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SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs. / Han, Alvin X.; Toporowski, Amy; Sacks, Jilian A. et al.

In: Nature genetics, Vol. 55, No. 1, 01.2023, p. 26-33.

Research output: Contribution to journal › Article › Academic › peer-review

Harvard

Han, AX, Toporowski, A, Sacks, JA, Perkins, MD, Briand, S, van Kerkhove, M, Hannay, E, Carmona, S, Rodriguez, B, Parker, E, Nichols, BE & Russell, CA 2023, 'SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs', Nature genetics, vol. 55, no. 1, pp. 26-33. https://doi.org/10.1038/s41588-022-01267-w

APA

Han, A. X., Toporowski, A., Sacks, J. A., Perkins, M. D., Briand, S., van Kerkhove, M., Hannay, E., Carmona, S., Rodriguez, B., Parker, E., Nichols, B. E., & Russell, C. A. (2023). SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs. Nature genetics, 55(1), 26-33. https://doi.org/10.1038/s41588-022-01267-w

Vancouver

Han AX, Toporowski A, Sacks JA, Perkins MD, Briand S, van Kerkhove M et al. SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs. Nature genetics. 2023 Jan;55(1):26-33. Epub 2023. doi: 10.1038/s41588-022-01267-w

Author

Han, Alvin X. ; Toporowski, Amy ; Sacks, Jilian A. et al. / SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs. In: Nature genetics. 2023 ; Vol. 55, No. 1. pp. 26-33.

BibTeX

@article{f2a50f0892a64b9996aec4aeb21cdc36,
title = "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.",
author = "Han, {Alvin X.} and Amy Toporowski and Sacks, {Jilian A.} and Perkins, {Mark D.} and Sylvie Briand and {van Kerkhove}, Maria and Emma Hannay and Sergio Carmona and Bill Rodriguez and Edyth Parker and Nichols, {Brooke E.} and Russell, {Colin A.}",
note = "Funding Information: We are pleased to acknowledge that all computational work reported in this paper was performed on the Shared Computing Cluster, which is administered by Boston University{\textquoteright}s Research Computing Services (www.bu.edu/tech/support/research/). This work was supported by the Rockefeller Foundation, and the Governments of Germany, Canada, UK, Australia, Norway, Saudi Arabia, Kuwait, the Netherlands and Portugal. A.X.H. and C.A.R. were supported by European Research Council NaviFlu (grant 818353). C.A.R. was also supported by a National Institutes of Health R01 grant (5R01AI132362-04) and a Dutch Research Council (NWO) Vici Award (09150182010027). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. The findings and conclusions in this manuscript are those of the authors and do not represent the official position of the World Health Organization. Funding Information: We are pleased to acknowledge that all computational work reported in this paper was performed on the Shared Computing Cluster, which is administered by Boston University{\textquoteright}s Research Computing Services ( www.bu.edu/tech/support/research/ ). This work was supported by the Rockefeller Foundation, and the Governments of Germany, Canada, UK, Australia, Norway, Saudi Arabia, Kuwait, the Netherlands and Portugal. A.X.H. and C.A.R. were supported by European Research Council NaviFlu (grant 818353). C.A.R. was also supported by a National Institutes of Health R01 grant (5R01AI132362-04) and a Dutch Research Council (NWO) Vici Award (09150182010027). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. The findings and conclusions in this manuscript are those of the authors and do not represent the official position of the World Health Organization. Publisher Copyright: {\textcopyright} 2023, The Author(s).",
year = "2023",
month = jan,
doi = "10.1038/s41588-022-01267-w",
language = "English",
volume = "55",
pages = "26--33",
journal = "Nature genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

TY - JOUR

T1 - SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

AU - Han, Alvin X.

AU - Toporowski, Amy

AU - Sacks, Jilian A.

AU - Perkins, Mark D.

AU - Briand, Sylvie

AU - van Kerkhove, Maria

AU - Hannay, Emma

AU - Carmona, Sergio

AU - Rodriguez, Bill

AU - Parker, Edyth

AU - Nichols, Brooke E.

AU - Russell, Colin A.

N1 - Funding Information: We are pleased to acknowledge that all computational work reported in this paper was performed on the Shared Computing Cluster, which is administered by Boston University’s Research Computing Services (www.bu.edu/tech/support/research/). This work was supported by the Rockefeller Foundation, and the Governments of Germany, Canada, UK, Australia, Norway, Saudi Arabia, Kuwait, the Netherlands and Portugal. A.X.H. and C.A.R. were supported by European Research Council NaviFlu (grant 818353). C.A.R. was also supported by a National Institutes of Health R01 grant (5R01AI132362-04) and a Dutch Research Council (NWO) Vici Award (09150182010027). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. The findings and conclusions in this manuscript are those of the authors and do not represent the official position of the World Health Organization. Funding Information: We are pleased to acknowledge that all computational work reported in this paper was performed on the Shared Computing Cluster, which is administered by Boston University’s Research Computing Services ( www.bu.edu/tech/support/research/ ). This work was supported by the Rockefeller Foundation, and the Governments of Germany, Canada, UK, Australia, Norway, Saudi Arabia, Kuwait, the Netherlands and Portugal. A.X.H. and C.A.R. were supported by European Research Council NaviFlu (grant 818353). C.A.R. was also supported by a National Institutes of Health R01 grant (5R01AI132362-04) and a Dutch Research Council (NWO) Vici Award (09150182010027). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. The findings and conclusions in this manuscript are those of the authors and do not represent the official position of the World Health Organization. Publisher Copyright: © 2023, The Author(s).

PY - 2023/1

Y1 - 2023/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85145904588&partnerID=8YFLogxK

U2 - 10.1038/s41588-022-01267-w

DO - 10.1038/s41588-022-01267-w

M3 - Article

C2 - 36624344

VL - 55

SP - 26

EP - 33

JO - Nature genetics

JF - Nature genetics

SN - 1061-4036

IS - 1

ER -

ID: 30840748