{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T18:47:24Z","timestamp":1776451644974,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013562","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000}}],"reference-count":45,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:00:00Z","timestamp":1775606400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2023-05905"],"award-info":[{"award-number":["RGPIN-2023-05905"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Canadian Network for Modelling Infectious Diseases","award":["560516-2020"],"award-info":[{"award-number":["560516-2020"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"\n The highly transmissible Omicron variant of SARS-CoV-2 caused many infections in Newfoundland and Labrador, Canada, and the fraction of infections that were unreported varied as PCR testing capacity was exceeded and eligibility rules changed. Due to these inconsistencies in the testing rate, we developed a mechanistic model that was calibrated to serological data (Dec 2021\u2013May 2022) to estimate underreporting and understand the impact of non-pharmaceutical interventions on transmission. Our model considers the epidemiology of SARS-CoV-2 spread, natural and vaccine-derived immunity, and the booster dose vaccination campaign that was ongoing in Newfoundland and Labrador. We found that during the early spread of the Omicron variant, when the eligibility for tests that were reported in the provincial counts was less restrictive, three or fewer infections were unreported per reported case. After March 17, 2022, when test eligibility was more restrictive, the underreporting rate increased steadily, with an average of 24.2 infections unreported infections per reported case. We found that Omicron transmission was lower when schools were closed (mean control reproduction number,\n \n \n \n \n \n \n \u211b<\/mml:mi>\n \n c<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n = 1.98, 95% CI: 1.58\u20132.37), higher when open (mean\n \n \n \n \n \n \n \u211b<\/mml:mi>\n \n c<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n = 2.71, 95% CI: 2.31\u20133.11), and of the alert levels, the strictest alert level reduced transmission the most (mean\n \n \n \n \n \n \n \u211b<\/mml:mi>\n \n c<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n = 2.23, 95% CI: 1.98\u20132.53). When underreporting rates vary, the impact of non-pharmaceutical interventions, such as alert level systems and school closures, cannot be determined from reported cases. Our findings highlight the value of combining serological data with modelling to determine the impact of non-pharmaceutical interventions during pandemics when surveillance systems are constrained.\n <\/jats:p>","DOI":"10.1371\/journal.pcbi.1013562","type":"journal-article","created":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T17:45:21Z","timestamp":1775670321000},"page":"e1013562","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Quantifying SARS-CoV-2 Omicron variant spread and the impact of non-pharmaceutical interventions in Newfoundland and Labrador, Canada"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6102-6592","authenticated-orcid":true,"given":"Francis","family":"Anokye","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael W. Z.","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steve","family":"Walker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy","family":"Hurford","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,4,8]]},"reference":[{"key":"pcbi.1013562.ref001","unstructured":"World Health Organization. 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Changing contact patterns in Newfoundland and Labrador, Canada in response to public health measures during the COVID-19 pandemic. MedRxiv. 2025.","DOI":"10.1101\/2025.09.16.25335524"},{"issue":"2","key":"pcbi.1013562.ref009","first-page":"83","article-title":"Projections of the transmission of the Omicron variant for Toronto, Ontario, and Canada using surveillance data following recent changes in testing policies","volume":"7","author":"P Yuan","year":"2022","journal-title":"Infect Dis Model"},{"issue":"4","key":"pcbi.1013562.ref010","doi-asserted-by":"crossref","first-page":"155","DOI":"10.14745\/ccdr.v49i04a08","article-title":"Extensive SARS-CoV-2 testing reveals BA.1\/BA.2 asymptomatic rates and underreporting in school children","volume":"49","author":"MM Martignoni","year":"2023","journal-title":"Can Commun Dis Rep"},{"issue":"3","key":"pcbi.1013562.ref011","doi-asserted-by":"crossref","first-page":"2000045","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045","volume":"25","author":"VM Corman","year":"2020","journal-title":"Eurosurveillance"},{"issue":"4","key":"pcbi.1013562.ref012","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1097\/EDE.0000000000001361","article-title":"Estimating the Cumulative Incidence of SARS-CoV-2 Infection and the Infection Fatality Ratio in Light of Waning Antibodies","volume":"32","author":"K Shioda","year":"2021","journal-title":"Epidemiology"},{"issue":"31","key":"pcbi.1013562.ref013","doi-asserted-by":"crossref","DOI":"10.1503\/cmaj.230249","article-title":"The evolution of SARS-CoV-2 seroprevalence in Canada: a time-series study, 2020\u20132023","volume":"195","author":"TJ Murphy","year":"2023","journal-title":"Cmaj"},{"issue":"12","key":"pcbi.1013562.ref014","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1001\/jamainternmed.2020.4130","article-title":"Seroprevalence of antibodies to SARS-CoV-2 in 10 sites in the United States, March 23-May 12, 2020","volume":"180","author":"FP Havers","year":"2020","journal-title":"JAMA Intern Med"},{"issue":"47","key":"pcbi.1013562.ref015","doi-asserted-by":"crossref","DOI":"10.1503\/cmaj.221335","article-title":"Serial cross-sectional estimation of vaccine-and infection-induced SARS-CoV-2 seroprevalence in British Columbia, Canada","volume":"194","author":"DM Skowronski","year":"2022","journal-title":"CMAJ"},{"issue":"1","key":"pcbi.1013562.ref016","doi-asserted-by":"crossref","first-page":"1524","DOI":"10.1186\/s12889-024-18980-2","article-title":"Non-pharmaceutical interventions in containing COVID-19 pandemic after the roll-out of coronavirus vaccines: a systematic review","volume":"24","author":"X He","year":"2024","journal-title":"BMC Public Health"},{"key":"pcbi.1013562.ref017","unstructured":"COVID-19 Immunity Task Force. Mandate & Strategy; 2024. Available from: https:\/\/www.covid19immunitytaskforce.ca\/mandate-strategy\/"},{"key":"pcbi.1013562.ref018","unstructured":"Public Health Agency of Canada. COVID-19 epidemiology update \u2013 Canada (archived 2022-10-07). 2022. Available from: https:\/\/health-infobase.canada.ca\/covid-19\/archive\/2022-10-07\/"},{"key":"pcbi.1013562.ref019","unstructured":"Government of Newfoundland and Labrador. NL COVID-19 Alert Level System: Implications for Municipalities. 2020. Available from: https:\/\/www.gov.nl.ca\/ecc\/files\/NL-COVID-Table-for-MNL-Final-March-2021.pdf"},{"key":"pcbi.1013562.ref020","unstructured":"Government of Newfoundland and Labrador. NL Public Health Orders. 2020. Available from: https:\/\/www.gov.nl.ca\/covid-19\/updates-resources\/previous-public-health-orders\/"},{"key":"pcbi.1013562.ref021","unstructured":"Public Health Agency of Canada. Canadian COVID-19 vaccination coverage report. 2024. Available from: https:\/\/health-infobase.canada.ca\/covid-19\/vaccination-coverage\/"},{"issue":"19","key":"pcbi.1013562.ref022","doi-asserted-by":"crossref","DOI":"10.1503\/cmaj.200476","article-title":"Mathematical modelling of COVID-19 transmission and mitigation strategies in the population of Ontario, Canada","volume":"192","author":"AR Tuite","year":"2020","journal-title":"CMAJ"},{"issue":"12","key":"pcbi.1013562.ref023","article-title":"Evaluating the impacts of non-pharmaceutical interventions on the transmission dynamics of COVID-19 in Canada based on mobile network","volume":"16","author":"L Xue","year":"2021","journal-title":"PLoS One"},{"issue":"1","key":"pcbi.1013562.ref024","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1186\/s12889-022-13432-1","article-title":"Impact of non-pharmaceutical interventions and vaccination on COVID-19 outbreaks in Nunavut, Canada: a Canadian Immunization Research Network (CIRN) study","volume":"22","author":"TN Vilches","year":"2022","journal-title":"BMC Public Health"},{"key":"pcbi.1013562.ref025","doi-asserted-by":"crossref","unstructured":"Gelman A. Prior distributions for variance parameters in hierarchical models (comment on article by Browne and Draper). 2006.","DOI":"10.1214\/06-BA117A"},{"issue":"7","key":"pcbi.1013562.ref026","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1111\/oik.05985","article-title":"Moving beyond noninformative priors: why and how to choose weakly informative priors in Bayesian analyses","volume":"128","author":"NP Lemoine","year":"2019","journal-title":"Oikos"},{"key":"pcbi.1013562.ref027","unstructured":"Statistics Canada. Census Profile. 2021 Census of Population. 2022. Available from: https:\/\/www12.statcan.gc.ca\/census-recensement\/2021\/dp-pd\/prof\/index.cfm?Lang=E"},{"issue":"7","key":"pcbi.1013562.ref028","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.3390\/vaccines10071049","article-title":"Percentage of Asymptomatic Infections among SARS-CoV-2 Omicron Variant-Positive Individuals: A Systematic Review and Meta-Analysis","volume":"10","author":"W Shang","year":"2022","journal-title":"Vaccines (Basel)"},{"issue":"1","key":"pcbi.1013562.ref029","doi-asserted-by":"crossref","DOI":"10.1001\/jamanetworkopen.2020.35057","article-title":"SARS-CoV-2 Transmission From People Without COVID-19 Symptoms","volume":"4","author":"MA Johansson","year":"2021","journal-title":"JAMA Netw Open"},{"issue":"5152","key":"pcbi.1013562.ref030","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.15585\/mmwr.mm705152e3","article-title":"Investigation of a SARS-CoV-2 B.1.1.529 (Omicron) Variant Cluster - Nebraska, November-December 2021","volume":"70","author":"L Jansen","year":"2021","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"pcbi.1013562.ref031","doi-asserted-by":"crossref","first-page":"1073387","DOI":"10.3389\/fpubh.2022.1073387","article-title":"Clinical characteristics and risk factors analysis of viral shedding time in mildly symptomatic and asymptomatic patients with SARS-CoV-2 Omicron variant infection in Shanghai","volume":"10","author":"R Li","year":"2023","journal-title":"Front Public Health"},{"issue":"16","key":"pcbi.1013562.ref032","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1056\/NEJMoa2119451","article-title":"Covid-19 vaccine effectiveness against the Omicron (B. 1.1. 529) variant","volume":"386","author":"N Andrews","year":"2022","journal-title":"New England J Med"},{"issue":"1","key":"pcbi.1013562.ref033","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1007\/s11538-013-9918-2","article-title":"Estimating initial epidemic growth rates","volume":"76","author":"J Ma","year":"2014","journal-title":"Bull Math Biol"},{"key":"pcbi.1013562.ref034","doi-asserted-by":"crossref","unstructured":"Butcher J. Runge\u2013Kutta methods for ordinary differential equations. Numerical Analysis and Optimization: NAO-III, Muscat, Oman, January 2014. 2015. p. 37\u201358.","DOI":"10.1007\/978-3-319-17689-5_2"},{"key":"pcbi.1013562.ref035","unstructured":"Walker S, Guan W, Freeman J, Bolker B, Flynn-Primrose D. Macpan2: Fast and flexible compartmental modelling. 2025. Available from: https:\/\/canmod.github.io\/macpan2\/."},{"key":"pcbi.1013562.ref036","unstructured":"Anokye F, Li MW, Walker S, Hurford A. francisanokye\/quantifying_omicron_burden_in_NL: v1.0.0; 2026. Available from: https:\/\/doi.org\/10.5281\/zenodo.18497732"},{"key":"pcbi.1013562.ref037","doi-asserted-by":"crossref","first-page":"292","DOI":"10.14745\/ccdr.v48i78a01","article-title":"Counterfactuals of effects of vaccination and public health measures on COVID-19 cases in Canada: What could have happened?","volume":"48","author":"NH Ogden","year":"2022","journal-title":"Can Commun Dis Rep"},{"issue":"1","key":"pcbi.1013562.ref038","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1186\/s12879-025-10968-6","article-title":"Impact of adjustment for differential testing by age and sex on apparent epidemiology of SARS-CoV- 2 infection in Ontario, Canada","volume":"25","author":"S Bosco","year":"2025","journal-title":"BMC Infect Dis"},{"issue":"12","key":"pcbi.1013562.ref039","doi-asserted-by":"crossref","first-page":"230621","DOI":"10.1098\/rsos.230621","article-title":"Pharmaceutical and non-pharmaceutical interventions for controlling the COVID-19 pandemic","volume":"10","author":"J Molla","year":"2023","journal-title":"R Soc Open Sci"},{"key":"pcbi.1013562.ref040","unstructured":"Ontario COVID-19 Science Advisory Table and Modelling Consensus Table. Update on COVID-19 Projections, March 17, 2022. 2022. Available from: https:\/\/pandemics.utoronto.ca\/resources\/update-on-covid-19-projections-18\/"},{"key":"pcbi.1013562.ref041","unstructured":"Khan A. Omicron driving up Canada\u2019s R value at \u2018unprecedented\u2019 rate. Here\u2019s what that means. 2021. Available from: https:\/\/globalnews.ca\/news\/8449946\/omicron-canada-r-value-rate\/"},{"issue":"3","key":"pcbi.1013562.ref042","article-title":"The effective reproductive number of the Omicron variant of SARS-CoV-2 is several times relative to Delta","volume":"29","author":"Y Liu","year":"2022","journal-title":"J Travel Med"},{"key":"pcbi.1013562.ref043","unstructured":"Government of Newfoundland and Labrador. Report to the House of Assembly on the COVID-19 Public Health Emergency. 2022. Available from: https:\/\/www.assembly.nl.ca"},{"issue":"6","key":"pcbi.1013562.ref044","doi-asserted-by":"crossref","first-page":"240186","DOI":"10.1098\/rsos.240186","article-title":"Is SARS-CoV-2 elimination or mitigation best? Regional and disease characteristics determine the recommended strategy","volume":"11","author":"MM Martignoni","year":"2024","journal-title":"R Soc Open Sci"},{"key":"pcbi.1013562.ref045","unstructured":"CBC News. As N.L. warns of COVID-19\u2019s inevitability, immunocompromised people fear they\u2019ve been forgotten; 2022. Available from: https:\/\/www.cbc.ca\/lite\/story\/1.6307769"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1013562","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013562","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T18:00:39Z","timestamp":1776448839000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013562"}},"subtitle":[],"editor":[{"given":"Tom","family":"Britton","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,8]]},"references-count":45,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,4,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1013562","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,8]]}}}