Activity- and gene-based quantification of enteric viruses, F- specific RNA phage genogroups, pepper mild mottle virus, and Escherichia coli in surface water

Akihiko Hata; Yuno Meuchi; Miaomiao Liu; Shotaro Torii; Hiroyuki Katayama

doi:10.1016/j.scitotenv.2023.166338

Activity- and gene-based quantification of enteric viruses, F- specific RNA phage genogroups, pepper mild mottle virus, and Escherichia coli in surface water

Sci Total Environ. 2023 Dec 15:904:166338. doi: 10.1016/j.scitotenv.2023.166338. Epub 2023 Aug 15.

Authors

Akihiko Hata¹, Yuno Meuchi², Miaomiao Liu³, Shotaro Torii³, Hiroyuki Katayama³

Affiliations

¹ Department of Environmental and Civil Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan. Electronic address: a-hata@pu-toyama.ac.jp.
² Department of Environmental and Civil Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
³ Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

PMID: 37591377
DOI: 10.1016/j.scitotenv.2023.166338

Abstract

Polymerase chain reaction (PCR) is widely applied for the monitoring of pathogenic viruses in water environments. To date, several pretreatments to selectively detect genes from infectious viruses via PCR have been developed. This study was aimed to characterize and validate methods for quantifying active viruses and indicators and to evaluate the proportion of their active fractions in surface water (n = 42). Active E. coli and F-specific RNA phage (FRNAPH) genogroups were quantified using culture assays. In addition to these microbes, norovirus genogroups I (GI) and II, Aichi virus 1, and pepper mild mottle virus (PMMoV) were quantified by (reverse transcription)-quantitative PCR (RT-qPCR) with and without cis-dichlorodiammineplatinum (CDDP) treatment to exclude genes in inactive viruses. CDDP-RT-qPCR showed concentrations and detection frequencies comparable to or higher than culture assays. Consequently, although CDDP-RT-qPCR can suggest the presence of an inactive virus, it can also overestimate the activity of the virus in the environment. Differences between culture and CDDP-RT-qPCR and between CDDP-RT-qPCR and RT-qPCR varied among the viruses. CDDP-RT-qPCR showed a concentration comparable to the culture assay (within 1 log₁₀ difference) in 93 % of positive samples for GI-FRNAPH but in <63 % of positive samples for GII- and GIII-FRNAPHs. GII-NoV was detected from 5 and 30 out of 42 samples via CDDP-RT-qPCR and RT-qPCR, respectively, and was suggested as inactivated by 2.0 log₁₀ or higher in most of the samples. By contrast, concentrations of PMMoV determined by these two assays were not notably different. It is suggested that the operational conditions of wastewater treatment plants around the sites, rather than environmental stresses, affected the microbial inactivation. To better understand the infectivity of viruses in the environment, it is important to investigate them using sensitive detection methods at various sites, including the source of contamination.

Keywords: CDDP-RT-qPCR; Enteric virus; Infectivity; Surface water.

MeSH terms

Enterovirus*
Escherichia coli
Genotype
RNA Phages* / genetics
Viruses*
Water

Substances

Water

Supplementary concepts

Pepper mild mottle virus