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. 2023 May 10:872:162058.
doi: 10.1016/j.scitotenv.2023.162058. Epub 2023 Feb 8.

Identification and genome sequencing of an influenza H3N2 variant in wastewater from elementary schools during a surge of influenza A cases in Las Vegas, Nevada

Van Vo  1 , Anthony Harrington  2 , Ching-Lan Chang  2 , Hayley Baker  2 , Michael A Moshi  2 , Nabih Ghani  2 , Jose Yani Itorralba  2 , Richard L Tillett  3 , Elizabeth Dahlmann  2 , Natnael Basazinew  2 , Richard Gu  2 , Tiffany D Familara  2 , Sage Boss  2 , Fritz Vanderford  2 , Moonis Ghani  2 , Austin J Tang  2 , Alice Matthews  2 , Katerina Papp  4 , Eakalak Khan  5 , Carolina Koutras  6 , Horng-Yuan Kan  7 , Cassius Lockett  7 , Daniel Gerrity  4 , Edwin C Oh  8
Affiliations

Identification and genome sequencing of an influenza H3N2 variant in wastewater from elementary schools during a surge of influenza A cases in Las Vegas, Nevada

Van Vo et al. Sci Total Environ. .

Abstract

Real-time surveillance of infectious diseases at schools or in communities is often hampered by delays in reporting due to resource limitations and infrastructure issues. By incorporating quantitative PCR and genome sequencing, wastewater surveillance has been an effective complement to public health surveillance at the community and building-scale for pathogens such as poliovirus, SARS-CoV-2, and even the monkeypox virus. In this study, we asked whether wastewater surveillance programs at elementary schools could be leveraged to detect RNA from influenza viruses shed in wastewater. We monitored for influenza A and B viral RNA in wastewater from six elementary schools from January to May 2022. Quantitative PCR led to the identification of influenza A viral RNA at three schools, which coincided with the lifting of COVID-19 restrictions and a surge in influenza A infections in Las Vegas, Nevada, USA. We performed genome sequencing of wastewater RNA, leading to the identification of a 2021-2022 vaccine-resistant influenza A (H3N2) 3C.2a1b.2a.2 subclade. We next tested wastewater samples from a treatment plant that serviced the elementary schools, but we were unable to detect the presence of influenza A/B RNA. Together, our results demonstrate the utility of near-source wastewater surveillance for the detection of local influenza transmission in schools, which has the potential to be investigated further with paired school-level influenza incidence data.

Keywords: COVID-19; Elementary schools, mutation; H3N2; Influenza; SARS-CoV-2; Wastewater.

PubMed Disclaimer

Conflict of interest statement

Declaration of competing interest Dr. Carolina Koutras is an employee of R-Zero Systems.

Figures

Unlabelled Image
Graphical abstract
Fig. 1
Fig. 1
Characterization of influenza trends in Southern Nevada, including clinical and wastewater surveillance data. (A) Trends in confirmed cases of influenza plotted over three years: 2019–2020, 2020–2021, and 2021–2022. (B) Distribution of influenza A strains among confirmed cases in 2021–2022. (C) Correlation of weekly 2021–2022 influenza cases (left y-axis) with wastewater concentrations of influenza A RNA (right y-axis) detected in three of six elementary schools. (D) Wastewater concentrations of PMMoV RNA at four of the six elementary schools during the sampling period.
Fig. 2
Fig. 2
Identification of a vaccine-resistant H3N2 subclade. Phylogenetic comparison of the three H3N2 genomes from the elementary schools with the 2022 Nevada reference (NV ref) and the 3C.2a1b.2a subclade.
Suppl. Fig. 1
Suppl. Fig. 1
Wastewater concentrations of PMMoV RNA at elementary school five and six during the sampling period.
See this image and copyright information in PMC

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