Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 31, Supplement—May 2025

SUPPLEMENT ISSUE
Supplement

SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA

Isla E. Emmen, William C. Vuyk, Andrew J. Lail, Sydney Wolf, Eli J. O’Connor, Rhea Dalvie, Maansi Bhasin, Aanya Virdi, Caroline White, Nura R. Hassan, Alex Richardson, Grace VanSleet, Andrea Weiler, Savannah Rounds-Dunn, Kenneth Van Horn, Marc Gartler, Jane Jorgenson, Michael Spelman, Sean Ottosen, Nicholas R. Minor, Nancy Wilson, Thomas C. Friedrich, and David H. O’ConnorComments to Author 
Author affiliation: University of Wisconsin–Madison School of Medicine and Public Health, Madison, Wisconsin, USA (I.E. Emmen, W.C. Vuyk, A.J. Lail, S. Wolf, E.J. O’Connor, R. Dalvie, M. Bhasin, A. Virdi, C. White, N.R. Hassan, N. Wilson, D.H. O’Connor); Madison West High School, Madison (E.J O’Connor); University of Wisconsin–Madison, Wisconsin National Primate Research Center, Madison (A. Richardson, G. VanSleet, A. Weiler, T.C. Friedrich); Public Health Madison Dane County, Madison (S. Rounds-Dunn, K. Van Horn); Madison Public Library, Madison (M. Gartler, J. Jorgensen, M. Spelman, S. Ottosen); University of Wisconsin–Madison School of Veterinary Medicine, Madison (T.C. Friedrich)

Main Article

Figure 4

Number of samples collected per week and viral lineages detected in a study of SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests (RATs), Wisconsin, USA. The chart shows the percentage of SARS-CoV-2 lineages by week for samples that passed quality control thresholds of >90% of the SARS-CoV-2 genome at >10× depth. The date used reflected the date the participant scanned a provided QR code attached to a RAT. Unscanned RATs were excluded from the analysis. The number of samples included in each week’s percentage is shown above the bar. We assigned Pango lineages by using Nextclade version 3.5.0 (25). From August to mid-November 2023, the most common lineages in our samples fell under XBB.1.5, XBB.1.9.2, XBB.1.16, and XBB.2.3. Beginning in early December 2023, we began to see an increase in the number of samples belonging to the lineage JN.1, which dominated RAT samples scanned in February 2024.

Figure 4. Number of samples collected per week and viral lineages detected in a study of SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests (RATs), Wisconsin, USA. The chart shows the percentage of SARS-CoV-2 lineages by week for samples that passed quality control thresholds of >90% of the SARS-CoV-2 genome at >10× depth. The date used reflected the date the participant scanned a provided QR code attached to a RAT. Unscanned RATs were excluded from the analysis. The number of samples included in each week’s percentage is shown above the bar. We assigned Pango lineages by using Nextclade version 3.5.0 (25). From August to mid-November 2023, the most common lineages in our samples fell under XBB.1.5, XBB.1.9.2, XBB.1.16, and XBB.2.3. Beginning in early December 2023, we began to see an increase in the number of samples belonging to the lineage JN.1, which dominated RAT samples scanned in February 2024.

Main Article

References
  1. Ladner  JT, Sahl  JW. Towards a post-pandemic future for global pathogen genome sequencing. PLoS Biol. 2023;21:e3002225. DOIPubMedGoogle Scholar
  2. Rasmussen  M, Møller  FT, Gunalan  V, Baig  S, Bennedbæk  M, Christiansen  LE, et al. First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023. Euro Surveill. 2023;28:36. DOIPubMedGoogle Scholar
  3. Oliveira Roster  KI, Kissler  SM, Omoregie  E, Wang  JC, Amin  H, Di Lonardo  S, et al. Surveillance strategies for the detection of new pathogen variants across epidemiological contexts. PLOS Comput Biol. 2024;20:e1012416. DOIPubMedGoogle Scholar
  4. Robishaw  JD, Alter  SM, Solano  JJ, Shih  RD, DeMets  DL, Maki  DG, et al. Genomic surveillance to combat COVID-19: challenges and opportunities. Lancet Microbe. 2021;2:e481–4. DOIPubMedGoogle Scholar
  5. World Health Organization. Recommendations for national SARS-CoV-2 testing strategies and diagnostic capacities [cited 2024 Apr 29]. https://www.who.int/publications/i/item/WHO-2019-nCoV-lab-testing-2021.1-eng
  6. Kates  J, Cubanski  J, Cox  C, Published  JT. Timeline of end dates for key health-related flexibilities provided through COVID-19 emergency declarations, legislation, and administrative actions [cited 2024 Nov 20]. https://www.kff.org/coronavirus-covid-19/issue-brief/timeline-of-end-dates-for-key-health-related-flexibilities-provided-through-covid-19-emergency-declarations-legislation-and-administrative-actions
  7. Centers for Disease Control and Prevention. COVID data tracker [cited 2024 May 9]. https://covid.cdc.gov/covid-data-tracker
  8. Centers for Disease Control and Prevention. COVID Museum COVID-19 timeline [cited 2025 Mar 6]. https://www.cdc.gov/museum/timeline/covid19.html
  9. Rader  B, Gertz  A, Iuliano  AD, Gilmer  M, Wronski  L, Astley  CM, et al. Use of at-home COVID-19 tests—United States, August 23, 2021–March 12, 2022. MMWR Morb Mortal Wkly Rep. 2022;71:489–94. DOIPubMedGoogle Scholar
  10. Khalid  MF, Selvam  K, Jeffry  AJN, Salmi  MF, Najib  MA, Norhayati  MN, et al. Performance of rapid antigen tests for COVID-19 diagnosis: a systematic review and meta-analysis. Diagnostics (Basel). 2022;12:110. DOIPubMedGoogle Scholar
  11. American Society for Microbiology. How the SARS-CoV-2 EUA antigen tests work [cited 2024 Jul 25]. https://asm.org:443/Articles/2020/August/How-the-SARS-CoV-2-EUA-Antigen-Tests-Work
  12. Food and Drug Administration. At-home OTC COVID-19 diagnostic tests [cited 2024 Jul 16]. https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/home-otc-covid-19-diagnostic-tests
  13. Martin  GE, Taiaroa  G, Taouk  ML, Savic  I, O’Keefe  J, Quach  R, et al. Maintaining genomic surveillance using whole-genome sequencing of SARS-CoV-2 from rapid antigen test devices. Lancet Infect Dis. 2022;22:1417–8. DOIPubMedGoogle Scholar
  14. Rector  A, Bloemen  M, Schiettekatte  G, Maes  P, Van Ranst  M, Wollants  E. Sequencing directly from antigen-detection rapid diagnostic tests in Belgium, 2022: a gamechanger in genomic surveillance? Euro Surveill. 2023;28:91. DOIPubMedGoogle Scholar
  15. Paull  JS, Petros  BA, Brock-Fisher  TM, Jalbert  SA, Selser  VM, Messer  KS, et al. Optimisation and evaluation of viral genomic sequencing of SARS-CoV-2 rapid diagnostic tests: a laboratory and cohort-based study. Lancet Microbe. 2024;5:e468–77. DOIPubMedGoogle Scholar
  16. Nguyen  PV, Carmola  LR, Wang  E, Bassit  L, Rao  A, Greenleaf  M, et al. SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 antigen self tests. J Clin Virol. 2023;162:105426. DOIPubMedGoogle Scholar
  17. Macori  G, Russell  T, Barry  G, McCarthy  SC, Koolman  L, Wall  P, et al. Inactivation and recovery of high quality RNA from positive SARS-CoV-2 rapid antigen tests suitable for whole virus genome sequencing. Front Public Health. 2022;10:863862. DOIPubMedGoogle Scholar
  18. Health Innovation Program. ZIP codes by rural and urban groupings: HIPxChange [cited 2025 Jan 3]. https://hipxchange.org/toolkit/ruralurbangroups
  19. Coelho  FF, da Silva  MA, Lopes  TB, Polatto  JM, de Castro  NS, Andrade  LAF, et al. SARS-CoV-2 rapid antigen test based on a new anti-nucleocapsid protein monoclonal antibody: development and real-time validation. Microorganisms. 2023;11:2422. DOIPubMedGoogle Scholar
  20. US Census Bureau. Geographic areas reference manual. Washington: the Bureau; 1994.
  21. Lu  X, Wang  L, Sakthivel  SK, Whitaker  B, Murray  J, Kamili  S, et al. US CDC real-time reverse transcription PCR panel for detection of severe acute respiratory syndrome coronavirus 2. Emerg Infect Dis. 2020;26:1654–65. DOIPubMedGoogle Scholar
  22. Patel  H, Monzón  S, Varona  S, Espinosa-Carrasco  J, Garcia  MU, Heuer  ML, et al. nf-core/viralrecon: nf-core/viralrecon v2.6.0–rhodium raccoon [cited 2024 May 29]. https://zenodo.org/record/7764938
  23. Ewels  PA, Peltzer  A, Fillinger  S, Patel  H, Alneberg  J, Wilm  A, et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38:276–8. DOIPubMedGoogle Scholar
  24. Wisconsin State Laboratory of Hygiene. SARS-CoV-2 wastewater genomic dashboard [cited 2024 Jun 7]. https://dataportal.slh.wisc.edu/sc2-ww-dashboard
  25. Aksamentov  I, Roemer  C, Hodcroft  E, Neher  R. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw. 2021;6:3773. DOIGoogle Scholar
  26. Tosta  S, Moreno  K, Schuab  G, Fonseca  V, Segovia  FMC, Kashima  S, et al. Global SARS-CoV-2 genomic surveillance: What we have learned (so far). Infect Genet Evol. 2023;108:105405. DOIPubMedGoogle Scholar
  27. Public Health Madison & Dane County. Respiratory illness dashboard [cited 2024 Jun 7]. https://publichealthmdc.com/health-services/respiratory-illness/dashboard
  28. US Postal Service. Postal Service delivery performance continues to average 2.6 days [cited 2024 Nov 13]. https://about.usps.com/newsroom/national-releases/2023/1222-usps-delivery-performance-continues-to-average-2-6-days.htm
  29. Chen  C, Nadeau  S, Yared  M, Voinov  P, Xie  N, Roemer  C, et al. CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants. Bioinformatics. 2022;38:1735–7. DOIPubMedGoogle Scholar
  30. Food and Drug Administration. Influenza diagnostic tests [cited 2024 Aug 2]. https://www.fda.gov/medical-devices/in-vitro-diagnostics/influenza-diagnostic-tests
  31. Therapeutic Goods Administration. Respiratory combo panel RSV/SARS-CoV-2/Influenza A/B Rapid Antigen Test Kit RAT-19 (self-test) (nasal swab) (combination self‐tests) [cited 2024 Nov 14]. https://www.tga.gov.au/resources/covid-19-test-kits/respiratory-combo-panel-rsv-sars-cov-2-influenza-ab-rapid-antigen-test-kit-rat-19-self-test-nasal-swab-combination-self-tests
  32. Therapeutic Goods Administration. COVID-19, Influenza A/B & RSV Antigen Nasal Test Kit for self-testing (Biolink Biopen) [cited 2024 Nov 14]. https://www.tga.gov.au/resources/covid-19-test-kits/covid-19-influenza-ab-rsv-antigen-nasal-test-kit-self-testing-biolink-biopen
  33. Smith-Jeffcoat  SE, Mellis  AM, Grijalva  CG, Talbot  HK, Schmitz  J, Lutrick  K, et al.; RVTN-Sentinel Study Group. SARS-CoV-2 viral shedding and rapid antigen test performance— respiratory virus transmission network, November 2022–May 2023. MMWR Morb Mortal Wkly Rep. 2024;73:365–71. DOIPubMedGoogle Scholar

Main Article

Page created: February 05, 2025
Page updated: May 12, 2025
Page reviewed: May 12, 2025
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external