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Increased viral read counts and metagenomic full genome characterization of porcine astrovirus 4 and Posavirus 1 in sows in a swine farm with unexplained neonatal piglet diarrhea

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Abstract

Neonatal diarrhea in piglets may cause major losses in affected pig herds. The present study used random high-throughput RNA sequencing (metagenomic next generation sequencing, mNGS) to investigate the virome of sows from a farm with persistent neonatal piglet diarrhea in comparison to two control farms without diarrhea problems. A variety of known swine gastrointestinal viruses was detected in the control farms as well as in the problem farm (Mamastrovirus, Enterovirus, Picobirnavirus, Posavirus 1, Kobuvirus, Proprismacovirus). A substantial increase in normalized viral read counts was observed in the affected farm compared to the control farms. The increase was attributable to a single viral species in each of the sampled sows (porcine astrovirus 4 and Posavirus 1). The complete genomes of a porcine astrovirus 4 and two co-infecting Posavirus 1 were de novo assembled and characterized. The 6734 nt single-stranded RNA genome of porcine astrovirus 4 (PoAstV-4) strain Belgium/2019 contains three overlapping open reading frames (nonstructural protein 1ab, nonstructural protein 1a, capsid protein). Posavirus 1 strains Belgium/01/2019 and Belgium/02/2019 have a 9814 nt single-stranded positive-sense RNA genome encoding a single open reading frame (polyprotein precursor) containing the five expected Picornavirales-conserved protein domains. The study highlights the potential of mNGS workflows to study unexplained neonatal diarrhea in piglets and contributes to the scarce availability of both PoAstV-4 and Posavirus-1 whole genome sequences from Western Europe.

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Data Availability

Raw NGS metagenomic data are publicly available in the Sequence Read Archive (SRA) under BioSample accession numbers SAMN14450565, SAMN1450544, SAMN14450538, SAMN14450540, SAMN14450542, and SAMN14450570. Viral genome sequences are available under Genbank accession numbers MT642666-MT642668.

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Acknowledgements

This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under Grant Agreement No 773830: One Health European Joint Programme as internal joint research project METASTAVA. Raw sequencing data were professionally generated by the Genomics Core Leuven and Laboratory for NGS and microarray diagnostics (Dr. D. Höper, Friedrich Loeffler Institut, Germany). The authors thank L. Weckx for excellent technical assistance and R. Winand for supporting the bioinformatic analyses.

Funding

This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme as internal joint research project METASTAVA.

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Authors and Affiliations

  1. Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium

    Steven Van Borm & Frank Vandenbussche

  2. Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium

    Kevin Vanneste & Qiang Fu

  3. Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium

    Dominiek Maes & Alexandra Schoos

  4. VetWorks BVBA, Poeke, Belgium

    Eline Vallaey

Authors
  1. Steven Van Borm
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  2. Kevin Vanneste
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  3. Qiang Fu
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  4. Dominiek Maes
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  7. Frank Vandenbussche
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Contributions

SVB, FV, DM, AS, and EV performed experiments; KV, RW, QF, SVB, and FV performed data analysis; SVB and FV designed the experiment and wrote the manuscript.

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Correspondence to Steven Van Borm.

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The authors declare that they have no conflict of interest.

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As only animal fecal samples were used, no approval from the ethical committee for animal experiments was needed. Laboratory work and data analysis at Sciensano was not subject to.

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Van Borm, S., Vanneste, K., Fu, Q. et al. Increased viral read counts and metagenomic full genome characterization of porcine astrovirus 4 and Posavirus 1 in sows in a swine farm with unexplained neonatal piglet diarrhea. Virus Genes 56, 696–704 (2020). https://doi.org/10.1007/s11262-020-01791-z

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