Wastewater-based epidemiology and long-read sequencing to identify enterovirus circulation in three municipalities in maricopa county, arizona, southwest united states between june and october 2020

Temitope O.C. Faleye, Devin A. Bowes, Erin M. Driver, Sangeet Adhikari, Deborah Adams, Arvind Varsani, Rolf U. Halden, Matthew Scotch

Research output: Contribution to journalArticlepeer-review

Abstract

We used wastewater-based epidemiology and amplicon-based long-read high-throughput sequencing for surveillance of enteroviruses (EVs) in Maricopa County, Arizona, Southwest United States. We collected 48 samples from 13 sites in three municipalities between 18 June and 1 October 2020, and filtered (175 mL each; 0.45 µm pore size) and extracted RNA from the filter-trapped solids. The RNA was converted to cDNA and processed through two workflows (Sanger sequencing (SSW) and long-read Illumina sequencing (LRISW)) each including a nested polymerase chain reaction (nPCR) assay. We subjected the ~350 bp amplicon from SSW to Sanger sequencing and the ~1900–2400 bp amplicon from LRISW to Illumina sequencing. We identified EV contigs from 11 of the 13 sites and 41.67% (20/48) of screened samples. Using the LRISW, we detected nine EV genotypes from three species (Enterovirus A (CVA4, EV-A76, EV-A90), Enterovirus B (E14) and Enterovirus C (CVA1, CVA11, CVA13, CVA19 and CVA24)) with Enterovirus C representing approximately 90% of the variants. However, the SSW only detected the five Enterovirus C types. Similarity and phylogenetic analysis showed that multiple Enterovirus C lineages were circulating, co-infecting and recombining in the population during the season despite the SARS-CoV-2 pandemic and the non-pharmaceutical public health measures taken to curb transmission.

Original languageEnglish (US)
Article number1803
JournalViruses
Volume13
Issue number9
DOIs
StatePublished - Sep 2021

Keywords

  • Arizona
  • Enterovirus C
  • Environmental monitoring
  • High-throughput nucleotide sequencing
  • Human
  • Wastewater-based epidemiological monitoring

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

Fingerprint

Dive into the research topics of 'Wastewater-based epidemiology and long-read sequencing to identify enterovirus circulation in three municipalities in maricopa county, arizona, southwest united states between june and october 2020'. Together they form a unique fingerprint.

Cite this