Detection of human, porcine and canine picornaviruses in municipal sewage sludge using pan-enterovirus amplicon-based long-read Illumina sequencing

Temitope O.C. Faleye, Erin M. Driver, Devin A. Bowes, Rochelle H. Holm, Daymond Talley, Ray Yeager, Aruni Bhatnagar, Ted Smith, Arvind Varsani, Rolf U. Halden, Matthew Scotch

Research output: Contribution to journalArticlepeer-review

Abstract

We describe the successful detection of human, porcine and canine picornaviruses (CanPV) in sewage sludge (at each stage of treatment) from Louisville, Kentucky, USA, using Pan-enterovirus amplicon-based long-read Illumina sequencing. Based on publicly available sequence data in GenBank, this is the first detection of CanPV in the USA and the first detection globally using wastewater-based epidemiology. Our findings also suggest there might be clusters of endemic porcine enterovirus (which have been shown capable of causing systemic infection in porcine) circulation in the USA that have not been sampled for around two decades. Our findings highlight the value of WBE coupled with amplicon based long-read Illumina sequencing for virus surveillance and demonstrates this approach can provide an avenue that supports a “One Health” model to virus surveillance. Finally, we describe a new CanPV assay targeting the capsid protein gene region that can be used globally, especially in resource limited settings for its detection and molecular epidemiology.

Original languageEnglish (US)
Pages (from-to)1339-1342
Number of pages4
JournalEmerging Microbes and Infections
Volume11
Issue number1
DOIs
StatePublished - 2022

Keywords

  • high-throughput nucleotide sequencing
  • Kentucky
  • One Health
  • Picornaviridae
  • wastewater-based epidemiological monitoring

ASJC Scopus subject areas

  • Parasitology
  • Epidemiology
  • Microbiology
  • Immunology
  • Drug Discovery
  • Virology
  • Infectious Diseases

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