{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T03:34:53Z","timestamp":1777865693269,"version":"3.51.4"},"reference-count":114,"publisher":"The Royal Society","issue":"1949","license":[{"start":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T00:00:00Z","timestamp":1777507200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T00:00:00Z","timestamp":1777507200000},"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","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Viral kinetics provide crucial insights into the biology and epidemiology of infections, with direct implications for basic science, therapeutics development and policy. The COVID-19 pandemic showcased the power of viral kinetics surveillance and modelling; however, our understanding of viral kinetics has been limited to retrospective analyses, convenience samples and bespoke models. To strengthen responses to ongoing and emerging outbreaks, we argue that viral kinetics should be a core component of pathogen surveillance. Building upon insights gained during the COVID-19 pandemic, we review ways that continuous viral kinetic surveillance supports infectious disease response by informing epidemiological parameters, development and deployment of therapeutics, and adaptive policy design. To achieve this, various challenges must be addressed regarding data standards, study design and communication. We advocate for the creation of a global, living library of viral kinetics data, with associated data sharing standards, modelling toolkits and on-demand epidemiological reports. Successfully integrating viral kinetics into active disease surveillance efforts will support both active outbreak response and improve the knowledge base vital for pandemic preparedness.<\/jats:p>\n                  <jats:p>This article is part of the Theo Murphy meeting issue \u2018Evaluating anti-infective drugs\u2019.<\/jats:p>","DOI":"10.1098\/rstb.2024.0347","type":"journal-article","created":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T07:16:12Z","timestamp":1777533372000},"source":"Crossref","is-referenced-by-count":0,"title":["Integrating viral kinetics into routine outbreak surveillance: challenges, opportunities and lessons from COVID-19"],"prefix":"10.1098","volume":"381","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1998-1844","authenticated-orcid":false,"given":"James A.","family":"Hay","sequence":"first","affiliation":[{"name":"University of Oxford 1 , ,","place":["Oxford, UK"],"department":["Pandemic Sciences Institute, Nuffield Department of Medicine"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5273-5234","authenticated-orcid":false,"given":"Daniel B.","family":"Larremore","sequence":"additional","affiliation":[{"name":"University of Colorado Boulder 2 , , ,","place":["Boulder, CO, USA"],"department":["BioFrontiers Institute"]},{"name":"University of Colorado Boulder 3 , , ,","place":["Boulder, CO, USA"],"department":["Department of Computer Science"]},{"name":"Santa Fe Institute 4 , , ,","place":["Santa Fe, NM, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9774-2435","authenticated-orcid":false,"given":"Aishani V.","family":"Aatresh","sequence":"additional","affiliation":[{"name":"Harvard Kennedy School 5 , , ,","place":["Cambridge, MA, USA, 02138"],"department":["Program on Science, Technology and Society"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6000-8387","authenticated-orcid":false,"given":"Stephen","family":"Kissler","sequence":"additional","affiliation":[{"name":"University of Colorado Boulder 3 , , ,","place":["Boulder, CO, USA"],"department":["Department of Computer Science"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2026,4,30]]},"reference":[{"key":"2026043003160550200_R1","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1085\/jgp.22.3.365","article-title":"The growth of bacteriophage","volume":"22","author":"Ellis","year":"1939","journal-title":"J. Gen. Physiol."},{"key":"2026043003160550200_R2","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1085\/jgp.13.5.557","article-title":"A method for the quantitative determination of bacteriophage","volume":"13","author":"Krueger","year":"1930","journal-title":"J. Gen. Physiol."},{"key":"2026043003160550200_R3","doi-asserted-by":"crossref","first-page":"4644","DOI":"10.1073\/pnas.86.12.4644","article-title":"Quantifying the infectivity of human immunodeficiency virus","volume":"86","author":"Layne","year":"1989","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2026043003160550200_R4","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1038\/s41564-022-01105-z","article-title":"Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness","volume":"7","author":"Ke","year":"2022","journal-title":"Nat. Microbiol."},{"key":"2026043003160550200_R5","doi-asserted-by":"crossref","first-page":"2489","DOI":"10.1056\/NEJMc2102507","article-title":"Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated persons","volume":"385","author":"Kissler","year":"2021","journal-title":"N. Engl. J. Med."},{"key":"2026043003160550200_R6","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.81849","article-title":"Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: a retrospective cohort study","volume":"11","author":"Hay","year":"2022","journal-title":"Elife"},{"key":"2026043003160550200_R7","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3002463","article-title":"Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants","volume":"22","author":"Russell","year":"2024","journal-title":"PLoS Biol."},{"key":"2026043003160550200_R8","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adk5108","article-title":"Modeling the transmission mitigation impact of testing for infectious diseases","volume":"10","author":"Middleton","year":"2024","journal-title":"Sci. Adv"},{"key":"2026043003160550200_R9","article-title":"This time is different: model-based evaluation of the implications of SARS-CoV-2 infection kinetics for disease control","author":"Johnson","year":"2020","journal-title":"bioRxiv"},{"key":"2026043003160550200_R10","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1002\/psp4.70055","article-title":"Viral dynamic models during COVID-19: are we ready for the next pandemic?","volume":"14","author":"Marc","year":"2025","journal-title":"CPT Pharmacometrics Syst. Pharmacol."},{"key":"2026043003160550200_R11","doi-asserted-by":"crossref","first-page":"e459","DOI":"10.1016\/S2666-5247(23)00398-1","article-title":"Viral clearance as a surrogate of clinical efficacy for COVID-19 therapies in outpatients: a systematic review and meta-analysis","volume":"5","author":"Elias","year":"2024","journal-title":"Lancet Microbe"},{"key":"2026043003160550200_R12","doi-asserted-by":"crossref","DOI":"10.1128\/aac.00192-22","article-title":"Characterizing SARS-CoV-2 viral clearance kinetics to improve the design of antiviral pharmacometric studies","volume":"66","author":"Watson","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"2026043003160550200_R13","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1093\/biostatistics\/kxac008","article-title":"Vaccine efficacy at a point in time","volume":"24","author":"Follmann","year":"2023","journal-title":"Biostatistics"},{"key":"2026043003160550200_R14","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1097\/EDE.0000000000001415","article-title":"Estimating vaccine efficacy against transmission via effect on viral load","volume":"32","author":"Kennedy-Shaffer","year":"2021","journal-title":"Epidemiology"},{"key":"2026043003160550200_R15","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1007\/s10928-014-9363-3","article-title":"Viral kinetic modeling: state of the art","volume":"41","author":"Canini","year":"2014","journal-title":"J. Pharmacokinet. Pharmacodyn."},{"key":"2026043003160550200_R16","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.69302","article-title":"Quantifying the relationship between SARS-CoV-2 viral load and infectiousness","volume":"10","author":"Marc","year":"2021","journal-title":"eLife"},{"key":"2026043003160550200_R17","doi-asserted-by":"crossref","DOI":"10.1172\/jci.insight.176286","article-title":"Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses","volume":"9","author":"Owens","year":"2024","journal-title":"JCI Insight"},{"key":"2026043003160550200_R18","doi-asserted-by":"crossref","DOI":"10.1126\/science.abi5273","article-title":"Estimating infectiousness throughout SARS-CoV-2 infection course","volume":"373","author":"Jones","year":"2021","journal-title":"Science"},{"key":"2026043003160550200_R19","article-title":"Just 2% of SARS-CoV-2\u2212positive individuals carry 90% of the virus circulating in communities","volume":"118","author":"Yang","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2026043003160550200_R20","doi-asserted-by":"crossref","DOI":"10.1126\/science.abe2424","article-title":"Transmission heterogeneities, kinetics, and controllability of SARS-CoV-2","volume":"371","author":"Sun","year":"2021","journal-title":"Science"},{"key":"2026043003160550200_R21","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1093\/jac\/dkg007","article-title":"Early administration of oral oseltamivir increases the benefits of influenza treatment","volume":"51","author":"Aoki","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"2026043003160550200_R22","doi-asserted-by":"crossref","first-page":"2252","DOI":"10.1093\/cid\/ciaa619","article-title":"To Interpret the SARS-CoV-2 test, consider the cycle threshold value","volume":"71","author":"Tom","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"2026043003160550200_R23","doi-asserted-by":"crossref","first-page":"e685","DOI":"10.1093\/cid\/ciaa1199","article-title":"College of American Pathologists (CAP) microbiology committee perspective: caution must be used in interpreting the cycle threshold (Ct) value","volume":"72","author":"Rhoads","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"2026043003160550200_R24","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3001333","article-title":"Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies","volume":"19","author":"Kissler","year":"2021","journal-title":"PLoS Biol."},{"key":"2026043003160550200_R25","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abc7112","article-title":"Potency and timing of antiviral therapy as determinants of duration of SARS-CoV-2 shedding and intensity of inflammatory response","volume":"6","author":"Goyal","year":"2020","journal-title":"Sci. Adv."},{"key":"2026043003160550200_R26","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/S1473-3099(23)00493-0","article-title":"Antiviral efficacy of molnupiravir versus ritonavir-boosted nirmatrelvir in patients with early symptomatic COVID-19 (PLATCOV): an open-label, phase 2, randomised, controlled, adaptive trial","volume":"24","author":"Schilling","year":"2024","journal-title":"Lancet Infect. Dis."},{"key":"2026043003160550200_R27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1012573","article-title":"Modelling the effectiveness of antiviral treatment strategies to prevent household transmission of acute respiratory viruses","volume":"20","author":"Zaaraoui","year":"2024","journal-title":"PLoS Comput. Biol."},{"key":"2026043003160550200_R28","doi-asserted-by":"crossref","DOI":"10.1002\/jmv.28854","article-title":"A mathematical model of SARS-CoV-2 immunity predicts paxlovid rebound","volume":"95","author":"Ranard","year":"2023","journal-title":"J. Med. Virol."},{"key":"2026043003160550200_R29","doi-asserted-by":"crossref","DOI":"10.1016\/j.epidem.2024.100812","article-title":"Enhanced testing can substantially improve defense against several types of respiratory virus pandemic","volume":"50","author":"Petrie","year":"2025","journal-title":"Epidemics"},{"key":"2026043003160550200_R30","doi-asserted-by":"crossref","first-page":"e184","DOI":"10.1016\/S2468-2667(21)00002-5","article-title":"Comparative cost-effectiveness of SARS-CoV-2 testing strategies in the USA: a modelling study","volume":"6","author":"Du","year":"2021","journal-title":"Lancet Public Health"},{"key":"2026043003160550200_R31","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1016\/S1473-3099(20)30630-7","article-title":"Comparison of molecular testing strategies for COVID-19 control: a mathematical modelling study","volume":"20","author":"Grassly","year":"2020","journal-title":"Lancet Infect. Dis."},{"key":"2026043003160550200_R32","doi-asserted-by":"crossref","DOI":"10.1017\/S0950268825100381","article-title":"A fundamental limit to the effectiveness of traveller screening with molecular tests","volume":"153","author":"Bubar","year":"2025","journal-title":"Epidemiol. Infect."},{"key":"2026043003160550200_R33","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abd5393","article-title":"Test sensitivity is secondary to frequency and turnaround time for COVID-19 screening","volume":"7","author":"Larremore","year":"2021","journal-title":"Sci. Adv."},{"key":"2026043003160550200_R34","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1186\/s12916-021-01982-x","article-title":"Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections","volume":"19","author":"Hellewell","year":"2021","journal-title":"BMC Med."},{"key":"2026043003160550200_R35","doi-asserted-by":"crossref","first-page":"e175","DOI":"10.1016\/S2468-2667(20)30308-X","article-title":"Quarantine and testing strategies in contact tracing for SARS-CoV-2: a modelling study","volume":"6","author":"Quilty","year":"2021","journal-title":"Lancet Public Health"},{"key":"2026043003160550200_R36","doi-asserted-by":"crossref","DOI":"10.1126\/science.abh0635","article-title":"Estimating epidemiologic dynamics from cross-sectional viral load distributions","volume":"373","author":"Hay","year":"2021","journal-title":"Science"},{"key":"2026043003160550200_R37","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.64683","article-title":"Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time","volume":"10","author":"Walker","year":"2021","journal-title":"eLife"},{"key":"2026043003160550200_R38","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-025-65237-6","article-title":"Nowcasting epidemic trends using hospital- and community-based virologic test data","volume":"16","author":"Lim","year":"2025","journal-title":"Nat. Commun."},{"key":"2026043003160550200_R39","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1013527","article-title":"Generalizing population RT-qPCR cycle threshold values-informed estimation of epidemiological dynamics: impact of surveillance practices and pathogen variability","volume":"21","author":"Lin","year":"2025","journal-title":"PLoS Comput. Biol."},{"key":"2026043003160550200_R40","article-title":"Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias","volume":"19","author":"Fryer","year":"2023","journal-title":"PLoS Pathog."},{"key":"2026043003160550200_R41","unstructured":"Total COVID-19 tests\n          . Our World in Data. Seehttps:\/\/ourworldindata.org\/grapher\/full-list-total-tests-for-covid-19?country=~GBR."},{"key":"2026043003160550200_R42","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S1473-3099(20)30196-1","article-title":"Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study","volume":"20","author":"To","year":"2020","journal-title":"Lancet Infect. Dis."},{"key":"2026043003160550200_R43","doi-asserted-by":"crossref","DOI":"10.1136\/bmjopen-2020-039856","article-title":"Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases","volume":"10","author":"Byrne","year":"2020","journal-title":"BMJ Open"},{"key":"2026043003160550200_R44","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1038\/s41591-020-1016-z","article-title":"Author correction: temporal dynamics in viral shedding and transmissibility of COVID-19","volume":"26","author":"He","year":"2020","journal-title":"Nat. Med."},{"key":"2026043003160550200_R45","doi-asserted-by":"crossref","first-page":"262","DOI":"10.7326\/M20-1495","article-title":"Variation in false-negative rate of reverse transcriptase polymerase chain reaction-based SARS-CoV-2 tests by time since exposure","volume":"173","author":"Kucirka","year":"2020","journal-title":"Ann. Intern. Med."},{"key":"2026043003160550200_R46","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":"Hellewell","year":"2020","journal-title":"Lancet Glob. Health"},{"key":"2026043003160550200_R47","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/s41586-020-2196-x","article-title":"Virological assessment of hospitalized patients with COVID-2019","volume":"581","author":"W\u00f6lfel","year":"2020","journal-title":"Nature"},{"key":"2026043003160550200_R48","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1011437","article-title":"How robust are estimates of key parameters in standard viral dynamic models?","volume":"20","author":"Zitzmann","year":"2024","journal-title":"PLoS Comput. Biol."},{"key":"2026043003160550200_R49","article-title":"Viral load kinetics of SARS-CoV-2 infection in saliva in Korean patients: a prospective multi-center comparative study","volume":"35","author":"Kim","year":"2020","journal-title":"J. Korean Med. Sci."},{"key":"2026043003160550200_R50","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2017962118","article-title":"Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort","volume":"118","author":"N\u00e9ant","year":"2021","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2026043003160550200_R51","doi-asserted-by":"crossref","first-page":"2127","DOI":"10.1111\/jgs.19499","article-title":"Kinetics of SARS-CoV-2 shedding in nursing home residents and staff","volume":"73","author":"Katz","year":"2024","journal-title":"J. Am. Geriatr. Soc."},{"key":"2026043003160550200_R52","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S1473-3099(21)00648-4","article-title":"Community transmission and viral load kinetics of the SARS-CoV-2 delta (B.1.617.2) variant in vaccinated and unvaccinated individuals in the UK: a prospective, longitudinal, cohort study","volume":"22","author":"Singanayagam","year":"2022","journal-title":"Lancet Infect. Dis."},{"key":"2026043003160550200_R53","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1016\/S2213-2600(22)00226-0","article-title":"Onset and window of SARS-CoV-2 infectiousness and temporal correlation with symptom onset: a prospective, longitudinal, community cohort study","volume":"10","author":"Hakki","year":"2022","journal-title":"Lancet Respir. Med."},{"key":"2026043003160550200_R54","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S1473-3099(20)30985-3","article-title":"Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study","volume":"21","author":"Marks","year":"2021","journal-title":"Lancet Infect. Dis."},{"key":"2026043003160550200_R55","doi-asserted-by":"crossref","first-page":"1975","DOI":"10.3201\/eid3009.240853","article-title":"SARS-CoV-2 dynamics in the Premier League testing program, United Kingdom","volume":"30","author":"Kucharski","year":"2024","journal-title":"Emerg. Infect. Dis."},{"key":"2026043003160550200_R56","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1093\/infdis\/jiab386","article-title":"Higher viral load drives infrequent severe acute respiratory syndrome Coronavirus 2 transmission between asymptomatic residence hall roommates","volume":"224","author":"Bjorkman","year":"2021","journal-title":"J. Infect. Dis."},{"key":"2026043003160550200_R57","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/S0140-6736(23)00917-0","article-title":"Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London","volume":"402","author":"Bailey","year":"2023","journal-title":"Lancet"},{"key":"2026043003160550200_R58","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2111477118","article-title":"In vivo kinetics of SARS-CoV-2 infection and its relationship with a person\u2019s infectiousness","volume":"118","author":"Ke","year":"2021","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2026043003160550200_R59","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.60122","article-title":"Quantifying antibody kinetics and RNA detection during early-phase SARS-CoV-2 infection by time since symptom onset","volume":"9","author":"Borremans","year":"2020","journal-title":"Elife"},{"key":"2026043003160550200_R60","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.jinf.2022.10.027","article-title":"Viral dynamics of the SARS-CoV-2 Omicron variant among household contacts with 2 or 3 COVID-19 vaccine doses","volume":"85","author":"Kandel","year":"2022","journal-title":"J. Infect."},{"key":"2026043003160550200_R61","doi-asserted-by":"crossref","DOI":"10.1186\/s12916-021-02220-0","article-title":"Modelling upper respiratory viral load dynamics of SARS-CoV-2","volume":"20","author":"Challenger","year":"2022","journal-title":"BMC Med."},{"key":"2026043003160550200_R62","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.1002\/psp4.13022","article-title":"SARS-CoV-2 viral dynamic modeling to inform model selection and timing and efficacy of antiviral therapy","volume":"12","author":"Zhang","year":"2023","journal-title":"CPT Pharmacometrics Syst. Pharmacol."},{"key":"2026043003160550200_R63","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2406303121","article-title":"The kinetics of SARS-CoV-2 infection based on a human challenge study","volume":"121","author":"Iyaniwura","year":"2024","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2026043003160550200_R64","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1111\/bcp.14486","article-title":"Model-informed drug repurposing: viral kinetic modelling to prioritize rational drug combinations for COVID-19","volume":"87","author":"Dodds","year":"2021","journal-title":"Br. J. Clin. Pharmacol."},{"key":"2026043003160550200_R65","doi-asserted-by":"crossref","first-page":"e370","DOI":"10.1016\/S1473-3099(22)00434-0","article-title":"The Johns Hopkins University Center for Systems Science and Engineering COVID-19 dashboard: data collection process, challenges faced, and lessons learned","volume":"22","author":"Dong","year":"2022","journal-title":"Lancet Infect. Dis."},{"key":"2026043003160550200_R66","doi-asserted-by":"crossref","first-page":"e75","DOI":"10.1016\/S1473-3099(20)30631-9","article-title":"SeroTracker: a global SARS-CoV-2 seroprevalence dashboard","volume":"21","author":"Arora","year":"2021","journal-title":"Lancet Infect. Dis."},{"key":"2026043003160550200_R67","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"2026043003160550200_R68","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.58989","article-title":"A global immunological observatory to meet a time of pandemics","volume":"9","author":"Mina","year":"2020","journal-title":"eLife"},{"key":"2026043003160550200_R69","unstructured":"GitHub\n          . GitHub\u2014mrc-ide\/epireviewhttps:\/\/github.com\/mrc-ide\/epireview"},{"key":"2026043003160550200_R70","unstructured":"Elsland\n              WSS\n            , Cuomo-DannenburgG, CoriA, Sangeeta BhatiaHJU, McCabeR, ImaiN. Systematic review of transmission and modelling parameters of nine WHO blue-print priority pathogens 2023. Seehttps:\/\/www.crd.york.ac.uk\/prospero\/display_record.php?ID=CRD42023393345."},{"key":"2026043003160550200_R71","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1007\/978-3-031-48408-7_16","volume-title":"Principles and practice of emergency research response","author":"Aatresh","year":"2024"},{"key":"2026043003160550200_R72","doi-asserted-by":"crossref","DOI":"10.1098\/rsif.2014.0094","article-title":"Within-host viral dynamics of dengue serotype 1 infection","volume":"11","author":"Clapham","year":"2014","journal-title":"J. R. Soc. Interface"},{"key":"2026043003160550200_R73","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1111\/imr.12697","article-title":"Within-host modeling of blood-stage malaria","volume":"285","author":"Khoury","year":"2018","journal-title":"Immunol. Rev."},{"key":"2026043003160550200_R74","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1111\/imr.12687","article-title":"Mathematical modeling of within-host Zika virus dynamics","volume":"285","author":"Best","year":"2018","journal-title":"Immunol. Rev."},{"key":"2026043003160550200_R75","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/nrgastro.2015.97","article-title":"Modelling hepatitis C therapy\u2014predicting effects of treatment","volume":"12","author":"Perelson","year":"2015","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"2026043003160550200_R76","first-page":"147","article-title":"SARS-CoV-2 viral load and shedding kinetics","volume":"21","author":"Puhach","year":"2023","journal-title":"Nat. Rev. Microbiol"},{"key":"2026043003160550200_R77","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1093\/infdis\/jiv225","article-title":"Influenza A virus shedding and infectivity in households","volume":"212","author":"Tsang","year":"2015","journal-title":"J. Infect. Dis."},{"key":"2026043003160550200_R78","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0154418","article-title":"Individual correlates of infectivity of influenza A virus infections in households","volume":"11","author":"Tsang","year":"2016","journal-title":"PLoS One"},{"key":"2026043003160550200_R79","doi-asserted-by":"crossref","DOI":"10.1016\/j.epidem.2022.100612","article-title":"The challenges of data in future pandemics","volume":"40","author":"Shadbolt","year":"2022","journal-title":"Epidemics"},{"key":"2026043003160550200_R80","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2026043003160550200_R81","doi-asserted-by":"crossref","DOI":"10.3390\/v14061294","article-title":"Nationwide harmonization effort for semi-quantitative reporting of SARS-CoV-2 PCR test results in Belgium","volume":"14","author":"Cuypers","year":"2022","journal-title":"Viruses"},{"key":"2026043003160550200_R82","doi-asserted-by":"crossref","first-page":"2554","DOI":"10.3390\/diagnostics13152554","article-title":"How South Africa used national Cycle Threshold (Ct) values to continuously monitor SARS-CoV-2 laboratory test quality","volume":"13","author":"Scott","year":"2023","journal-title":"Diagnostics"},{"key":"2026043003160550200_R83","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1111\/irv.12068","article-title":"The consortium for the standardization of influenza seroepidemiology (CONSISE): a global partnership to standardize influenza seroepidemiology and develop influenza investigation protocols to inform public health policy","volume":"7","author":"Van Kerkhove","year":"2013","journal-title":"Influenza Other Respir. Viruses"},{"key":"2026043003160550200_R84","doi-asserted-by":"crossref","DOI":"10.3390\/v16071057","article-title":"ct2vl: A robust public resource for converting SARS-CoV-2 Ct values to viral loads","volume":"16","author":"Hill","year":"2024","journal-title":"Viruses"},{"key":"2026043003160550200_R85","doi-asserted-by":"crossref","DOI":"10.3389\/fpubh.2024.1408193","article-title":"Infectious disease surveillance needs for the United States: lessons from Covid-19","volume":"12","author":"Lipsitch","year":"2024","journal-title":"Front. Public Health"},{"key":"2026043003160550200_R86","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1038\/s41586-024-07029-4","article-title":"Prevalence of persistent SARS-CoV-2 in a large community surveillance study","volume":"626","author":"Ghafari","year":"2024","journal-title":"Nature"},{"key":"2026043003160550200_R87","doi-asserted-by":"crossref","DOI":"10.1126\/science.abg0821","article-title":"SARS-CoV-2 within-host diversity and transmission","volume":"372","author":"Lythgoe","year":"2021","journal-title":"Science"},{"key":"2026043003160550200_R88","doi-asserted-by":"crossref","first-page":"e218","DOI":"10.1016\/S2589-7500(20)30059-5","article-title":"Improving epidemic surveillance and response: big data is dead, long live big data","volume":"2","author":"Buckee","year":"2020","journal-title":"Lancet Digit. Health"},{"key":"2026043003160550200_R89","doi-asserted-by":"crossref","DOI":"10.1016\/j.jcv.2023.105420","article-title":"Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: a longitudinal cohort study","volume":"161","author":"Drain","year":"2023","journal-title":"J. Clin. Virol."},{"key":"2026043003160550200_R90","doi-asserted-by":"crossref","first-page":"1615","DOI":"10.1093\/cid\/cis238","article-title":"Nomenclature for immune correlates of protection after vaccination","volume":"54","author":"Plotkin","year":"2012","journal-title":"Clin. Infect. Dis."},{"key":"2026043003160550200_R91","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1002\/sim.4780080407","article-title":"Surrogate endpoints in clinical trials: definition and operational criteria","volume":"8","author":"Prentice","year":"1989","journal-title":"Stat. Med"},{"key":"2026043003160550200_R92","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.jinf.2021.03.018","article-title":"Exhaled SARS-CoV-2 quantified by face-mask sampling in hospitalised patients with COVID-19","volume":"82","author":"Williams","year":"2021","journal-title":"J. Infect."},{"key":"2026043003160550200_R93","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.01612-24","article-title":"Influenza virus infection and aerosol shedding kinetics in a controlled human infection model","volume":"98","author":"Shetty","year":"2024","journal-title":"J. Virol."},{"key":"2026043003160550200_R94","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/j.cmi.2022.07.005","article-title":"Exhaled SARS-CoV-2 RNA viral load kinetics measured by facemask sampling associates with household transmission","volume":"29","author":"Pan","year":"2023","journal-title":"Clin. Microbiol. Infect."},{"key":"2026043003160550200_R95","doi-asserted-by":"crossref","DOI":"10.1016\/j.fhj.2024.100175","article-title":"Implementation of facemask sampling for the detection of infectious individuals with SARS-CoV-2 in high stakes clinical examinations-a feasibility study","volume":"11","author":"Pan","year":"2024","journal-title":"Future Healthc. J."},{"key":"2026043003160550200_R96","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1008704","article-title":"Minimal transmission in an influenza A (H3N2) human challenge-transmission model within a controlled exposure environment","volume":"16","author":"Nguyen-Van-Tam","year":"2020","journal-title":"PLoS Pathog."},{"key":"2026043003160550200_R97","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/s41467-022-35652-0","article-title":"Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa","volume":"14","author":"Sun","year":"2023","journal-title":"Nat. Commun."},{"key":"2026043003160550200_R98","unstructured":"Chen\n              M\n            \n          . 2020COVID-19 pharmacology resource center. Seehttps:\/\/web.archive.org\/web\/20240419040027\/https:\/\/www.covidpharmacology.com\/."},{"key":"2026043003160550200_R99","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1008409","article-title":"Practical considerations for measuring the effective reproductive number, Rt","volume":"16","author":"Gostic","year":"2020","journal-title":"PLoS Comput. Biol."},{"key":"2026043003160550200_R100","doi-asserted-by":"crossref","first-page":"112","DOI":"10.12688\/wellcomeopenres.16006.2","article-title":"Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts","volume":"5","author":"Abbott","year":"2020","journal-title":"Wellcome Open Res."},{"key":"2026043003160550200_R101","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1011439","article-title":"Estimating the epidemic reproduction number from temporally aggregated incidence data: a statistical modelling approach and software tool","volume":"19","author":"Nash","year":"2023","journal-title":"PLoS Comput. Biol."},{"key":"2026043003160550200_R102","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1002\/cpt.2223","article-title":"Systematic review and patient-level meta-analysis of SARS-CoV-2 viral dynamics to model response to antiviral therapies","volume":"110","author":"Gastine","year":"2021","journal-title":"Clin. Pharmacol. Ther."},{"key":"2026043003160550200_R103","doi-asserted-by":"crossref","DOI":"10.1016\/j.epidem.2022.100569","article-title":"RAMPVIS: answering the challenges of building visualisation capabilities for large-scale emergency responses","volume":"39","author":"Chen","year":"2022","journal-title":"Epidemics"},{"key":"2026043003160550200_R104","first-page":"924","article-title":"Visual preferences for communicating modelling: a global analysis of COVID-19 policy and decision makers","volume":"10","author":"Hadley","year":"2025","journal-title":"Infect. Dis. Model."},{"key":"2026043003160550200_R105","doi-asserted-by":"crossref","DOI":"10.1016\/j.epidem.2021.100520","article-title":"Communicating uncertainty in epidemic models","volume":"37","author":"McCabe","year":"2021","journal-title":"Epidemics"},{"key":"2026043003160550200_R106","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.1016\/S2666-5247(20)30172-5","article-title":"SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis","volume":"2","author":"Cevik","year":"2021","journal-title":"Lancet Microbe"},{"key":"2026043003160550200_R107","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1017\/S0022172400062410","article-title":"Effect of specific humoral immunity and some non-specific factors on resistance of volunteers to respiratory coronavirus infection","volume":"95","author":"Callow","year":"1985","journal-title":"J. Hyg."},{"key":"2026043003160550200_R108","doi-asserted-by":"crossref","first-page":"7590","DOI":"10.1128\/JVI.01623-05","article-title":"Kinetics of influenza A virus infection in humans","volume":"80","author":"Baccam","year":"2006","journal-title":"J. Virol."},{"key":"2026043003160550200_R109","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-014-0538-4","article-title":"Epidemiologic data and pathogen genome sequences: a powerful synergy for public health","volume":"15","author":"Grad","year":"2014","journal-title":"Genome Biol."},{"key":"2026043003160550200_R110","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.00480-18","article-title":"Real-time analysis and visualization of pathogen sequence data","volume":"56","author":"Neher","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"2026043003160550200_R111","doi-asserted-by":"crossref","DOI":"10.1016\/j.epidem.2024.100755","article-title":"Nowcasting and forecasting the 2022 U.S. mpox outbreak: support for public health decision making and lessons learned","volume":"47","author":"Charniga","year":"2024","journal-title":"Epidemics"},{"key":"2026043003160550200_R112","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1111\/irv.12629","article-title":"Longitudinal active sampling for respiratory viral infections across age groups","volume":"13","author":"Galanti","year":"2019","journal-title":"Influenza Other Respir. Viruses"},{"key":"2026043003160550200_R113","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1093\/cid\/civ486","article-title":"Community surveillance of respiratory viruses among families in the Utah Better Identification of Germs-Longitudinal Viral Epidemiology (BIG-LoVE) study","volume":"61","author":"Byington","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"2026043003160550200_R114","doi-asserted-by":"crossref","first-page":"e30","DOI":"10.1016\/S2468-2667(20)30282-6","article-title":"Community prevalence of SARS-CoV-2 in England from April to November, 2020: results from the ONS Coronavirus infection survey","volume":"6","author":"Pouwels","year":"2021","journal-title":"Lancet Public Health"}],"container-title":["Philosophical Transactions B"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/royalsocietypublishing.org\/rstb\/article-pdf\/doi\/10.1098\/rstb.2024.0347\/6135601\/rstb.2024.0347.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/royalsocietypublishing.org\/rstb\/article-pdf\/doi\/10.1098\/rstb.2024.0347\/6135601\/rstb.2024.0347.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T07:16:29Z","timestamp":1777533389000},"score":1,"resource":{"primary":{"URL":"https:\/\/royalsocietypublishing.org\/rstb\/article\/381\/1949\/20240347\/481550\/Integrating-viral-kinetics-into-routine-outbreak"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,30]]},"references-count":114,"journal-issue":{"issue":"1949","published-online":{"date-parts":[[2026,4,30]]},"published-print":{"date-parts":[[2026,4,30]]}},"URL":"https:\/\/doi.org\/10.1098\/rstb.2024.0347","relation":{},"ISSN":["0962-8436","1471-2970"],"issn-type":[{"value":"0962-8436","type":"print"},{"value":"1471-2970","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,30]]},"article-number":"20240347"}}