A multiplex-NGS approach to identifying respiratory RNA viruses during the COVID-19 pandemic

Arch Virol. 2023 Feb 14;168(3):87. doi: 10.1007/s00705-023-05717-6.

Abstract

A methodological approach based on reverse transcription (RT)-multiplex PCR followed by next-generation sequencing (NGS) was implemented to identify multiple respiratory RNA viruses simultaneously. A convenience sampling from respiratory surveillance and SARS-CoV-2 diagnosis in 2020 and 2021 in Montevideo, Uruguay, was analyzed. The results revealed the cocirculation of SARS-CoV-2 with human rhinovirus (hRV) A, B and C, human respiratory syncytial virus (hRSV) B, influenza A virus, and metapneumovirus B1. SARS-CoV-2 coinfections with hRV or hRSV B and influenza A virus coinfections with hRV C were identified in adults and/or children. This methodology combines the benefits of multiplex genomic amplification with the sensitivity and information provided by NGS. An advantage is that additional viral targets can be incorporated, making it a helpful tool to investigate the cocirculation and coinfections of respiratory viruses in pandemic and post-pandemic contexts.

Keywords: COVID-19 pandemic; SARS-CoV-2; human respiratory RNA viruses; multiplex PCR-NGS; viral coinfections.

MeSH terms

  • Adult
  • COVID-19 Testing
  • COVID-19* / diagnosis
  • COVID-19* / epidemiology
  • Child
  • Coinfection* / diagnosis
  • Coinfection* / epidemiology
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Influenza A virus* / genetics
  • Influenza, Human* / epidemiology
  • Pandemics
  • RNA
  • RNA Viruses* / genetics
  • Respiratory Syncytial Virus, Human* / genetics
  • Respiratory Tract Infections* / diagnosis
  • Respiratory Tract Infections* / epidemiology
  • SARS-CoV-2 / genetics

Substances

  • RNA