Maintaining genomic surveillance using whole-genome sequencing of SARS-CoV-2 from rapid antigen test devices

Martin, Geneviève; Taiaroa, George; Taouk, Mona L; Savic, Ivana; O'Keefe, Jacinta; Quach, Robert; Prestedge, Jacqueline; Krysiak, Marcelina; Caly, Leon; Williamson, Deborah A

doi:10.1016/s1473-3099(22)00512-6

Cited by 14 publications

(9 citation statements)

References 5 publications

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“…Whereas a reflexive PCR test after a positive Ag-RDT diagnosis is currently performed to obtain samples suitable for sequencing (and is possible in many tertiary facilities in LMICs), this presents additional cost and logistical barriers. Recent studies showed that SARS-CoV-2 sequencing can be performed using materials obtained from Ag-RDTs performed at point of care 36 – 38 . Importantly, whole genomes can be recovered up to 8 days after testing, providing opportunities for sequencing to be performed on samples performed through self-testing as well 36 .…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2023

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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.

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Section: Discussionmentioning

confidence: 99%

“…Recent studies showed that SARS-CoV-2 sequencing can be performed using materials obtained from Ag-RDTs performed at point of care 36 – 38 . Importantly, whole genomes can be recovered up to 8 days after testing, providing opportunities for sequencing to be performed on samples performed through self-testing as well 36 .…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2023

View full text Add to dashboard Cite

show abstract

“…While a reflexive PCR test after a positive Ag-RDT diagnosis is currently performed to obtain samples suitable for sequencing (and is possible in many tertiary facilities in LMICs), this presents additional cost and logistical barriers. Recent studies showed that SARS-CoV-2 sequencing can be performed using materials obtained from Ag-RDTs performed at point-of-care [33][34][35] . Importantly, whole genomes can be recovered up to eight days after testing, providing opportunities for sequencing to be performed on samples performed through selftesting as well 33 .…”

Section: Discussionmentioning

confidence: 99%

“…Recent studies showed that SARS-CoV-2 sequencing can be performed using materials obtained from Ag-RDTs performed at point-of-care [33][34][35] . Importantly, whole genomes can be recovered up to eight days after testing, providing opportunities for sequencing to be performed on samples performed through selftesting as well 33 .…”

Section: Discussionmentioning

confidence: 99%

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

Han

Toporowski

Sacks

et al. 2022

Preprint

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Background Genomic surveillance is essential for monitoring the emergence and spread of SARS-CoV-2 variants. SARS-CoV-2 diagnostic testing is the starting point for SARS-CoV-2 genomic sequencing. However, testing rates in many low- and middle-income countries (LMICs) are low (mean = 27 tests/100,000 people/day) and global testing rates are falling in the post-crisis phase of the pandemic, leading to spatiotemporal biases in sample collection. Various public health agencies and academic groups have produced recommendations on sample sizes and sequencing strategies for effective genomic surveillance. However, these recommendations assume very high volumes of diagnostic testing that are currently well beyond reach in most LMICs. Methods To investigate how testing rates, sequencing strategies and the degree of spatiotemporal bias in sample collection impact variant detection and monitoring outcomes, we used an individual-based model to simulate COVID-19 epidemics in a prototypical LMIC. Within the model, we simulated a range of testing rates, accounted for likely testing demand and applied various genomic surveillance strategies, including sentinel surveillance. Findings Diagnostic testing rates play a substantially larger role in monitoring the prevalence and emergence of new variants than the proportion of samples sequenced. To enable timely detection and monitoring of emerging variants, programs should achieve average testing rates of at least 100 tests/100,000 people/day and sequence 5-10% of test-positive specimens, which may be accomplished through sentinel or other routine surveillance systems. Under realistic assumptions, this averages to ~10 samples for sequencing/1,000,000 people/week. Interpretation For countries where testing capacities are low and sample collection is spatiotemporally biased, surveillance programs should prioritize investments in wider access to diagnostic testing to enable more representative sampling, ahead of simply increasing quantities of sequenced samples. Funding European Research Council, the Rockefeller Foundation, and the Governments of Germany, Canada, UK, Australia, Norway, Saudi Arabia, Kuwait, Netherlands and Portugal.

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“…Antiviral treatment. One participant (20) with longitudinal sampling received Paxlovid, and Binax results and SARS-CoV-2 RNA converted from positive to negative on day 3 of antiviral treatment (Figure 1A). However, the day following discontinuation, the participant experienced a return of symptoms and a rebound in both Binax and RNA positivity.…”

Section: Specific Applications Of Sars-cov-2 Sequencing From Binax Swabsmentioning

confidence: 99%

SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests

Nguyen

Carmola

Wang

et al. 2023

Preprint

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Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.

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Maintaining genomic surveillance using whole-genome sequencing of SARS-CoV-2 from rapid antigen test devices

Cited by 14 publications

References 5 publications

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

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

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

SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests

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