Evidence map›Paper›PMID 40708015›Full record

ArticlePorcine health management2025

Characterization of the enteric virome of clinically healthy pigs around weaning on commercial farms in the Netherlands using next generation sequencing and qPCR.

M A R Schyns, R van den Braak, J Peijnenborg, S Coppens, M Deijs, M G J M Burggraaff, W I Kuller, S Theuns, L van der Hoek, A de Groof

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Article in Porcine health management, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

M A R SchynsBusiness Unit Intensive Livestock, MSD Animal Health Benelux, Wim de Körverstraat 35, Boxmeer, 5830 AA, The Netherlands.
R van den BraakDepartment Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, Boxmeer, 5830 AA, The Netherlands.
J PeijnenborgDepartment Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, Boxmeer, 5830 AA, The Netherlands.
S CoppensPathoSense BV, Pastoriestraat 10, Lier, 2500, Belgium.
M DeijsLaboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
M G J M BurggraaffLaboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
W I KullerUniversity Farm Animal Practice, Reijerscopse Overgang 1, Harmelen, 3481 LZ, The Netherlands.
S TheunsPathoSense BV, Pastoriestraat 10, Lier, 2500, Belgium.
L van der HoekLaboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
A de GroofDepartment Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, Boxmeer, 5830 AA, The Netherlands. ad.de.groof@merck.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundEnteric virus infections around time of weaning have always been related to pig diseases such as postweaning diarrhea. Little, however, is known about the virus infection pattern (species, timing and viral load) in clinically healthy pigs. Virus infections may help to train and shape the immune system and presumably only lead to clinical disease when uncontrolled. Next Generation Sequencing (NGS) is a relatively new technique that can uncover the composition of the enteric virome. This study describes the dynamics of the enteric virome in clinically healthy pigs using NGS and qPCR until 10 weeks of age.

methodsSeven farms were selected based on the following criteria: diarrhea after weaning was visible in less than 5% of the pens, piglets reached 25 kg of body weight before 10 weeks of age and no antimicrobial batch treatment had been used on the farm for the last six months. Rectal swabs were taken in five different age groups: 2, 3.5, 5, 7 and 10 weeks of age, 10 piglets per age group, in a cross-sectional setup. Two NGS platforms were used to detect enteric viruses. Eleven virus-specific qPCRs were used to corroborate the results of the NGS analyses.

resultsRotavirus A, Porcine Kobuvirus, Enterovirus G and Porcine Astrovirus 3 and 4 were first detected at two weeks of age, followed by detection of Porcine Astrovirus 5 at 3.5 weeks of age, just before weaning. One week after weaning, at 5 weeks of age, Porcine Astrovirus 3 was undetectable, but now Porcine Astrovirus 1 and 2 had successively made their entry. Although Rotavirus B & C, Porcine Sapelovirus and Porcine Sapovirus were already detected just before weaning, the amount of virus peaked one week after weaning. Rotavirus H was first detected one week after weaning and peaked at 7 weeks of age. Many viruses were cleared by the age of 10 weeks.

conclusionsThe timing and magnitude of subclinical enteric virus infections across farms were remarkably similar. Our study offers insight into the dynamics of enteric virome development in healthy pigs and provides essential context to NGS-based diagnostics.

Indexed as

AstrovirusEnteric virusesKobuvirusNGSRectal swabsRotavirusVirome dynamics

Identifiers

PMID40708015
PMCPMC12291374

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.