In the United States, SARS-CoV-2 genomic surveillance initially relied almost entirely on residual diagnostic specimens from nucleic acid amplification–based tests. However, use of those tests waned after the end of the COVID-19 Public Health Emergency on May 11, 2023. In Dane County, Wisconsin, we partnered with local- and state-level public health agencies and the South Central Library System to continue genomic surveillance by obtaining SARS-CoV-2 genome sequences from freely available community rapid antigen tests (RATs). During August 15, 2023–February 29, 2024, we received 227 RAT samples, from which we generated 127 sequences with >10× depth of coverage for >90% of the SARS-CoV-2 genome. In a subset of tests, lower cycle threshold values correlated with sequence success. Our results demonstrated that collecting and sequencing results from RATs in partnership with community sites is a practical approach for sustaining SARS-CoV-2 genomic surveillance.

在美国，SARS-CoV-2 基因组监测最初几乎完全依赖于基于核酸扩增的检测中的残留诊断样本。然而，在 2023 年 5 月 11 日 COVID-19 突发公共卫生事件结束后，这些测试的使用有所减少。在威斯康星州戴恩县，我们与地方和州级公共卫生机构以及中南部图书馆系统合作，通过从免费提供的社区快速抗原检测 （RAT） 中获取 SARS-CoV-2 基因组序列来继续进行基因组监测。在 2023 年 8 月 15 日至 2024 年 2 月 29 日期间，我们收到了 227 个 RAT 样本，从中生成了 127 个序列，覆盖深度为 >10× >90% 的 SARS-CoV-2 基因组。在测试子集中，较低的周期阈值与序列成功相关。我们的结果表明，与社区站点合作收集和测序 RAT 结果是维持 SARS-CoV-2 基因组监测的实用方法。