Wastewater surveillance of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus (RSV), rhinovirus, and seasonal coronaviruses during the COVID-19 pandemic

Abstract

Background: Respiratory disease is a major cause of morbidity and mortality; however, current surveillance for circulating respiratory viruses is passive and biased. Seasonal circulation of respiratory viruses changed dramatically during the COVID-19 pandemic. More active methods for understanding respiratory disease dynamics are needed to better inform public health response and to guide clinical decision making. Wastewater-based epidemiology has been used to understand COVID-19, influenza A, and RSV infection rates at a community level, but has not been used to investigate other respiratory viruses. Methods: We measured concentrations of influenza A and B, RSV A and B, human parainfluenza (1-4), rhinovirus, seasonal human coronaviruses, and human metapneumovirus RNA in wastewater solids three times per week for 17 months spanning the COVID-19 pandemic at a wastewater treatment plant in California, USA. Novel probe-based assays were developed and validated for non-influenza viral targets. We compared viral concentrations to positivity rates for viral infections from clinical specimens submitted to sentinel laboratories. Findings: We detected RNA from all target viruses in wastewater solids. Human rhinovirus and seasonal coronaviruses were found at highest concentrations. Concentrations of viruses correlated significantly and positively with positivity rates of associated viral diseases from sentinel laboratories. Measurements from wastewater indicated limited circulation of RSV A and influenza B, and human coronavirus OC43 dominated the seasonal human coronavirus infections while human parainfluenza 1 and 4A dominated among parainfluenza infections. Interpretation: Wastewater-based epidemiology can be used to obtain information on circulation of respiratory viruses at a community level without the need to test many individuals because a single sample of wastewater represents the entire contributing community. Results from wastewater can be available within 24 hours of sample collection, allowing real time information to inform public health response, clinical decision making, and individual behavior modifications.

Respiratory virus concentrations in human excretions that contribute to wastewater: A systematic review

“…For the 32 data sets, some of them differentiated between the types of parainfluenza virus. Seven (7) data sets measured parainfluenza virus 1, six (6) measured parainfluenza virus 2, nine (9) measured parainfluenza virus 3, three (3) measured parainfluenza virus 4, and seven (7) did not specify a single type of parainfluenza virus. See Supporting Information Figure S1 for the weighted average positivity rate by parainfluenza type.…”

“…More recently, wastewater surveillance of RSV (4) and influenza (5) has been shown to be strongly correlated with the clinical incidence of these diseases. Additionally, rhinovirus (6), parainfluenza viruses, metapneumovirus, and seasonal coronaviruses 229E, HKU1, OC43, and NL63 have all been detected in wastewater where they are correlated to clinical measures of disease occurrence (7), indicating that wastewater surveillance of respiratory viruses may be a viable tool for public health officials to implement alongside conventional surveillance methods.…”

Influenza transmission dynamics quantified from wastewater

“…Our results demonstrate that both RT-qPCR and dRT-PCR based quantification methods are capable of sufficiently sensitive detection to reconstruct estimated infection incidence and estimate Re. In particular we plan to extend the dPCR assay to detect more pathogens as Boehm et al did in the U.S. (Boehm et al 2022).…”

“…Test-seeking behavior also changed during the pandemic, reportedly increasing compared to pre-pandemic in the U.S. (CDC 2022b). Finally, pandemic-related public health measures and associated behavioral changes have disrupted typical seasonal influenza transmission dynamics (Dhanasekaran et al 2022; Boehm et al 2022). Thus, pandemic-related changes have simultaneously changed influenza transmission dynamics and decreased the reliability of ongoing influenza surveillance efforts.…”

“…They also extended wastewater surveillance by sub-typing the detected IAV. Most recently, Boehm et al (2022) developed a multiplexed method to quantify influenza A and B alongside several other respiratory viruses in wastewater. They confirmed that IAV concentrations in wastewater at the municipal level were associated with laboratory-confirmed cases at the state level.…”