SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 antigen self tests

Nguyen, Phuong-Vi; Carmola, Ludy Registre; Wang, Yuanxun Ethan; Bassit, Leda; Rao, Anuradha; Greenleaf, Morgan; Sullivan, Julie; Martin, Greg S.; Lam, Wilbur A.; Waggoner, Jesse J.; Piantadosi, Anne

doi:10.1016/j.jcv.2023.105426

Cited by 3 publications

References 20 publications

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SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests

Emmen,

Vuyk,

Lail

et al. 2024

Preprint

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For the first several years of the pandemic, SARS-CoV-2 genomic surveillance relied almost entirely on residual diagnostic specimens from nucleic acid amplification-based tests (NAATs). The use of NAATs waned after the end of the Stafford Act Emergency Declaration for COVID-19 in the US. To continue to monitor the spread and evolution of SARS-CoV-2, we partnered with local- and state-level public health agencies and the Dane County Public Library System to obtain SARS-CoV-2 genome sequence from freely available community rapid antigen tests (RATs). From August 15, 2023 to February 29, 2024 we received 227 tests through this system, from which we generated 127 sequences with >10x depth of coverage for ≥90% of the SARS-CoV-2 genome. Our results demonstrate that collecting and sequencing from RATs in partnership with trusted community stakeholders is a practical, useful approach for sustaining genomic surveillance for SARS-CoV-2.

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SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests

Emmen,

Vuyk,

Lail

et al. 2024

Preprint

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Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests

Jules,

Decker,

Bixler

et al. 2024

Preprint

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The Suitability of RNA from Positive SARS-CoV-2 Rapid Antigen Tests for Whole Virus Genome Sequencing and Variant Identification to Maintain Genomic Surveillance

Cucina,

Contino,

Brunacci

et al. 2023

Diagnostics

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The COVID-19 pandemic has transformed laboratory management, with a surge in demand for diagnostic tests prompting the adoption of new diagnostic assays and the spread of variant surveillance tools. Rapid antigen tests (RATs) were initially used only for screening and later as suitable infection assessment tools. This study explores the feasibility of sequencing the SARS-CoV-2 genome from the residue of the nasopharyngeal swab extraction buffers of rapid antigen tests (RATs) to identify different COVID-19 lineages and sub-lineages. Methods: Viral RNA was extracted from the residue of the nasopharyngeal swab extraction buffers of RATs and, after a confirmation of positivity through a reaction of RT-PCR, viral genome sequencing was performed. Results: Overall, the quality of the sequences obtained from the RNA extracted from the residue of the nasopharyngeal swab extraction buffers of RATs was adequate and allowed us to identify the SARS-CoV-2 variants’ circulation and distribution in a period when the use of molecular swabs had been drastically reduced. Conclusions: This study demonstrates the potential for genomic surveillance by sequencing SARS-CoV-2 from the residue of the nasopharyngeal swab extraction buffers of RATs, highlighting alternative possibilities for tracking variants.

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SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 antigen self tests

Cited by 3 publications

References 20 publications

SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests

SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests

Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests

The Suitability of RNA from Positive SARS-CoV-2 Rapid Antigen Tests for Whole Virus Genome Sequencing and Variant Identification to Maintain Genomic Surveillance

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