Targeted Resequencing of Wetland Sediment as a Tool for Avian Influenza Virus Surveillance

Abstract

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Extraction and Detection of Avian Influenza Virus From Wetland Sediment Using Enrichment-Based Targeted Resequencing

“…In this study, we demonstrate that AIV RNA can be successfully extracted from environmental sediment samples, detected using RT-qPCR and characterized using AIV-specific probes for targeted resequencing [clade analysis detailed in Himsworth et al (25)].…”

“…Five sampling sites per wetland area were chosen and four 50 mL subsamples were collected per site (n = 300), with subsamples ∼1 m apart from each other and in from the shore. Collection was performed by walking 1-2 m into the water and collecting the superficial layer of submerged sediment into a sterile 50 mL conical falcon tube (25). Samples were transported to the lab and frozen without preservatives at −80 • C within 4-8 h of collection (26).…”

“…Identification and characterization of AIV subtypes in the samples were done using an in-house-developed bioinformatics analysis pipeline (https://github.com/duanjunhyq/AIV_ seeker) as previously described (25). All sequence data were deposited into the NCBI sequence read archive PRJNA353856 (ncbi.nlm.nih.gov/sra).…”

A literature review of the use of environmental sampling in the surveillance of avian influenza viruses

“…Studies using targeted resequencing and genomics have now been reported but additional work is needed to confirm the validity of this approach (Himsworth et al, 2019). (Deboosere et al, 2011(Deboosere et al, , 2012Ronnqvist, Ziegler, von Bonsdorff, & Maunula, 2012) and erythrocyte absorption using chicken red blood cells (Horm, Gutierrez, Sorn, et al, 2012;Khalenkov, Laver, & Webster, 2008).…”

Preparing for Emerging Zoonotic Viruses

“…However, sewage could have great potential to be used for virus discovery and emerging disease detection ( Fernandez-Cassi et al ., 2018 ; Nordahl Petersen et al ., 2015 ). Other sample types, representing large numbers of animals, that can be can be used to monitor circulating of pathogens are: manure composting plants, bulk milk and ponds ( Himsworth et al ., 2019 ; Garcia et al ., 2014 ; Balmer et al ., 2014 ).…”