Respiratory Virus Detection and Sequencing from SARS-CoV-2-Negative Rapid Antigen Tests

Emerg Infect Dis. 2025 May;31(13):39-44. doi: 10.3201/eid3113.241191.

Abstract

Genomic epidemiology offers insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 rapid antigen tests to identify a wide range of respiratory viruses and generate full genome sequences. This process offers a streamlined mechanism for broad respiratory virus genomic surveillance.

Keywords: COVID-19; SARS-CoV-2; coronavirus disease; molecular epidemiology; public health surveillance; respiratory infections; respiratory tract infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

MeSH terms

  • Antigens, Viral
  • COVID-19 / diagnosis
  • COVID-19 / virology
  • Genome, Viral
  • Humans
  • Phylogeny
  • Respiratory Tract Infections* / diagnosis
  • Respiratory Tract Infections* / virology
  • SARS-CoV-2* / genetics
  • Viruses* / classification
  • Viruses* / genetics
  • Viruses* / isolation & purification

Substances

  • Antigens, Viral