SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

Alvin X. Han, Amy Toporowski, Jilian A. Sacks, Mark D. Perkins, Sylvie Briand, Maria van Kerkhove, Emma Hannay, Sergio Carmona, Bill Rodriguez, Edyth Parker, Brooke E. Nichols, Colin A. Russell

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)26-33
Number of pages8
JournalNature Genetics
Volume55
Issue number1
Early online date2023
DOIs
Publication statusPublished - Jan 2023

Cite this