{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:17:59Z","timestamp":1772173079320,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010375","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,8,25]],"date-time":"2022-08-25T00:00:00Z","timestamp":1661385600000}}],"reference-count":57,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2022,8,15]],"date-time":"2022-08-15T00:00:00Z","timestamp":1660521600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2031536"],"award-info":[{"award-number":["2031536"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["NU38OT000297"],"award-info":[{"award-number":["NU38OT000297"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"\n To define appropriate planning scenarios for future pandemics of respiratory pathogens, it is important to understand the initial transmission dynamics of COVID-19 during 2020. Here, we fit an age-stratified compartmental model with a flexible underlying transmission term to daily COVID-19 death data from states in the contiguous U.S. and to national and sub-national data from around the world. The daily death data of the first months of the COVID-19 pandemic was qualitatively categorized into one of four main profile types: \u201cspring single-peak\u201d, \u201csummer single-peak\u201d, \u201cspring\/summer two-peak\u201d and \u201cbroad with shoulder\u201d. We estimated a reproduction number\n R<\/jats:italic>\n as a function of calendar time\n t<\/jats:italic>\n \n c<\/jats:italic>\n <\/jats:sub>\n and as a function of time since the first death reported in that population (local pandemic time,\n t<\/jats:italic>\n \n p<\/jats:italic>\n <\/jats:sub>\n ). Contrary to the diversity of categories and range of magnitudes in death incidence profiles, the\n R<\/jats:italic>\n (\n t<\/jats:italic>\n \n p<\/jats:italic>\n <\/jats:sub>\n ) profiles were much more homogeneous. We found that in both the contiguous U.S. and globally, the initial value of both\n R<\/jats:italic>\n (\n t<\/jats:italic>\n \n c<\/jats:italic>\n <\/jats:sub>\n ) and\n R<\/jats:italic>\n (\n t<\/jats:italic>\n \n p<\/jats:italic>\n <\/jats:sub>\n ) was substantial: at or above two. However, during the early months, pandemic time\n R<\/jats:italic>\n (\n t<\/jats:italic>\n \n p<\/jats:italic>\n <\/jats:sub>\n ) decreased exponentially to a value that hovered around one. This decrease was accompanied by a reduction in the variance of\n R<\/jats:italic>\n (\n t<\/jats:italic>\n \n p<\/jats:italic>\n <\/jats:sub>\n ). For calendar time\n R<\/jats:italic>\n (\n t<\/jats:italic>\n \n c<\/jats:italic>\n <\/jats:sub>\n ), the decrease in magnitude was slower and non-exponential, with a smaller reduction in variance. Intriguingly, similar trends of exponential decrease and reduced variance were not observed in raw death data. Our findings suggest that the combination of specific government responses and spontaneous changes in behaviour ensured that transmissibility dropped, rather than remaining constant, during the initial phases of a pandemic. Future pandemic planning scenarios should include models that assume similar decreases in transmissibility, which lead to longer epidemics with lower peaks when compared with models based on constant transmissibility.\n <\/jats:p>","DOI":"10.1371\/journal.pcbi.1010375","type":"journal-article","created":{"date-parts":[[2022,8,15]],"date-time":"2022-08-15T13:39:22Z","timestamp":1660570762000},"page":"e1010375","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Consistent pattern of epidemic slowing across many geographies led to longer, flatter initial waves of the COVID-19 pandemic"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9164-0008","authenticated-orcid":true,"given":"Michal","family":"Ben-Nun","sequence":"first","affiliation":[]},{"given":"Pete","family":"Riley","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0735-7769","authenticated-orcid":true,"given":"James","family":"Turtle","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7904-4804","authenticated-orcid":true,"given":"Steven","family":"Riley","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,8,15]]},"reference":[{"key":"pcbi.1010375.ref001","unstructured":"The COVID Tracking Project;. https:\/\/covidtracking.com\/."},{"key":"pcbi.1010375.ref002","unstructured":"Coronavirus (COVID-19) Vaccinations;. https:\/\/ourworldindata.org\/covid-vaccinations."},{"key":"pcbi.1010375.ref003","doi-asserted-by":"crossref","DOI":"10.1126\/science.abg3055","article-title":"Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England","volume":"372","author":"NG Davies","year":"2021","journal-title":"Science"},{"key":"pcbi.1010375.ref004","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/s41586-021-03470-x","article-title":"Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England","volume":"593","author":"E Volz","year":"2021","journal-title":"Nature"},{"key":"pcbi.1010375.ref005","unstructured":"Tang JW, Tambyah PA, Hui DSC. Emergence of a new SARS-CoV-2 variant in the UK. J Infect;."},{"key":"pcbi.1010375.ref006","unstructured":"Tang JW, Toovey OTR, Harvey KN, Hui DDS. Introduction of the South African SARS-CoV-2 variant 501Y.V2 into the UK. J Infect;."},{"key":"pcbi.1010375.ref007","unstructured":"PANGO lineages;. https:\/\/cov-lineages.org\/global_report.html."},{"issue":"1","key":"pcbi.1010375.ref008","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/s41597-020-00609-9","article-title":"A structured open dataset of government interventions in response to COVID-19","volume":"7","author":"A Desvars-Larrive","year":"2020","journal-title":"Sci Data"},{"key":"pcbi.1010375.ref009","unstructured":"Coronavirus Government Response Tracker;. https:\/\/www.bsg.ox.ac.uk\/research\/research-projects\/coronavirus-government-response-tracker."},{"key":"pcbi.1010375.ref010","unstructured":"Tracking Public Health and Social Measures;. https:\/\/www.who.int\/emergencies\/diseases\/novel-coronavirus-2019\/phsm."},{"issue":"10","key":"pcbi.1010375.ref011","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1016\/S1473-3099(20)30457-6","article-title":"Effectiveness of isolation, testing, contact tracing and physical distancing on reducing transmission of SARS-CoV-2 in different settings","volume":"20","author":"A Kucharski","year":"2021","journal-title":"The Lancet"},{"issue":"8","key":"pcbi.1010375.ref012","doi-asserted-by":"crossref","first-page":"e0239352","DOI":"10.1371\/journal.pone.0239352","article-title":"Mitigation Strategies and Compliance in the Covid-19 Fight; How Much Compliance is Enough?","volume":"16","author":"S Mukerjee","year":"2021","journal-title":"PLOS ONE"},{"issue":"4","key":"pcbi.1010375.ref013","doi-asserted-by":"crossref","first-page":"e488","DOI":"10.1016\/S2214-109X(20)30074-7","article-title":"Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts","volume":"8","author":"J Hellewell","year":"2020","journal-title":"Lancet Glob Health"},{"key":"pcbi.1010375.ref014","article-title":"Effect of early application of social distancing interventions on COVID-19 mortality over the first pandemic wave: An analysis of longitudinal data from 37 countries","author":"D Piovani","year":"2020","journal-title":"J Infect"},{"key":"pcbi.1010375.ref015","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1038\/s41562-020-01009-0","article-title":"Ranking the effectiveness of worldwide COVID-19 government interventions","volume":"4","author":"N Haug","year":"2020","journal-title":"Nature Human Behaviour"},{"issue":"40","key":"pcbi.1010375.ref016","article-title":"The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories","volume":"19","author":"CMMID COVID-19 Working Group","year":"2021","journal-title":"BMC Medicine"},{"key":"pcbi.1010375.ref017","article-title":"The basic reproduction number of SARS-CoV-2: a scoping review of available evidence","author":"A Barber","year":"2020","journal-title":"medRxiv"},{"key":"pcbi.1010375.ref018","doi-asserted-by":"crossref","first-page":"100445","DOI":"10.1016\/j.epidem.2021.100445","article-title":"Estimating the global reduction in transmission and rise in detection capacity of the novel coronavirus SARS-CoV-2 in early 2020","volume":"35","author":"A Belloir","year":"2021","journal-title":"Epidemics"},{"issue":"6","key":"pcbi.1010375.ref019","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1016\/S1473-3099(20)30162-6","article-title":"Interventions to mitigate early spread of SARS-CoV-2 in Singapore: a modelling study","volume":"20","author":"JR Koo","year":"2020","journal-title":"The Lancet Infectious Diseases"},{"issue":"7820","key":"pcbi.1010375.ref020","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s41586-020-2405-7","article-title":"Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe","volume":"584","author":"S Flaxman","year":"2020","journal-title":"Nature"},{"issue":"6531","key":"pcbi.1010375.ref021","doi-asserted-by":"crossref","DOI":"10.1126\/science.abd9338","article-title":"The effectiveness of eight nonpharmaceutical interventions against COVID-19 in 41 countries","volume":"371","author":"JM Brauner","year":"2020","journal-title":"Science"},{"key":"pcbi.1010375.ref022","article-title":"Physical distancing interventions and incidence of coronavirus disease 2019: natural experiment in 149 countries","volume":"370","author":"N Islam","year":"2020","journal-title":"BMJ"},{"issue":"6489","key":"pcbi.1010375.ref023","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1126\/science.aba9757","article-title":"The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak","volume":"368","author":"M Chinazzi","year":"2020","journal-title":"Science"},{"issue":"5","key":"pcbi.1010375.ref024","doi-asserted-by":"crossref","first-page":"e261","DOI":"10.1016\/S2468-2667(20)30073-6","article-title":"The effect of control strategies to reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China: a modelling study","volume":"5","author":"K Prem","year":"2020","journal-title":"The Lancet Public Health"},{"issue":"10","key":"pcbi.1010375.ref025","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1038\/s41591-020-1036-8","article-title":"Using a real-world network to model localized COVID-19 control strategies","volume":"26","author":"JA Firth","year":"2020","journal-title":"Nat Med"},{"issue":"10","key":"pcbi.1010375.ref026","doi-asserted-by":"crossref","first-page":"e1008388","DOI":"10.1371\/journal.pcbi.1008388","article-title":"A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies","volume":"16","author":"A McCombs","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010375.ref027","first-page":"376","article-title":"Estimates of regional infectivity of COVID-19 in the United Kingdom following imposition of social distancing measures","author":"R Challen","year":"2021","journal-title":"Philosophical Transactions of the Royal Society B"},{"issue":"9","key":"pcbi.1010375.ref028","doi-asserted-by":"crossref","first-page":"e1004392","DOI":"10.1371\/journal.pcbi.1004392","article-title":"Early Characterization of the Severity and Transmissibility of Pandemic Influenza Using Clinical Episode Data from Multiple Populations","volume":"11","author":"P Riley","year":"2015","journal-title":"PLoS Comput Biol"},{"issue":"5","key":"pcbi.1010375.ref029","doi-asserted-by":"crossref","first-page":"e1007013","DOI":"10.1371\/journal.pcbi.1007013","article-title":"Forecasting national and regional influenza-like illness for the USA","volume":"15","author":"M Ben-Nun","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010375.ref030","doi-asserted-by":"crossref","first-page":"e1009230","DOI":"10.1371\/journal.pcbi.1009230","article-title":"Accurate influenza forecasts using type-specific incidence data for small geographical units","author":"J Turtle","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010375.ref031","doi-asserted-by":"crossref","DOI":"10.1201\/b14835","volume-title":"Markov Chain Monte Carlo in Practice","author":"WR Gilks","year":"1995"},{"key":"pcbi.1010375.ref032","unstructured":"COVID-19 Map\u2014Johns Hopkins Coronavirus Resource Center;. https:\/\/coronavirus.jhu.edu\/map.html."},{"issue":"7823","key":"pcbi.1010375.ref033","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/d41586-020-02497-w","article-title":"How many people has the coronavirus killed?","volume":"585","author":"G Viglione","year":"2020","journal-title":"Nature"},{"key":"pcbi.1010375.ref034","doi-asserted-by":"crossref","DOI":"10.15585\/mmwr.mm6942e2","article-title":"Excess Deaths Associated with COVID-19, by Age and Race and Ethnicity \u2014 United States, January 26\u2013October 3, 2020","volume":"69","author":"LM Rossen","year":"2020","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"pcbi.1010375.ref035","unstructured":"United Nations Population Division. wpp2019: World Population Prospects 2019; 2020."},{"key":"pcbi.1010375.ref036","unstructured":"Walker K, Herman M. tidycensus: Load US Census Boundary and Attribute Data; 2020."},{"key":"pcbi.1010375.ref037","unstructured":"U S Census Bureau. American Community Survey 2014-2018 5-Year Estimates; 2019."},{"issue":"6","key":"pcbi.1010375.ref038","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/S1473-3099(20)30243-7","article-title":"Estimates of the severity of coronavirus disease 2019: a model-based analysis","volume":"20","author":"R Verity","year":"2020","journal-title":"Lancet Infect Dis"},{"issue":"6502","key":"pcbi.1010375.ref039","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1126\/science.abc0035","article-title":"The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries","volume":"369","author":"PGT Walker","year":"2020","journal-title":"Science"},{"issue":"6","key":"pcbi.1010375.ref040","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A new look at the statistical model identification","volume":"19","author":"H Akaike","year":"1974","journal-title":"IEEE Trans Automat Contr"},{"issue":"10","key":"pcbi.1010375.ref041","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1056\/NEJMoa2001191","article-title":"First Case of 2019 Novel Coronavirus in the United States","volume":"382","author":"ML Holshue","year":"2020","journal-title":"N Engl J Med"},{"issue":"9","key":"pcbi.1010375.ref042","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1093\/aje\/kwt133","article-title":"A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics","volume":"178","author":"A Cori","year":"2013","journal-title":"Am J Epidemiol"},{"key":"pcbi.1010375.ref043","unstructured":"Cori A, Kamvar Z, Stockwin J, Jombart T, Dahlqwist E, FitzJohn R, et al. EpiEstim v2.2-3: A tool to estimate time varying instantaneous reproduction number during epidemics; 2021. https:\/\/github.com\/mrc-ide\/EpiEstim."},{"key":"pcbi.1010375.ref044","first-page":"312","article-title":"The pandemic\u2019s true death toll: millions more than official counts","volume":"601","author":"A David","journal-title":"Nature"},{"key":"pcbi.1010375.ref045","doi-asserted-by":"crossref","first-page":"e69336","DOI":"10.7554\/eLife.69336","article-title":"Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset","volume":"10","author":"K Ariel","year":"2021","journal-title":"eLife"},{"issue":"3","key":"pcbi.1010375.ref046","doi-asserted-by":"crossref","DOI":"10.1136\/bmjgh-2020-004564","article-title":"Excess mortality during the COVID-19 pandemic: a geospatial and statistical analysis in Aden governorate, Yemen","volume":"6","author":"ES Koum Besson","year":"2021","journal-title":"BMJ Global Health"},{"key":"pcbi.1010375.ref047","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.ijid.2021.09.049","article-title":"Excess mortality during the COVID-19 pandemic: a geospatial and statistical analysis in Mogadishu, Somalia","volume":"113","author":"A Warsame","year":"2021","journal-title":"Int J Infect Dis"},{"key":"pcbi.1010375.ref048","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/s41586-021-03914-4","article-title":"Burden and characteristics of COVID-19 in the United States during 2020","author":"S Pei","year":"2021","journal-title":"Nature"},{"key":"pcbi.1010375.ref049","first-page":"1469","article-title":"Variation in the COVID-19 infection\u2013fatality ratio by age, time, and geography during the pre-vaccine era: a systematic analysis","author":"The COVID-19 Forecast Team","year":"2022","journal-title":"The Lancet"},{"key":"pcbi.1010375.ref050","unstructured":"Emergency Use Authorization;. https:\/\/www.fda.gov\/emergency-preparedness-and-response\/mcm-legal-regulatory-and-policy-framework\/emergency-use-authorization#coviddrugs."},{"key":"pcbi.1010375.ref051","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1007\/s00466-020-01880-8","article-title":"The reproduction number of COVID-19 and its correlation with public health interventions","volume":"66","author":"K Linka","year":"2020","journal-title":"Comput Mech"},{"key":"pcbi.1010375.ref052","article-title":"A SEIR-like model with a time-dependent contagion factor describes the dynamics of the Covid-19 pandemic","author":"R Dickman","year":"2020","journal-title":"medRxiv"},{"issue":"12","key":"pcbi.1010375.ref053","doi-asserted-by":"crossref","first-page":"e1008274","DOI":"10.1371\/journal.pcbi.1008274","article-title":"Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing","volume":"16","author":"SC Anderson","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"33","key":"pcbi.1010375.ref054","doi-asserted-by":"crossref","first-page":"19873","DOI":"10.1073\/pnas.2009033117","article-title":"Timing social distancing to avert unmanageable COVID-19 hospital surges","volume":"117","author":"D Duque","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010375.ref055","unstructured":"Covid Data Tracker;. https:\/\/covid.cdc.gov\/covid-data-tracker\/#variant-proportions."},{"key":"pcbi.1010375.ref056","unstructured":"Tracking SARS-CoV-2 Variants;. https:\/\/www.who.int\/en\/activities\/tracking-SARS-CoV-2-variants\/."},{"key":"pcbi.1010375.ref057","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/nature03063","article-title":"Transmissibility of 1918 pandemic influenza","volume":"432","author":"CE Mills","year":"2004","journal-title":"Nature"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1010375","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,8,25]],"date-time":"2022-08-25T00:00:00Z","timestamp":1661385600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010375","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,25]],"date-time":"2022-08-25T13:59:32Z","timestamp":1661435972000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010375"}},"subtitle":[],"editor":[{"given":"Eric","family":"Lofgren","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,8,15]]},"references-count":57,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2022,8,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010375","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.03.31.22273267","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,15]]}}}