Investigating Environmental Matrices for Use in Avian Influenza Virus Surveillance—Surface Water, Sediments, and Avian Fecal Samples

Abstract

Avian influenza viruses (AIV) have a wide host range in the avian metapopulation and, occasionally, transmission to humans also occurs. Surface water plays a particularly important role in the epidemiology of AIV, as the natural virus reservoir is found in aquatic wild birds.

An algorithm for the characterization of influenza A viruses from various host species and environments

“…If virus grows, repeat conventional RT‐PCR for HA, NA, and matrix genes and submit for Sanger sequence. For samples with a high qRT‐PCR Ct value between 29 and 33, or for samples types that are known to have PCR inhibitory substances limiting PCR sensitivity, such as fecal samples, 11 or for samples with high Ct values where the quality of RNA is in question, culture may be required in either cell culture or eggs first, where possible, to obtain good sequence data. In this instance, cultured samples should undergo conventional RT‐PCR for HA, NA, and matrix genes followed by Sanger sequencing.…”

A systematic review of influenza virus in water environments across human, poultry, and wild bird habitats

“…Of these, 169 were excluded for various reasons, including lack of influenza data in water matrices ( n = 129), language limitations ( n = 32), being a review ( n = 7), and duplication ( n = 1). Seven additional articles were found through the citation search, giving a total of 43 articles that met the inclusion criteria ( Fig 1 ) ( Ahmed et al., 2023a ; Ahmed et al., 2023b ; Ahrens et al., 2023 ; Ando et al., 2023 ; Asadi et al., 2023 ; Bo et al., 2021 ; Boehm et al., 2023a ; Boehm et al., 2023b ; Borchardt et al., 2017 ; de Melo et al. 2023 ; Dumke et al., 2022 ; Germeraad et al., 2020 ; Hayes et al., 2023 ; He et al., 2017 ; Heijnen and Medema 2011a ; Henaux et al., 2012 ; Hinshaw et al., 1979 ; Horm et al., 2012 ; Horm et al., 2013 ; Ito et al., 1995 ; Khalil et al., 2022 ; Lai and McPhillips 1999 ; Leung et al., 2007 ; Li et al., 2022 ; Markt et al., 2023 ; Markwell and Shortridge 1982 ; Mercier et al., 2022 ; Munoz-Aguayo et al., 2019 ; Okuya et al., 2015 ; Okuya et al., 2023 ; Ornelas-Eusebio et al., 2015 ; Pawar et al., 2019 ; Rector et al., 2022 ; Rothman et al., 2021 ; Toribio-Avedillo et al., 2023 ; Vo et al., 2023 ; Vong et al., 2008 ; Wolfe et al., 2022 ; Wolken et al., 2023 ; Zafeiriadou et al., 2023 ; Zhang et al., 2011 ; Zhang et al., 2022 ; Zhang et al., 2012 ).…”

“…Influenza A subtypes were reported in 25 of the 43 studies (Table S7). Within this range, five studies were associated with water matrices from WTPs ( Ando et al., 2023 ; Boehm et al., 2023b ; Dumke et al., 2022 ; Heijnen and Medema 2011a ; Vo et al., 2023 ), ten with poultry environments ( Borchardt et al., 2017 ; Germeraad et al., 2020 ; He et al., 2017 ; Horm et al., 2012 ; Horm et al., 2013 ; Leung et al., 2007 ; Li et al., 2022 ; Markwell and Shortridge 1982 ; Vong et al., 2008 ; Zhang et al., 2012 ), nine with bird habitats ( Ahrens et al., 2023 ; Hinshaw et al., 1979 ; Ito et al., 1995 ; Khalil et al., 2022 ; Okuya et al., 2015 ; Okuya et al., 2023 ; Ornelas-Eusebio et al., 2015 ; Zhang et al., 2011 ), and one with both bird and poultry environments ( Bo et al., 2021 ). In water from WTPs, subtypes mainly included seasonal human influenza, such as pandemic influenza A (H1N1) 2009 and H3N2.…”

Enhanced detection of viruses for improved water safety

“…Likewise, reports on the occurrence of INFA viruses in freshwater environments are still limited. Current research has primarily focused on avian influenza virus subtypes in surface waters, often with low recoverable viral loads 53 , 54 . Only two previous studies have documented the detection of SARS-CoV-2 in freshwater environments 55 , 56 .…”