Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch–German border region

Leonard Schuele, Erley Lizarazo-Forero, Katrin Strutzberg-Minder, Sabine Schütze, Sandra Löbert, Claudia Lambrecht, Jürgen Harlizius, Alex W. Friedrich, Silke Peter, John W.A. Rossen, Natacha Couto

Research output: Contribution to journalArticlepeer-review

5 Citations (SciVal)

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.

Original languageEnglish
Pages (from-to)2306-2319
Number of pages14
JournalTransboundary and Emerging Diseases
Volume69
Issue number4
Early online date4 Aug 2021
DOIs
Publication statusPublished - 31 Jul 2022

Bibliographical note

Funding Information:
informationThe Food Pro-tec-ts project is carried out within the framework of the INTERREG V A programme 'Deutschland-Nederland' and is co-financed by the European Regional Development Fund (ERDF) and the Dutch Ministry of Economic Affairs and Climate Change, the Ministry of Economic Affairs, Innovation, Digitalisation and Energy of North Rhine-Westphalia and the provinces of Gelderland, Limburg and North Brabant. It is accompanied by the programme management at the Euregio Rhein-Waal. LS received a grant from the Marie Skłodowska-Curie Actions (Grant Agreement number: 713660—PRONKJEWAIL—H2020—MSCA-COFUND-2015). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.We thank Erwin C. Raangs, Liana Kafetzopoulou and Hayley Cassidy for expert technical support and the farmers for their participation in the study. The Food Protects project is carried out within the framework of the INTERREG V A programme “Deutschland-Nederland” and is co-financed by the European Regional Development Fund (ERDF) and the Dutch Ministry of Economic Affairs and Climate Change, the Ministry of Economic Affairs, Innovation, Digitalization and Energy of North Rhine-Westphalia and the provinces of Gelderland, Limburg and North Brabant. It is accompanied by the programme management at the Euregio Rhein-Waal. Leonard Schuele received the Marie Skłodowska-Curie Actions (Grant Agreement number: 713660 PRONKJEWAIL H2020 MSCA-COFUND-2015). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Funding Information:
The Food Pro‐tec‐ts project is carried out within the framework of the INTERREG V A programme 'Deutschland‐Nederland' and is co‐financed by the European Regional Development Fund (ERDF) and the Dutch Ministry of Economic Affairs and Climate Change, the Ministry of Economic Affairs, Innovation, Digitalisation and Energy of North Rhine‐Westphalia and the provinces of Gelderland, Limburg and North Brabant. It is accompanied by the programme management at the Euregio Rhein‐Waal. LS received a grant from the Marie Skłodowska‐Curie Actions (Grant Agreement number: 713660—PRONKJEWAIL—H2020—MSCA‐COFUND‐2015). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Funding Information:
We thank Erwin C. Raangs, Liana Kafetzopoulou and Hayley Cassidy for expert technical support and the farmers for their participation in the study. The Food Protects project is carried out within the framework of the INTERREG V A programme “Deutschland‐Nederland” and is co‐financed by the European Regional Development Fund (ERDF) and the Dutch Ministry of Economic Affairs and Climate Change, the Ministry of Economic Affairs, Innovation, Digitalization and Energy of North Rhine‐Westphalia and the provinces of Gelderland, Limburg and North Brabant. It is accompanied by the programme management at the Euregio Rhein‐Waal. Leonard Schuele received the Marie Skłodowska‐Curie Actions (Grant Agreement number: 713660 PRONKJEWAIL H2020 MSCA‐COFUND‐2015). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Publisher Copyright:
© 2021 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.

Keywords

  • influenza A virus
  • one health
  • porcine virome
  • shotgun metagenomics sequencing
  • surveillance
  • targeted sequence capture

ASJC Scopus subject areas

  • General Immunology and Microbiology
  • General Veterinary

Fingerprint

Dive into the research topics of 'Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch–German border region'. Together they form a unique fingerprint.

Cite this