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Shenoy A, Sharma B, Xu G, Kapoor R, Rho HA, Sangha K. God is in the rain: The impact of rainfall-induced early social distancing on COVID-19 outbreaks. JOURNAL OF HEALTH ECONOMICS 2022; 81:102575. [PMID: 34923344 PMCID: PMC8654737 DOI: 10.1016/j.jhealeco.2021.102575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 10/25/2021] [Accepted: 12/04/2021] [Indexed: 05/05/2023]
Abstract
We measure the benefit to society created by preventing COVID-19 deaths through a marginal increase in early social distancing. We exploit county-level rainfall on the last weekend before statewide lockdown in the early phase of the pandemic. After controlling for historical rainfall, temperature, and state fixed-effects, current rainfall is a plausibly exogenous instrument for social distancing. A one percent decrease in the population leaving home on the weekend before lockdown creates an average of 132 dollars of benefit per county resident within 2 weeks. The impacts of earlier distancing compound over time and mainly arise from lowering the risk of a major outbreak, yielding large but unevenly distributed social benefit.
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Affiliation(s)
- Ajay Shenoy
- University of California, Santa Cruz, United States. http://people.ucsc.edu/~azshenoy
| | - Bhavyaa Sharma
- University of California, Santa Cruz, United States. https://economics.ucsc.edu/about/people/phd.html
| | - Guanghong Xu
- University of California, Santa Cruz, United States. https://economics.ucsc.edu/about/people/phd.html
| | - Rolly Kapoor
- University of California, Santa Cruz, United States. https://economics.ucsc.edu/about/people/phd.html
| | - Haedong Aiden Rho
- University of California, Santa Cruz, United States. https://economics.ucsc.edu/about/people/phd.html
| | - Kinpritma Sangha
- Siemens Healthineers. https://www.linkedin.com/in/kinpritma-sangha-31100b92/
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2
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Muenchhoff M, Graf A, Krebs S, Quartucci C, Hasmann S, Hellmuth JC, Scherer C, Osterman A, Boehm S, Mandel C, Becker-Pennrich AS, Zoller M, Stubbe HC, Munker S, Munker D, Milger K, Gapp M, Schneider S, Ruhle A, Jocham L, Nicolai L, Pekayvaz K, Weinberger T, Mairhofer H, Khatamzas E, Hofmann K, Spaeth PM, Bender S, Kääb S, Zwissler B, Mayerle J, Behr J, von Bergwelt-Baildon M, Reincke M, Grabein B, Hinske CL, Blum H, Keppler OT. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020. ACTA ACUST UNITED AC 2021; 26. [PMID: 34713795 PMCID: PMC8555370 DOI: 10.2807/1560-7917.es.2021.26.43.2002066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background In the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data. Aim We applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata. Methods We investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission. Results We identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions. Conclusions Early spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.
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Affiliation(s)
- Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Caroline Quartucci
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sandra Hasmann
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Johannes C Hellmuth
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Clemens Scherer
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stephan Boehm
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Mandel
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Andrea Sabine Becker-Pennrich
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany
| | - Michael Zoller
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Hans Christian Stubbe
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Stefan Munker
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Dieter Munker
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Katrin Milger
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Madeleine Gapp
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stephanie Schneider
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Adrian Ruhle
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Linda Jocham
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Leo Nicolai
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Kami Pekayvaz
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Tobias Weinberger
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Helga Mairhofer
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Elham Khatamzas
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Katharina Hofmann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Spaeth
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Bernhard Zwissler
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Juergen Behr
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Michael von Bergwelt-Baildon
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Martin Reincke
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Beatrice Grabein
- Department of Clinical Microbiology and Hospital Hygiene, University Hospital, LMU Munich, Munich, Germany
| | - Christian Ludwig Hinske
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
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3
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Kerr CC, Stuart RM, Mistry D, Abeysuriya RG, Rosenfeld K, Hart GR, Núñez RC, Cohen JA, Selvaraj P, Hagedorn B, George L, Jastrzębski M, Izzo AS, Fowler G, Palmer A, Delport D, Scott N, Kelly SL, Bennette CS, Wagner BG, Chang ST, Oron AP, Wenger EA, Panovska-Griffiths J, Famulare M, Klein DJ. Covasim: An agent-based model of COVID-19 dynamics and interventions. PLoS Comput Biol 2021; 17:e1009149. [PMID: 34310589 DOI: 10.1101/2020.05.10.20097469] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/05/2021] [Accepted: 06/05/2021] [Indexed: 05/24/2023] Open
Abstract
The COVID-19 pandemic has created an urgent need for models that can project epidemic trends, explore intervention scenarios, and estimate resource needs. Here we describe the methodology of Covasim (COVID-19 Agent-based Simulator), an open-source model developed to help address these questions. Covasim includes country-specific demographic information on age structure and population size; realistic transmission networks in different social layers, including households, schools, workplaces, long-term care facilities, and communities; age-specific disease outcomes; and intrahost viral dynamics, including viral-load-based transmissibility. Covasim also supports an extensive set of interventions, including non-pharmaceutical interventions, such as physical distancing and protective equipment; pharmaceutical interventions, including vaccination; and testing interventions, such as symptomatic and asymptomatic testing, isolation, contact tracing, and quarantine. These interventions can incorporate the effects of delays, loss-to-follow-up, micro-targeting, and other factors. Implemented in pure Python, Covasim has been designed with equal emphasis on performance, ease of use, and flexibility: realistic and highly customized scenarios can be run on a standard laptop in under a minute. In collaboration with local health agencies and policymakers, Covasim has already been applied to examine epidemic dynamics and inform policy decisions in more than a dozen countries in Africa, Asia-Pacific, Europe, and North America.
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Affiliation(s)
- Cliff C Kerr
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Robyn M Stuart
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
- Burnet Institute, Melbourne, Victoria, Australia
| | - Dina Mistry
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | | | - Katherine Rosenfeld
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Gregory R Hart
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Rafael C Núñez
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Jamie A Cohen
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Prashanth Selvaraj
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Brittany Hagedorn
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Lauren George
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | | | - Amanda S Izzo
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Greer Fowler
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Anna Palmer
- Burnet Institute, Melbourne, Victoria, Australia
| | | | - Nick Scott
- Burnet Institute, Melbourne, Victoria, Australia
| | | | - Caroline S Bennette
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Bradley G Wagner
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Stewart T Chang
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Assaf P Oron
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Edward A Wenger
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Jasmina Panovska-Griffiths
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wolfson Centre for Mathematical Biology and The Queen's College, University of Oxford, Oxford, United Kingdom
| | - Michael Famulare
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Daniel J Klein
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
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4
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Kirkegaard JB, Mathiesen J, Sneppen K. Superspreading of airborne pathogens in a heterogeneous world. Sci Rep 2021; 11:11191. [PMID: 34045593 PMCID: PMC8160272 DOI: 10.1038/s41598-021-90666-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/13/2021] [Indexed: 12/23/2022] Open
Abstract
Epidemics are regularly associated with reports of superspreading: single individuals infecting many others. How do we determine if such events are due to people inherently being biological superspreaders or simply due to random chance? We present an analytically solvable model for airborne diseases which reveal the spreading statistics of epidemics in socio-spatial heterogeneous spaces and provide a baseline to which data may be compared. In contrast to classical SIR models, we explicitly model social events where airborne pathogen transmission allows a single individual to infect many simultaneously, a key feature that generates distinctive output statistics. We find that diseases that have a short duration of high infectiousness can give extreme statistics such as 20% infecting more than 80%, depending on the socio-spatial heterogeneity. Quantifying this by a distribution over sizes of social gatherings, tracking data of social proximity for university students suggest that this can be a approximated by a power law. Finally, we study mitigation efforts applied to our model. We find that the effect of banning large gatherings works equally well for diseases with any duration of infectiousness, but depends strongly on socio-spatial heterogeneity.
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Affiliation(s)
| | - Joachim Mathiesen
- Niels Bohr Institute, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Kim Sneppen
- Niels Bohr Institute, University of Copenhagen, 2100, Copenhagen, Denmark
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5
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Goyal A, Reeves DB, Cardozo-Ojeda EF, Schiffer JT, Mayer BT. Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events. eLife 2021; 10:e63537. [PMID: 33620317 PMCID: PMC7929560 DOI: 10.7554/elife.63537] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/22/2021] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 is difficult to contain because many transmissions occur during pre-symptomatic infection. Unlike influenza, most SARS-CoV-2-infected people do not transmit while a small percentage infect large numbers of people. We designed mathematical models which link observed viral loads with epidemiologic features of each virus, including distribution of transmissions attributed to each infected person and duration between symptom onset in the transmitter and secondarily infected person. We identify that people infected with SARS-CoV-2 or influenza can be highly contagious for less than 1 day, congruent with peak viral load. SARS-CoV-2 super-spreader events occur when an infected person is shedding at a very high viral load and has a high number of exposed contacts. The higher predisposition of SARS-CoV-2 toward super-spreading events cannot be attributed to additional weeks of shedding relative to influenza. Rather, a person infected with SARS-CoV-2 exposes more people within equivalent physical contact networks, likely due to aerosolization.
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Affiliation(s)
- Ashish Goyal
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Daniel B Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - E Fabian Cardozo-Ojeda
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Joshua T Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Medicine, University of WashingtonSeattleUnited States
- Clinical Research Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Bryan T Mayer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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6
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Resende PC, Delatorre E, Gräf T, Mir D, Motta FC, Appolinario LR, da Paixão ACD, Mendonça ACDF, Ogrzewalska M, Caetano B, Wallau GL, Docena C, dos Santos MC, de Almeida Ferreira J, Sousa Junior EC, da Silva SP, Fernandes SB, Vianna LA, Souza LDC, Ferro JFG, Nardy VB, Santos CA, Riediger I, do Carmo Debur M, Croda J, Oliveira WK, Abreu A, Bello G, Siqueira MM. Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil. Front Microbiol 2021; 11:615280. [PMID: 33679622 PMCID: PMC7925893 DOI: 10.3389/fmicb.2020.615280] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
A previous study demonstrates that most of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Brazilian strains fell in three local clades that were introduced from Europe around late February 2020. Here we investigated in more detail the origin of the major and most widely disseminated SARS-CoV-2 Brazilian lineage B.1.1.33. We recovered 190 whole viral genomes collected from 13 Brazilian states from February 29 to April 31, 2020 and combined them with other B.1.1 genomes collected globally. Our genomic survey confirms that lineage B.1.1.33 is responsible for a variable fraction of the community viral transmissions in Brazilian states, ranging from 2% of all SARS-CoV-2 genomes from Pernambuco to 80% of those from Rio de Janeiro. We detected a moderate prevalence (5-18%) of lineage B.1.1.33 in some South American countries and a very low prevalence (<1%) in North America, Europe, and Oceania. Our study reveals that lineage B.1.1.33 evolved from an ancestral clade, here designated B.1.1.33-like, that carries one of the two B.1.1.33 synapomorphic mutations. The B.1.1.33-like lineage may have been introduced from Europe or arose in Brazil in early February 2020 and a few weeks later gave origin to the lineage B.1.1.33. These SARS-CoV-2 lineages probably circulated during February 2020 and reached all Brazilian regions and multiple countries around the world by mid-March, before the implementation of air travel restrictions in Brazil. Our phylodynamic analysis also indicates that public health interventions were partially effective to control the expansion of lineage B.1.1.33 in Rio de Janeiro because its median effective reproductive number (R e ) was drastically reduced by about 66% during March 2020, but failed to bring it to below one. Continuous genomic surveillance of lineage B.1.1.33 might provide valuable information about epidemic dynamics and the effectiveness of public health interventions in some Brazilian states.
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Affiliation(s)
- Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Daiana Mir
- Unidad de Genomica y Bioinformatica, Centro Universitario Regional del Litoral Norte, Universidad de la Republica, Salto, Uruguay
| | - Fernando Couto Motta
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Luciana Reis Appolinario
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Anna Carolina Dias da Paixão
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Ana Carolina da Fonseca Mendonça
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Maria Ogrzewalska
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Braulia Caetano
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | | | - Cássia Docena
- Instituto Aggeu Magalhaes, Fundação Oswaldo Cruz, Recife, Brazil
| | | | | | | | | | | | - Lucas Alves Vianna
- Laboratorio Central de Saude Publica do Estado Espirito Santo (LACEN-ES), Vitoria, Brazil
| | | | - Jean F. G. Ferro
- Laboratorio Central de Saude Publica de Alagoas (LACEN-AL), Maceio, Brazil
| | - Vanessa B. Nardy
- Laboratorio Central de Saude Publica da Bahia (LACEN-BA), Salvador, Brazil
| | - Cliomar A. Santos
- Laboratorio Central de Saude Publica de Sergipe (LACEN-SE), Aracaju, Brazil
| | - Irina Riediger
- Laboratorio Central de Saude Publica de Parana (LACEN-PR), Curitiba, Brazil
| | | | - Júlio Croda
- Fiocruz Mato Grosso do Sul, Campo Grande, Brazil
- Universidade Federal de Mato Grosso do Sul – UFMS, Campo Grande, Brazil
| | | | - André Abreu
- Coordenadoria Geral de Laboratorios – Ministério da Saude, Brazilia, Brazil
| | - Gonzalo Bello
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marilda M. Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
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7
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Komissarov AB, Safina KR, Garushyants SK, Fadeev AV, Sergeeva MV, Ivanova AA, Danilenko DM, Lioznov D, Shneider OV, Shvyrev N, Spirin V, Glyzin D, Shchur V, Bazykin GA. Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia. Nat Commun 2021; 12:649. [PMID: 33510171 PMCID: PMC7844267 DOI: 10.1038/s41467-020-20880-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/17/2020] [Indexed: 01/19/2023] Open
Abstract
The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from at least 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions were not from China, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-3) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.0 [1.9, 4.3].
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Affiliation(s)
| | - Ksenia R Safina
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.,A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Artem V Fadeev
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Mariia V Sergeeva
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Anna A Ivanova
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia.,First Pavlov State Medical University, Saint Petersburg, Russia
| | - Olga V Shneider
- Vreden Russian Research Institute of Traumatology and Orthopaedics, Saint Petersburg, Russia
| | - Nikita Shvyrev
- National Research University Higher School of Economics, Moscow, Russia
| | - Vadim Spirin
- National Research University Higher School of Economics, Moscow, Russia
| | - Dmitry Glyzin
- National Research University Higher School of Economics, Moscow, Russia
| | - Vladimir Shchur
- National Research University Higher School of Economics, Moscow, Russia
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia. .,A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
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8
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Masui K. Interpretation of laboratory tests for prevention of the SARS-CoV-2 transmission. J Anesth 2020; 35:374-377. [PMID: 33161443 PMCID: PMC7648661 DOI: 10.1007/s00540-020-02872-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/23/2020] [Indexed: 01/07/2023]
Abstract
With the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), medical providers should take care to prevent the transmission of SARS-CoV-2 in hospitals including super-spreading. Understanding super-spreading would be useful to reduce future transmission. Some publications have shown clusters of SARS-CoV-2 such as at choir practice and in hospitals. Aerosol can be considered as a primary transmission route. As SARS-CoV-2 stability in aerosol is similar to SARS-CoV-1 with the higher reproductive number of SARS-CoV-2 than SARS-CoV-1, another factor causes rapidly spread-out, e.g. a higher discharge ratio from infected people or a higher viral intake ratio to human body. A basic research suggests higher infectivity of SARS-CoV-2 in the nose than the peripheral lung. Universal masking would be important to prevent the exposure of SARS-CoV-2 droplet to uninfected people. To detect SARS-CoV-2 infection, laboratory tests such as reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assays are applied. Although sensitivity and specificity are provided for the ability of the test, positive or negative prediction values are useful to indicate the possiblity of infection or non-infection in clinical practice. We have to realize that the positive and negative prediction values depend on the sensitivity, specificity, and infection probability of the patient.
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Affiliation(s)
- Kenichi Masui
- Department of Anesthesiology, Showa University School of Medicine, Hatanodai 1-5-8, Shinagawa, Tokyo, 142-8666, Japan.
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9
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Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread. Nat Commun 2020; 11:5558. [PMID: 33144575 PMCID: PMC7609670 DOI: 10.1038/s41467-020-19346-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/06/2020] [Indexed: 12/25/2022] Open
Abstract
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.
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Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Kasen K Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael A Martin
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - John J Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Anna S Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Manjeet Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, USA
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- The William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- The William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Trivikram Dasu
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, USA
| | | | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Katia Koelle
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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10
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Goyal A, Reeves DB, Cardozo-Ojeda EF, Schiffer JT, Mayer BT. Wrong person, place and time: viral load and contact network structure predict SARS-CoV-2 transmission and super-spreading events. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.08.07.20169920. [PMID: 33024978 PMCID: PMC7536880 DOI: 10.1101/2020.08.07.20169920] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 is difficult to contain because many transmissions occur during the pre-symptomatic phase of infection. Moreover, in contrast to influenza, while most SARS-CoV-2 infected people do not transmit the virus to anybody, a small percentage secondarily infect large numbers of people. We designed mathematical models of SARS-CoV-2 and influenza which link observed viral shedding patterns with key epidemiologic features of each virus, including distributions of the number of secondary cases attributed to each infected person (individual R0) and the duration between symptom onset in the transmitter and secondarily infected person (serial interval). We identify that people with SARS-CoV-2 or influenza infections are usually contagious for fewer than one day congruent with peak viral load several days after infection, and that transmission is unlikely below a certain viral load. SARS-CoV-2 super-spreader events with over 10 secondary infections occur when an infected person is briefly shedding at a very high viral load and has a high concurrent number of exposed contacts. The higher predisposition of SARS-CoV-2 towards super-spreading events is not due to its 1-2 additional weeks of viral shedding relative to influenza. Rather, a person infected with SARS-CoV-2 exposes more people within equivalent physical contact networks than a person infected with influenza, likely due to aerosolization of virus. Our results support policies that limit crowd size in indoor spaces and provide viral load benchmarks for infection control and therapeutic interventions intended to prevent secondary transmission.
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Affiliation(s)
- Ashish Goyal
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | - Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | | | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
- Department of Medicine, University of Washington, Seattle
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Bryan T. Mayer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
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11
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Maor M, Sulitzeanu-Kenan R, Chinitz D. When COVID-19, constitutional crisis, and political deadlock meet: the Israeli case from a disproportionate policy perspective. POLICY & SOCIETY 2020; 39:442-457. [PMID: 35039730 PMCID: PMC8754702 DOI: 10.1080/14494035.2020.1783792] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
This article describes the efforts made by the Israeli government to contain the spread of COVID-19, which were implemented amidst a constitutional crisis and a yearlong electoral impasse, under the leadership of Prime Minister Benjamin Netanyahu, who was awaiting a trial for charges of fraud, bribery, and breach of trust. It thereafter draws on the disproportionate policy perspective to ascertain the ideas and sensitivities that placed key policy responses on trajectories which prioritized differential policy responses over general, nation-wide solutions (and vice versa), even though data in the public domain supported the selection of opposing policy solutions on epidemiological or social welfare grounds. The article also gauges the consequences and implications of the policy choices made in the fight against COVID-19 for the disproportionate policy perspective. It argues that Prime Minister Netanyahu employed disproportionate policy responses both at the rhetorical level and on the ground in the fight against COVID-19; that during the crisis, Netanyahu enjoyed wide political leeway to employ disproportionate policy responses, and the general public exhibited a willingness to tolerate this; and (iii) that ascertaining the occurrence of disproportionate policy responses is not solely a matter of perception.
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Affiliation(s)
- Moshe Maor
- Department of Political Science, The Hebrew University of Jerusalem, Jerusalem, Israel
- CONTACT Moshe Maor
| | - Raanan Sulitzeanu-Kenan
- Department of Political Science & the Federmann School of Public Policy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Chinitz
- School of Public Health, The Hebrew University of Jerusalem, Jerusalem, Israel
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12
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Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.07.09.20149104. [PMID: 32676620 PMCID: PMC7359545 DOI: 10.1101/2020.07.09.20149104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide Safer-at-Home public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.
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Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Kasen K Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michael A Martin
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, United States of America
- Department of Biology, Emory University, Atlanta, GA, United States of America
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Trent Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - John J Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anna S Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mitchell Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Manjeet Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of 26 America and the William S. Middleton Memorial Veterans Hospital
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of 26 America and the William S. Middleton Memorial Veterans Hospital
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of 28 Medicine and Public Health, Madison, WI
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of 28 Medicine and Public Health, Madison, WI
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 30 Madison, WI, United States of America
| | - Trivikram Dasu
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Sanjib Bhattacharyya
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Katia Koelle
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, United States of America
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
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13
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Kain MP, Childs ML, Becker AD, Mordecai EA. Chopping the tail: how preventing superspreading can help to maintain COVID-19 control. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.06.30.20143115. [PMID: 32637966 PMCID: PMC7340192 DOI: 10.1101/2020.06.30.20143115] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Disease transmission is notoriously heterogeneous, and SARS-CoV-2 is no exception. A skewed distribution where few individuals or events are responsible for the majority of transmission can result in explosive, superspreading events, which produce rapid and volatile epidemic dynamics, especially early or late in epidemics. Anticipating and preventing superspreading events can produce large reductions in overall transmission rates. Here, we present a compartmental (SEIR) epidemiological model framework for estimating transmission parameters from multiple imperfectly observed data streams, including reported cases, deaths, and mobile phone-based mobility that incorporates individual-level heterogeneity in transmission using previous estimates for SARS-CoV-1 and SARS-CoV-2. We parameterize the model for COVID-19 epidemic dynamics by estimating a time-varying transmission rate that incorporates the impact of non-pharmaceutical intervention strategies that change over time, in five epidemiologically distinct settings---Los Angeles and Santa Clara Counties, California; Seattle (King County), Washington; Atlanta (Dekalb and Fulton Counties), Georgia; and Miami (Miami-Dade County), Florida. We find the effective reproduction number R E dropped below 1 rapidly following social distancing orders in mid-March, 2020 and remained there into June in Santa Clara County and Seattle, but climbed above 1 in late May in Los Angeles, Miami, and Atlanta, and has trended upward in all locations since April. With the fitted model, we ask: how does truncating the tail of the individual-level transmission rate distribution affect epidemic dynamics and control? We find interventions that truncate the transmission rate distribution while partially relaxing social distancing are broadly effective, with impacts on epidemic growth on par with the strongest population-wide social distancing observed in April, 2020. Given that social distancing interventions will be needed to maintain epidemic control until a vaccine becomes widely available, "chopping off the tail" to reduce the probability of superspreading events presents a promising option to alleviate the need for extreme general social distancing.
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Affiliation(s)
- Morgan P Kain
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Natural Capital Project, Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA
| | - Marissa L Childs
- Emmett Interdisciplinary Program in Environment and Resources, Stanford University, Stanford, CA, 94305, USA
| | | | - Erin A Mordecai
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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14
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Small M, Cavanagh D. Modelling Strong Control Measures for Epidemic Propagation With Networks-A COVID-19 Case Study. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2020; 8:109719-109731. [PMID: 34192104 PMCID: PMC8043504 DOI: 10.1109/access.2020.3001298] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/07/2020] [Indexed: 05/18/2023]
Abstract
We show that precise knowledge of epidemic transmission parameters is not required to build an informative model of the spread of disease. We propose a detailed model of the topology of the contact network under various external control regimes and demonstrate that this is sufficient to capture the salient dynamical characteristics and to inform decisions. Contact between individuals in the community is characterised by a contact graph, the structure of that contact graph is selected to mimic community control measures. Our model of city-level transmission of an infectious agent (SEIR model) characterises spread via a (a) scale-free contact network (no control); (b) a random graph (elimination of mass gatherings); and (c) small world lattice (partial to full lockdown-"social" distancing). This model exhibits good qualitative agreement between simulation and data from the 2020 pandemic spread of a novel coronavirus. Estimates of the relevant rate parameters of the SEIR model are obtained and we demonstrate the robustness of our model predictions under uncertainty of those estimates. The social context and utility of this work is identified, contributing to a highly effective pandemic response in Western Australia.
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Affiliation(s)
- Michael Small
- Integrated Energy Pty Ltd.ComoWA6152Australia
- Complex Systems GroupDepartment of Mathematics and StatisticsThe University of Western AustraliaPerthWA6009Australia
- Mineral ResourcesCommonwealth Scientific and Industrial Research OrganisationKensingtonWA6151Australia
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