ArticleFrontiers in veterinary science2020
Extraction and Detection of Avian Influenza Virus From Wetland Sediment Using Enrichment-Based Targeted Resequencing.
Article in Frontiers in veterinary science, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.
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5 citing papers in PubMed, 1 synthesis or guideline pooled it, 12 citations in OpenAlex.
- A Systematic Review of New, Enhanced Surveillance Systems and Methodologies for Zoonotic Influenza Viruses in Animals and Human-Animal Interface.Influenza and other respiratory viruses · 2025Pooled it
- Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.Applied and environmental microbiology · 2026Article
- Gene flow and its sporadic spillover: H10 and N5 avian influenza viruses from wild birds and the H10N5 human cases in China.Virologica Sinica · 2025Article
- Targeted genomic sequencing of avian influenza viruses in wetland sediment from wild bird habitats.Applied and environmental microbiology · 2024Article
- Exploring surface water as a transmission medium of avian influenza viruses - systematic infection studies in mallards.Emerging microbes & infections · 2022Article
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Early virus detection and characterization is key to successful avian influenza virus (AIV) surveillance for the health of humans as well as domestic poultry. We explored a novel sampling approach and molecular strategy using sediment from wetlands and outdoor waterbodies on poultry farms as a population-level proxy of AIV activity in waterfowls. RNA was extracted using the MoBio RNA PowerSoil Total RNA isolation kit with additional chloroform extraction steps to reduce PCR inhibition. AIV matrix protein (MP) gene was detected in 42/345 (12.2%) samples by RT-qPCR; an additional 64 (18.6%) samples showed evidence of amplification below the threshold and were categorized as "suspect positive." Enrichment-based targeted resequencing (TR) identified AIV sequences in 79/345 (22.9%) samples. TR probes were designed for MP, hemagglutinin (HA), and neuraminidase (NA), however PB2 and PA were also identified. Although RT-qPCR and TR only had fair-moderate agreement, RT-qPCR positivity was predictive of TR-positivity both when using only strictly positive RT-qPCR samples (OR = 11.29) and when coding suspect positives as positive (OR = 7.56). This indicates that RT-qPCR could be used as a screening tool to select samples for virus characterization by TR and that future studies should consider RT-qPCR suspect positives to be positive samples for subsequent resequencing when avoiding false negatives is the priority, for instance in a diagnostic test, and to consider suspect positives to be negative samples when cost efficiency over a large number of samples is the priority, for instance in a surveillance program. A total of 13 HA (H1-7, H9-13, H16) and 9 NA (N1-9) subtypes were identified, with a maximum of 8 HA and 8 NA subtypes detected in a single sample. The optimized RNA extraction and targeted resequencing methods provided increased virus detection and subtyping characterization that could be implemented in an AIV surveillance system.
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