SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests
Emmen, I. E.; Vuyk, W. C.; Lail, A. J.; Wolf, S.; O'Connor, E. J.; Dalvie, R.; Bhasin, M.; Virdi, A.; White, C.; Hassan, N. R.; Richardson, A.; VanSleet, G.; Weiler, A. M.; Rounds-Dunn, S.; Van Horn, K.; Gartler, M.; Jorgenson, J.; Spelman, M.; Ottosen, S.; Minor, N. R.; Wilson, N.; Friedrich, T.; O'Connor, D.
Show abstract
In the United States, SARS-CoV-2 genomic surveillance initially relied almost entirely on residual diagnostic specimens from nucleic acid amplification-based tests (NAATs). The use of NAATs waned after the end of the COVID-19 Public Health Emergency. We partnered with local- and state-level public health agencies and the Dane County Public Library System to continue genomic surveillance by obtaining SARS-CoV-2 genome sequences from freely available community rapid antigen tests (RATs). From August 15, 2023 to February 29, 2024 we received 227 tests, from which we generated 127 sequences with >10x depth of coverage for [≥]90% of the genome. In a subset of tests, lower Ct values correlated with sequence success. Our results demonstrate that collecting and sequencing from RATs in partnership with community sites is a practical approach for sustaining SARS-CoV-2 genomic surveillance.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): a point-of-care PCR test for rapid detection of SARS-CoV-2 infection 94%
- Sequencing SARS-CoV-2 from Antigen Tests 94%
- SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis 94%
Similar papers in this journal
- Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights 95%
- Real-time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with Variants of Concern 93%
- Understanding the barriers to pooled SARS-CoV-2 testing in the United States 93%
Similar papers in this journal
Similar papers in this journal
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.