Estimating Population Infection Rates from Non-random Testing Data: Evidence from the COVID-19 Pandemic

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2024 Sep 26

PMID 39325815

Authors

David Benatia

Raphael Godefroy

Joshua Lewis

Affiliations

Soon will be listed here.

Abstract

To effectively respond to an emerging infectious disease outbreak, policymakers need timely and accurate measures of disease prevalence in the general population. This paper presents a new methodology to estimate real-time population infection rates from non-random testing data. The approach compares how the observed positivity rate varies with the size of the tested population and applies this gradient to infer total population infections. Applying this methodology to daily testing data across U.S. states during the first wave of the COVID-19 pandemic, we estimated widespread undiagnosed COVID-19 infections. Nationwide, we found that for every identified case, there were 12 population infections. Our prevalence estimates align with results from seroprevalence surveys, alternate approaches to measuring COVID-19 infections, and total excess mortality during the first wave of the pandemic.

References

Billah M, Miah M, Khan M . Reproductive number of coronavirus: A systematic review and meta-analysis based on global level evidence. PLoS One. 2020; 15(11):e0242128. PMC: 7657547. DOI: 10.1371/journal.pone.0242128. View

Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y . Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia. N Engl J Med. 2020; 382(13):1199-1207. PMC: 7121484. DOI: 10.1056/NEJMoa2001316. View

Manski C, Molinari F . Estimating the COVID-19 infection rate: Anatomy of an inference problem. J Econom. 2020; 220(1):181-192. PMC: 7200382. DOI: 10.1016/j.jeconom.2020.04.041. View

Li R, Pei S, Chen B, Song Y, Zhang T, Yang W . Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2). Science. 2020; 368(6490):489-493. PMC: 7164387. DOI: 10.1126/science.abb3221. View

Linton N, Kobayashi T, Yang Y, Hayashi K, Akhmetzhanov A, Jung S . Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data. J Clin Med. 2020; 9(2). PMC: 7074197. DOI: 10.3390/jcm9020538. View

Pei S, Kandula S, Shaman J . Differential effects of intervention timing on COVID-19 spread in the United States. Sci Adv. 2020; 6(49). PMC: 7821895. DOI: 10.1126/sciadv.abd6370. View

Zeller M, Gangavarapu K, Anderson C, Smither A, Vanchiere J, Rose R . Emergence of an early SARS-CoV-2 epidemic in the United States. Cell. 2021; 184(19):4939-4952.e15. PMC: 8313480. DOI: 10.1016/j.cell.2021.07.030. View

Garcia-Garcia D, Vigo M, Fonfria E, Herrador Z, Navarro M, Bordehore C . Retrospective methodology to estimate daily infections from deaths (REMEDID) in COVID-19: the Spain case study. Sci Rep. 2021; 11(1):11274. PMC: 8163852. DOI: 10.1038/s41598-021-90051-7. View

Ai T, Yang Z, Hou H, Zhan C, Chen C, Lv W . Correlation of Chest CT and RT-PCR Testing for Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases. Radiology. 2020; 296(2):E32-E40. PMC: 7233399. DOI: 10.1148/radiol.2020200642. View

10.

Pan X, Chen D, Xia Y, Wu X, Li T, Ou X . Asymptomatic cases in a family cluster with SARS-CoV-2 infection. Lancet Infect Dis. 2020; 20(4):410-411. PMC: 7158985. DOI: 10.1016/S1473-3099(20)30114-6. View

11.

Maurano M, Ramaswami S, Zappile P, Dimartino D, Boytard L, Ribeiro-Dos-Santos A . Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region. Genome Res. 2020; 30(12):1781-1788. PMC: 7706732. DOI: 10.1101/gr.266676.120. View

12.

Xie X, Zhong Z, Zhao W, Zheng C, Wang F, Liu J . Chest CT for Typical Coronavirus Disease 2019 (COVID-19) Pneumonia: Relationship to Negative RT-PCR Testing. Radiology. 2020; 296(2):E41-E45. PMC: 7233363. DOI: 10.1148/radiol.2020200343. View

13.

Alene M, Yismaw L, Assemie M, Ketema D, Mengist B, Kassie B . Magnitude of asymptomatic COVID-19 cases throughout the course of infection: A systematic review and meta-analysis. PLoS One. 2021; 16(3):e0249090. PMC: 7987199. DOI: 10.1371/journal.pone.0249090. View

14.

Worobey M, Pekar J, Larsen B, Nelson M, Hill V, Joy J . The emergence of SARS-CoV-2 in Europe and North America. Science. 2020; 370(6516):564-570. PMC: 7810038. DOI: 10.1126/science.abc8169. View

15.

Sorci G, Faivre B, Morand S . Explaining among-country variation in COVID-19 case fatality rate. Sci Rep. 2020; 10(1):18909. PMC: 7609641. DOI: 10.1038/s41598-020-75848-2. View

16.

Bai Y, Yao L, Wei T, Tian F, Jin D, Chen L . Presumed Asymptomatic Carrier Transmission of COVID-19. JAMA. 2020; 323(14):1406-1407. PMC: 7042844. DOI: 10.1001/jama.2020.2565. View

17.

Verity R, Okell L, Dorigatti I, Winskill P, Whittaker C, Imai N . Estimates of the severity of coronavirus disease 2019: a model-based analysis. Lancet Infect Dis. 2020; 20(6):669-677. PMC: 7158570. DOI: 10.1016/S1473-3099(20)30243-7. View

18.

Perkins T, Cavany S, Moore S, Oidtman R, Lerch A, Poterek M . Estimating unobserved SARS-CoV-2 infections in the United States. Proc Natl Acad Sci U S A. 2020; 117(36):22597-22602. PMC: 7486725. DOI: 10.1073/pnas.2005476117. View

19.

Deng X, Gu W, Federman S, du Plessis L, Pybus O, Faria N . Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science. 2020; 369(6503):582-587. PMC: 7286545. DOI: 10.1126/science.abb9263. View

20.

Garcia-Garcia D, Morales E, de la Fuente-Nunez C, Vigo I, Fonfria E, Bordehore C . Identification of the first COVID-19 infections in the US using a retrospective analysis (REMEDID). Spat Spatiotemporal Epidemiol. 2022; 42:100517. PMC: 9087146. DOI: 10.1016/j.sste.2022.100517. View