A pooled testing strategy for identifying SARS-CoV-2 at low prevalence.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
13
05
2020
accepted:
12
10
2020
pubmed:
22
10
2020
medline:
23
1
2021
entrez:
21
10
2020
Statut:
ppublish
Résumé
Suppressing infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will probably require the rapid identification and isolation of individuals infected with the virus on an ongoing basis. Reverse-transcription polymerase chain reaction (RT-PCR) tests are accurate but costly, which makes the regular testing of every individual expensive. These costs are a challenge for all countries around the world, but particularly for low-to-middle-income countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups
Identifiants
pubmed: 33086375
doi: 10.1038/s41586-020-2885-5
pii: 10.1038/s41586-020-2885-5
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
276-280Commentaires et corrections
Type : ErratumIn
Références
Dorfman, R. The detection of defective members of large populations. Ann. Math. Stat. 14, 436–440 (1943).
doi: 10.1214/aoms/1177731363
Hwang, F. K. A method for detecting all defective members in a population by group testing. J. Am. Stat. Assoc. 67, 605–608 (1972).
doi: 10.1080/01621459.1972.10481257
Allemann, A. in Information Theory, Combinatorics, and Search Theory. Lecture Notes in Computer Science Vol. 7777 (Aydinian, H. et al.) 569–596 (Springer, 2013).
Aldridge, M., Johnson, O. & Scarlett, J. Group testing: an information theory perspective. Found. Trends Commun. Inf. Theory 15, 196–392 (2019).
doi: 10.1561/0100000099
Ghosh, S. et al. A compressed sensing approach to group-testing for COVID-19 detection. Preprint at https://arxiv.org/abs/2005.07895 (2020).
Heng, B. W. & Scarlett, J. Non-adaptive group testing in the linear regime: strong converse and approximate recovery. Preprint at https://arxiv.org/abs/2006.01325 (2020).
Broder, A. Z. & Kumar, R. A note on double pooling tests. Preprint at https://arxiv.org/abs/2004.01684 (2020).
Arevalo-Rodriguez, I. et al. False negative results of initial RT-PCR assays for COVID-19: a systematic review. Preprint at https://doi.org/10.1101/2020.04.16.20066787 (2020).
Lohse, S. et al. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people. Lancet Infect. Dis. 20, 1231–1232 (2020).
doi: 10.1016/S1473-3099(20)30362-5
pubmed: 32530425
pmcid: 7194818
Yelin, I. et al. Evaluation of COVID-19 RT-qPCR test in multi sample pools. Clin. Infect. Dis. https://doi.org/10.1093/cid/ciaa531 (2020).
Shental, N. et al. Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers. Sci. Adv. 6, eabc5961 (2020).
doi: 10.1126/sciadv.abc5961
pubmed: 32917716
pmcid: 7485993
Medicare. Medicare Administrative Contractor (MAC) COVID-19 Test Pricing. https://www.cms.gov/files/document/mac-covid-19-test-pricing.pdf (2020).
Corman, V. M. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 25, 2000045 (2020).
pmcid: 6988269
Sanche, S. et al. High contagiousness and rapid spread of severe acute respiratory syndrome coronavirus 2. Emerg. Infect. Dis. 26, 1470–1477 (2020).
doi: 10.3201/eid2607.200282
pubmed: 32255761
pmcid: 7323562
Office of National Statistics. Coronavirus (COVID-19) Infection Survey pilot: England and Wales, 4 September 2020. https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/englandandwales4september2020 (UK Department of Health & Social Care, 2020).
Pouwels, K. B. et al. Community prevalence of SARS-CoV-2 in England: results from the ONS Coronavirus Infection Survey Pilot. Preprint at https://doi.org/10.1101/2020.07.06.20147348 (2020).
Office of National Statistics. COVID-19 Infection Survey (Pilot): Methods and Further Information: Test Sensitivity and Specificity. https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/methodologies/covid19infectionsurveypilotmethodsandfurtherinformation#test-sensitivity-and-specificity (UK Department of Health & Social Care, 2020).
Office of National Statistics. Weekly Statistics for NHS Test and Trace (England) and coronavirus testing (UK): 27 August to 2 September. Annex Table 1: People newly tested for COVID-19 under Pillars 1 and 2, England. https://www.gov.uk/government/publications/nhs-test-and-trace-england-and-coronavirus-testing-uk-statistics-27-august-to-2-september-2020/weekly-statistics-for-nhs-test-and-trace-england-and-coronavirus-testing-uk-27-august-to-2-september#annex-table-1 (UK Department of Health & Social Care, 2020).
Reijns M. A. M. et al. A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection. Preprint at https://doi.org/10.1101/2020.07.14.20154005 (2020).
Wölfel, R. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469 (2020).
doi: 10.1038/s41586-020-2196-x
pubmed: 32235945
Long, Q. X. et al. Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nat. Med. 26, 1200–1204 (2020).
doi: 10.1038/s41591-020-0965-6
pubmed: 32555424
Watson, J., Whiting, P. F. & Brush, J. E. Interpreting a covid-19 test result. Br. Med. J. 369, m1808 (2020).
doi: 10.1136/bmj.m1808
Kucirka, L. M., Lauer, S. A., Laeyendecker, O., Boon, D. & Lessler, J. Variation in false-negative rate of reverse transcriptase polymerase chain reaction-based SARS-CoV-2 by time since exposure. Ann. Intern. Med. 173, 262–267 (2020)
doi: 10.7326/M20-1495
pubmed: 32422057
Jaafar, R. et al. Correlation between 3790 qPCR positives samples and positive cell cultures including 1941 SARS-CoV-2 isolates. Clin. Infect. Dis. https://doi.org/10.1093/cid/ciaa1491 (2020).
Service, R. F. One number could help reveal how infectious a COVID-19 patient is. Should test results include it? Science https://www.sciencemag.org/news/2020/09/one-number-could-help-reveal-how-infectious-covid-19-patient-should-test-results (2020).
Afshordi, N., Holder, B., Bahrami, M. & Lichtblau, D. Diverse local epidemics reveal the distinct effects of population density, demographics, climate, depletion of susceptibles, and intervention in the first wave of covid-19 in the United States. Preprint at https://arxiv.org/abs/2007.00159 (2020).