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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)

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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.

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Page created: February 05, 2025
Page updated: May 02, 2025
Page reviewed: May 02, 2025
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