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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs
Nature Genetics, Volume 55, No. 1, Year 2023
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Description
The first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (mean = 27 tests per 100,000 people per day). We simulated COVID-19 epidemics in a prototypical low- and middle-income country to investigate how testing rates, sampling strategies and sequencing proportions jointly impact surveillance outcomes, and showed that low testing rates and spatiotemporal biases delay time to detection of new variants by weeks to months and can lead to unreliable estimates of variant prevalence, even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of approximately 100 tests per 100,000 people per day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing. © 2023, The Author(s).
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC9839449/bin/41588_2022_1267_MOESM1_ESM.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC9839449/bin/41588_2022_1267_MOESM2_ESM.pdf
Authors & Co-Authors
Han, Alvin X.
Netherlands, Amsterdam
Universiteit Van Amsterdam
Toporowski, Amy
Switzerland, Geneva
Foundation for Innovative new Diagnostics, Switzerland
Sacks, Jilian Amber
Switzerland, Geneva
Organisation Mondiale de la Santé
Perkins, Mark D.
Switzerland, Geneva
Organisation Mondiale de la Santé
Briand, Sylvie C.
Switzerland, Geneva
Organisation Mondiale de la Santé
van Kerkhove, Maria D.
Switzerland, Geneva
Organisation Mondiale de la Santé
Hannay, Emma Jane
Switzerland, Geneva
Foundation for Innovative new Diagnostics, Switzerland
Carmona, Sergio C.
Switzerland, Geneva
Foundation for Innovative new Diagnostics, Switzerland
Parker, Edyth
United States, San Diego
Scripps Research Institute
Nichols, Brooke E.
Netherlands, Amsterdam
Universiteit Van Amsterdam
Switzerland, Geneva
Foundation for Innovative new Diagnostics, Switzerland
United States, Boston
Boston University
Russell, Colin A.
Netherlands, Amsterdam
Universiteit Van Amsterdam
United States, Boston
Boston University
Statistics
Citations: 18
Authors: 11
Affiliations: 5
Identifiers
Doi:
10.1038/s41588-022-01267-w
ISSN:
10614036
Research Areas
Covid
Health System And Policy
Study Design
Cross Sectional Study