ArticleTransboundary and emerging diseases2022
Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region.
Article in Transboundary and emerging diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it, 17 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
- Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.Molecular biology and evolution · 2025Article
- From Panels to Pathogen Networks: The Expanding Role of Targeted Sequencing in Veterinary Medicine.Biology · 2025Review
- Advancements in Modern Nucleic Acid-Based Multiplex Testing Methodologies for the Diagnosis of Swine Infectious Diseases.Veterinary sciences · 2025Review
- Mining Porcine Blood Whole-DNA Sequencing Datasets to Uncover Pig Viromes: An Exploratory Application to Identify Potential Infecting Agents of an Undefined Disease Outbreak.Veterinary sciences · 2025Article
- Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases.Veterinary sciences · 2024Review
- Screening for Viruses in Indigenous Greek Black Pigs.Microorganisms · 2024Article
- Application of Host-Depleted Nanopore Metagenomic Sequencing in the Clinical Detection of Pathogens in Pigs and Cats.Animals : an open access journal from MDPI · 2023Article
- The impact and complete genome characterisation of viruses involved in outbreaks of gastroenteritis in a farrow-to-finish holding.Scientific reports · 2023Article
- Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region.Transboundary and emerging diseases · 2022Article
- Swine Norovirus: Past, Present, and Future.Viruses · 2022Review
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Porcine viruses have been emerging in recent decades, threatening animal and human health, as well as economic stability for pig farmers worldwide. Next-generation sequencing (NGS) can detect and characterize known and unknown viruses but has limited sensitivity when an unbiased approach, such as shotgun metagenomics sequencing, is used. To increase the sensitivity of NGS for the detection of viruses, we applied and evaluated a broad viral targeted sequence capture (TSC) panel and compared it to an unbiased shotgun metagenomic approach. A cohort of 36 pooled porcine nasal swab and blood serum samples collected from both sides of the Dutch-German border region were evaluated. Overall, we detected 46 different viral species using TSC, compared to 40 viral species with a shotgun metagenomics approach. Furthermore, we performed phylogenetic analysis on recovered influenza A virus (FLUAV) genomes from Germany and revealed a close similarity to a zoonotic influenza strain previously detected in the Netherlands. Although TSC introduced coverage bias within the detected viruses, it improved sensitivity, genome sequence depth and contig length. In-depth characterization of the swine virome, coupled with developing new enrichment techniques, can play a crucial role in the surveillance of circulating porcine viruses and emerging zoonotic pathogens.
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Registered trials
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