemic. Activity of the epidemic in Oman is examined. Other factors, like the return of overseas students, have increased the epidemic activity. Responses to NPI are different between migrants and natives.
Background COVID-19’s emergence carries with it many uncertainties and challenges, including strategies to manage the epidemic. Oman has implemented non-pharmaceutical interventions (NPIs) to mitigate the impact of COVID-19. However, responses to NPIs may be different across different populations within a country with a large number of migrants, such as Oman. This study investigated the different responses to NPIs, and assessed the use of the time-varying reproduction number (Rt) to monitor them. Methods Polymerase chain reaction (PCR) laboratory-confirmed COVID-19 data for Oman, from February 24 to June 3, 2020, were used alongside demographic and epidemiological information. Data were arranged into pairs of infector–infectee, and two main libraries of R software were used to estimate reproductive number (Rt). Rt was calculated for both Omanis and non-Omanis. Findings A total of 13,538 cases were included, 44.9% of which were Omanis. Among all these cases we identified 2769 infector–infectee pairs for calculating Rt. There was a sharp drop in Rt from 3.7 (95% confidence interval [CI] 2.8–4.6) in mid-March to 1.4 (95% CI 1.2–1.7) in late March in response to NPIs. Rt then decreased further to 1.2 (95% CI 1.1–1.3) in late April after which it rose, corresponding to the easing of NPIs. Comparing the two groups, the response to major public health controls was more evident in Omanis in reducing Rt to 1.09 (95% CI 0.84–1.3) by the end of March. Interpretation Use of real-time estimation of Rt allowed us to follow the effects of NPIs. The migrant population responded differently than the Omani population.
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Affiliation(s)
- Adil Al Wahaibi
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman.
| | - Abdullah Al Manji
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
| | - Amal Al Maani
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
| | - Bader Al Rawahi
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
| | - Khalid Al Harthy
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
| | - Fatma Alyaquobi
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
| | - Amina Al-Jardani
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
| | - Eskild Petersen
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
| | - Seif Al Abri
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
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7
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Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM, Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A. Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'. Nature 2020; 584:425-429. [PMID: 32604404 DOI: 10.1038/s41586-020-2488-1] [Citation(s) in RCA: 623] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/23/2020] [Indexed: 01/12/2023]
Abstract
On 21 February 2020, a resident of the municipality of Vo', a small town near Padua (Italy), died of pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection1. This was the first coronavirus disease 19 (COVID-19)-related death detected in Italy since the detection of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. Here we collected information on the demography, clinical presentation, hospitalization, contact network and the presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. From the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI): 2.1-3.3%). From the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI: 0.8-1.8%). Notably, 42.5% (95% CI: 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (that is, did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI: 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (P = 0.62 and 0.74 for E and RdRp genes, respectively, exact Wilcoxon-Mann-Whitney test). This study sheds light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides insights into its transmission dynamics and the efficacy of the implemented control measures.
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Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Nicolò Navarin
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Davide Abate
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Saverio G Parisi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Silvia Cocchio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessandro Sperduti
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Renato Salvador
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | | | | | - Ludovico Fava
- School of Medicine, University of Padova, Padua, Italy
| | - Matteo Drigo
- School of Medicine, University of Padova, Padua, Italy
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Vincenzo Baldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
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8
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Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM, Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A. Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'. Nature 2020. [PMID: 32604404 DOI: 10.1101/2020.04.17.20053157] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
On 21 February 2020, a resident of the municipality of Vo', a small town near Padua (Italy), died of pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection1. This was the first coronavirus disease 19 (COVID-19)-related death detected in Italy since the detection of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. Here we collected information on the demography, clinical presentation, hospitalization, contact network and the presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. From the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI): 2.1-3.3%). From the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI: 0.8-1.8%). Notably, 42.5% (95% CI: 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (that is, did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI: 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (P = 0.62 and 0.74 for E and RdRp genes, respectively, exact Wilcoxon-Mann-Whitney test). This study sheds light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides insights into its transmission dynamics and the efficacy of the implemented control measures.
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Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Nicolò Navarin
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Davide Abate
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Saverio G Parisi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Silvia Cocchio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessandro Sperduti
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Renato Salvador
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | | | | | - Ludovico Fava
- School of Medicine, University of Padova, Padua, Italy
| | - Matteo Drigo
- School of Medicine, University of Padova, Padua, Italy
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Vincenzo Baldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
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9
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Polonsky JA, Baidjoe A, Kamvar ZN, Cori A, Durski K, Edmunds WJ, Eggo RM, Funk S, Kaiser L, Keating P, de Waroux OLP, Marks M, Moraga P, Morgan O, Nouvellet P, Ratnayake R, Roberts CH, Whitworth J, Jombart T. Outbreak analytics: a developing data science for informing the response to emerging pathogens. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180276. [PMID: 31104603 PMCID: PMC6558557 DOI: 10.1098/rstb.2018.0276] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Despite continued efforts to improve health systems worldwide, emerging pathogen epidemics remain a major public health concern. Effective response to such outbreaks relies on timely intervention, ideally informed by all available sources of data. The collection, visualization and analysis of outbreak data are becoming increasingly complex, owing to the diversity in types of data, questions and available methods to address them. Recent advances have led to the rise of outbreak analytics, an emerging data science focused on the technological and methodological aspects of the outbreak data pipeline, from collection to analysis, modelling and reporting to inform outbreak response. In this article, we assess the current state of the field. After laying out the context of outbreak response, we critically review the most common analytics components, their inter-dependencies, data requirements and the type of information they can provide to inform operations in real time. We discuss some challenges and opportunities and conclude on the potential role of outbreak analytics for improving our understanding of, and response to outbreaks of emerging pathogens. This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control‘. This theme issue is linked with the earlier issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’.
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Affiliation(s)
- Jonathan A Polonsky
- 1 Department of Health Emergency Information and Risk Assessment, World Health Organization , Avenue Appia 20, 1211 Geneva , Switzerland.,3 Faculty of Medicine, University of Geneva , 1 rue Michel-Servet, 1211 Geneva , Switzerland
| | - Amrish Baidjoe
- 4 Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London , Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG , UK
| | - Zhian N Kamvar
- 4 Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London , Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG , UK
| | - Anne Cori
- 4 Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London , Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG , UK
| | - Kara Durski
- 2 Department of Infectious Hazard Management, World Health Organization , Avenue Appia 20, 1211 Geneva , Switzerland
| | - W John Edmunds
- 5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK.,6 Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK
| | - Rosalind M Eggo
- 5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK.,6 Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK
| | - Sebastian Funk
- 5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK.,6 Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK
| | - Laurent Kaiser
- 3 Faculty of Medicine, University of Geneva , 1 rue Michel-Servet, 1211 Geneva , Switzerland
| | - Patrick Keating
- 5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK.,8 UK Public Health Rapid Support Team , London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT , UK
| | - Olivier le Polain de Waroux
- 5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK.,8 UK Public Health Rapid Support Team , London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT , UK.,9 Public Health England , Wellington House, 133-155 Waterloo Road, London SE1 8UG , UK
| | - Michael Marks
- 7 Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK
| | - Paula Moraga
- 10 Centre for Health Informatics, Computing and Statistics (CHICAS), Lancaster Medical School, Lancaster University , Lancaster LA1 4YW , UK
| | - Oliver Morgan
- 1 Department of Health Emergency Information and Risk Assessment, World Health Organization , Avenue Appia 20, 1211 Geneva , Switzerland
| | - Pierre Nouvellet
- 4 Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London , Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG , UK.,11 School of Life Sciences, University of Sussex , Sussex House, Brighton BN1 9RH , UK
| | - Ruwan Ratnayake
- 5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK.,6 Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK
| | - Chrissy H Roberts
- 7 Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK
| | - Jimmy Whitworth
- 5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK.,8 UK Public Health Rapid Support Team , London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT , UK
| | - Thibaut Jombart
- 4 Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London , Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG , UK.,5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine , Keppel St, London WC1E 7HT , UK.,8 UK Public Health Rapid Support Team , London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT , UK
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10
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Routledge I, Lai S, Battle KE, Ghani AC, Gomez-Rodriguez M, Gustafson KB, Mishra S, Unwin J, Proctor JL, Tatem AJ, Li Z, Bhatt S. Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach. PLoS Comput Biol 2020; 16:e1007707. [PMID: 32203520 PMCID: PMC7117777 DOI: 10.1371/journal.pcbi.1007707] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/02/2020] [Accepted: 02/03/2020] [Indexed: 01/02/2023] Open
Abstract
In order to monitor progress towards malaria elimination, it is crucial to be able to measure changes in spatio-temporal transmission. However, common metrics of malaria transmission such as parasite prevalence are under powered in elimination contexts. China has achieved major reductions in malaria incidence and is on track to eliminate, having reporting zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain elimination and prevent re-emergence. This is particularly pertinent in Yunnan province, where the potential for local transmission is highest. Using a geo-located individual-level dataset of cases recorded in Yunnan province between 2011 and 2016, we introduce a novel Bayesian framework to model a latent diffusion process and estimate the joint likelihood of transmission between cases and the number of cases with unobserved sources of infection. This is used to estimate the case reproduction number, Rc. We use these estimates within spatio-temporal geostatistical models to map how transmission varied over time and space, estimate the timeline to elimination and the risk of resurgence. We estimate the mean Rc between 2011 and 2016 to be 0.171 (95% CI = 0.165, 0.178) for P. vivax cases and 0.089 (95% CI = 0.076, 0.103) for P. falciparum cases. From 2014 onwards, no cases were estimated to have a Rc value above one. An unobserved source of infection was estimated to be moderately likely (p>0.5) for 19/ 611 cases and high (p>0.8) for 2 cases, suggesting very high levels of case ascertainment. Our estimates suggest that, maintaining current intervention efforts, Yunnan is unlikely to experience sustained local transmission up to 2020. However, even with a mean of 0.005 projected up to 2020, locally-acquired cases are possible due to high levels of importation.
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Affiliation(s)
| | - Shengjie Lai
- University of Southampton, Southampton, United Kingdom
| | | | | | | | - Kyle B. Gustafson
- Institute for Disease Modelling, Bellevue, Washington, United States of America
| | | | | | - Joshua L. Proctor
- Institute for Disease Modelling, Bellevue, Washington, United States of America
| | | | - Zhongjie Li
- Chinese Centers for Disease Control and Prevention, Beijing, China
| | - Samir Bhatt
- Imperial College London, London, United Kingom
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11
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Moraga P, Dorigatti I, Kamvar ZN, Piatkowski P, Toikkanen SE, Nagraj VP, Donnelly CA, Jombart T. epiflows: an R package for risk assessment of travel-related spread of disease. F1000Res 2018; 7:1374. [PMID: 31543947 PMCID: PMC6738191 DOI: 10.12688/f1000research.16032.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 11/20/2022] Open
Abstract
As international travel increases worldwide, new surveillance tools are needed to help identify locations where diseases are most likely to be spread and prevention measures need to be implemented. In this paper we present epiflows, an R package for risk assessment of travel-related spread of disease. epiflows produces estimates of the expected number of symptomatic and/or asymptomatic infections that could be introduced to other locations from the source of infection. Estimates (average and confidence intervals) of the number of infections introduced elsewhere are obtained by integrating data on the cumulative number of cases reported, population movement, length of stay and information on the distributions of the incubation and infectious periods of the disease. The package also provides tools for geocoding and visualization. We illustrate the use of epiflows by assessing the risk of travel-related spread of yellow fever cases in Southeast Brazil in December 2016 to May 2017.
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Affiliation(s)
- Paula Moraga
- Department of Mathematical Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK
| | - Zhian N. Kamvar
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK
| | - Pawel Piatkowski
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - VP Nagraj
- School of Medicine, Research Computing, University of Virginia, Virginia, USA
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Thibaut Jombart
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
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12
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Moraga P, Dorigatti I, Kamvar ZN, Piatkowski P, Toikkanen SE, Nagraj VP, Donnelly CA, Jombart T. epiflows: an R package for risk assessment of travel-related spread of disease. F1000Res 2018; 7:1374. [PMID: 31543947 PMCID: PMC6738191 DOI: 10.12688/f1000research.16032.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 11/28/2022] Open
Abstract
As international travel increases worldwide, new surveillance tools are needed to help identify locations where diseases are most likely to be spread and prevention measures need to be implemented. In this paper we present epiflows, an R package for risk assessment of travel-related spread of disease. epiflows produces estimates of the expected number of symptomatic and/or asymptomatic infections that could be introduced to other locations from the source of infection. Estimates (average and confidence intervals) of the number of infections introduced elsewhere are obtained by integrating data on the cumulative number of cases reported, population movement, length of stay and information on the distributions of the incubation and infectious periods of the disease. The package also provides tools for geocoding and visualization. We illustrate the use of epiflows by assessing the risk of travel-related spread of yellow fever cases in Southeast Brazil in December 2016 to May 2017.
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Affiliation(s)
- Paula Moraga
- Department of Mathematical Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK
| | - Zhian N. Kamvar
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK
| | - Pawel Piatkowski
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - VP Nagraj
- School of Medicine, Research Computing, University of Virginia, Virginia, USA
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Thibaut Jombart
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
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