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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)

Main Article

Table 2

Lineages detected during SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests, Wisconsin, USA*

Date†
 Highest percentage‡
Second highest percentage§
 No. RATs with passing sequence¶
 Other lineages detected via RAT sequencing
Wastewater lineage
 Matching RAT lineages
 Wastewater lineage
 Matching RAT lineages
2023 Aug 28
 EG.5.1
 EG.5.1.4
XBB.1.16
 XBB.1.16.11
 5
 FL.1.5.1, XBB.2.3
2023 Sep 11
 EG.5.1
 EG.5.1.13
XBB.1.16
 XBB.1.16
 8
 XBB.1.5.10, XBB.1.5, GE.1,HK.9, JF.1.1, HH.1
2023 Sep 25
 EG.5.1
 EG.5.1.4
XBB.1.16
 XBB.1.16
 4
 GJ.1.2, FL.1.5.1
2023 Oct 9
 EG.5.1
 HV.1, HV.1.8
XBB.1.9
 None
 8
 HK.29, JN.1.1, XBB.1.16.9
2023 Oct 23
 EG.5.1
 None
XBB.1.16
 None
 2
 XCH.1, DV.7.1
2023 Nov 6
 EG.5.1
 EG.5.1.1, EG.5.1.6
XBB.1.16
 None
 6
 FL.1.5.1, HK.13.2.1, HK.26
2023 No 20
 EG.5.1
 EG.5.1.1, EG.5.1.6, HV.1
XBB.1.16
 XBB.1.16.6
 10
 HK.26, GK.1.1, JN.1.4.5, HK.3, JN.1
2023 Dec 4
 EG.5.1
 HV.1, HV.1.2, HV.1.6
BA.2.86
 JN.1, JN.1.1, JN.1.38
 14
 XDA, XCV, GK.1.8
2023 Dec 18
 BA.2.86
 JN.1, JN.1.1, JN.1.4, JN.1.42
EG.5.1
 EG.5.1, EG.5.1.8, HV.1
 11
 JG.3, GW.5.1.1, GK.1.6.1
2024 Jan 1
 BA.2.86
 JN.1, JN.1.39
EG.5.1
 None
 3
 None
2024 Jan 15
 BA.2.86
 JN.1, JN.1.38, JN.1.4, JN.1.42
EG.5.1
 HV.1
 15
 JG.3, XDD, XDP, JC.5.1, HK.3.2
2024 Jan 29
 BA.2.86
 JN.1, JN.1.1
EG.5.1
 None
 9
 None
2024 Feb 12 BA.2.86 JN.1, JN.1.42 XBB.2.3 None 4 None

*Lineages represent successful rapid antigen test sequences that corresponded to the 2 most prevalent lineage groups in the wastewater signal in the state of Wisconsin for each 2-week period. RAT, rapid antigen test. †Dates represent first day of each 2-week reporting period. ‡Lineage group comprising the first largest percentage of wastewater data. §Lineage group comprising the second largest percentage of wastewater data. ¶Passing sequences had >90% genome coverage at >10× depth.

Main Article

Page created: February 05, 2025
Page updated: May 12, 2025
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