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

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.

Estimating the potential impact and diagnostic requirements for SARS-CoV-2 test-and-treat programs

“…individuals who present with similar respiratory symptoms): Based on the range of test positivity rates reported by various countries during the second-half of 2021 (when community testing was assumed to still be prevalent in most countries), 45 we assumed that test positivity rate was 10% at the start as well as end of an epidemic wave, and a 20% test positivity rate at the peak, linearly interpolating the demand for periods between these time points. 11,12…”

“…individuals who present with similar respiratory symptoms): Based on the range of test positivity rates reported by various countries during the second-half of 2021 (when community testing was assumed to still be prevalent in most countries), 45 we assumed that test positivity rate was 10% at the start as well as end of an epidemic wave, and a 20% test positivity rate at the peak, linearly interpolating the demand for periods between these time points. 11,12 We also simulated scenarios where household contacts of clinic-provided positively-tested individuals were given Ag-RDTs for self-testing for three consecutive days following the positive clinical test of the latter. Adherence (likelihood) to testing by asymptomatic household contacts was assumed to decrease linearly to 50% by the third day.…”

“…Here, we used an agent-based model (PATAT) 11,12 to demonstrate how testing rates and strategies affect the use and impact of antivirals. In the model, we focused on antigen rapid diagnostic tests (Ag-RDTs) which can easily be performed at point-of-care or be used as self-tests with short turnaround time needed to quickly identify high-risk infected individuals.…”

Tackling covid-19 variants

“…To tackle this issue, the World Health Organization launched the International Pathogen Surveillance Network (IPSN) in May 2023 as a part of its 10 year strategy for pathogen genomic surveillance 1112. Expanding access to genomic surveillance is important, but it is equally crucial to ensure a sufficiently large volume of testing so that sampled viruses accurately represent those circulating in the population 13…”

Direct immunoassay on a polyester microwell plate for colorimetric detection of the spike protein in swab and saliva samples

“…They only perform 27 tests per 100 000 people per day. 3 In response to this problem, there has been a major effort to develop new point-of-care (POC) methods that can rapidly detect the disease in individuals who have been infected. This is especially important in areas with limited laboratory resources, where testing options are limited.…”