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Volume 17
Issue 2
10.3390/v17020193
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Multiple Co-Infecting Caliciviruses in Oral Fluid and Enteric Samples of Swine Detected by a Novel RT-qPCR Assay and a 3′RACE-PCR-NGS Method

by
Zoltán László
1,
Péter Pankovics
1,
Péter Urbán
2,
Róbert Herczeg
2,
Gyula Balka
3,4,
Barbara Igriczi
3,4,
Attila Cságola
5,
Mihály Albert
5,
Fruzsina Tóth
1,
Gábor Reuter
1 and
Ákos Boros
1,*
1
Department of Medical Microbiology and Immunology, Medical School, University of Pecs, 7624 Pecs, Hungary
2
Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, János Szentagothai Research Centre, University of Pecs, 7624 Pecs, Hungary
3
Department of Pathology, University of Veterinary Medicine, István Str 2., 1078 Budapest, Hungary
4
National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1078 Budapest, Hungary
5
Ceva Phylaxia Ltd., 1107 Budapest, Hungary
*
Author to whom correspondence should be addressed.
Viruses 2025, 17(2), 193; https://doi.org/10.3390/v17020193
Submission received: 6 January 2025 / Revised: 23 January 2025 / Accepted: 24 January 2025 / Published: 30 January 2025
(This article belongs to the Special Issue Porcine Viruses 2024)
Versions Notes

Abstract

Caliciviruses including noro- and sapoviruses of family Caliciviridae are important enteric human and swine pathogens, while others, like valoviruses, are less known. In this study, we developed a detection and typing pipeline for the most prevalent swine enteric caliciviruses—sapovirus GIII (Sw-SaV), norovirus GII (Sw-NoV), and valovirus GI (Sw-VaV). The pipeline integrates triplex RT-qPCR, 3′RACE semi-nested PCR, and next-generation sequencing (NovaSeq, Illumina) techniques. A small-scale epidemiological investigation was conducted on archived enteric and, for the first time, on oral fluid/saliva samples of diarrheic and asymptomatic swine of varying ages from Hungary and Slovakia. In enteric samples, Sw-SaV was the most prevalent, detected in 26.26% of samples, primarily in diarrheic pigs with low Cq values, followed by Sw-NoV (2.53%) in nursery pigs. In oral fluid samples, Sw-NoV predominated (7.46%), followed by Sw-SaV (4.39%). Sw-VaVs were sporadically found in both sample types. A natural, asymptomatic Sw-SaV outbreak was retrospectively detected where the transient shedding of the virus was <2 weeks. Complete capsid sequences (n = 59; 43 Sw-SaV, 13 Sw-NoV, and 3 Sw-VaV) including multiple (up to five) co-infecting variants were identified. Sw-SaV sequences belong to seven genotypes, while Sw-NoV and Sw-VaV strains clustered into distinct sub-clades, highlighting the complex diversity of these enteric caliciviruses in swine.
Keywords: norovirus; sapovirus; valovirus; calicivirus; swine; saliva; oral fluid; NGS; co-infection norovirus; sapovirus; valovirus; calicivirus; swine; saliva; oral fluid; NGS; co-infection

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MDPI and ACS Style

László, Z.; Pankovics, P.; Urbán, P.; Herczeg, R.; Balka, G.; Igriczi, B.; Cságola, A.; Albert, M.; Tóth, F.; Reuter, G.; et al. Multiple Co-Infecting Caliciviruses in Oral Fluid and Enteric Samples of Swine Detected by a Novel RT-qPCR Assay and a 3′RACE-PCR-NGS Method. Viruses 2025, 17, 193. https://doi.org/10.3390/v17020193

AMA Style

László Z, Pankovics P, Urbán P, Herczeg R, Balka G, Igriczi B, Cságola A, Albert M, Tóth F, Reuter G, et al. Multiple Co-Infecting Caliciviruses in Oral Fluid and Enteric Samples of Swine Detected by a Novel RT-qPCR Assay and a 3′RACE-PCR-NGS Method. Viruses. 2025; 17(2):193. https://doi.org/10.3390/v17020193

Chicago/Turabian Style

László, Zoltán, Péter Pankovics, Péter Urbán, Róbert Herczeg, Gyula Balka, Barbara Igriczi, Attila Cságola, Mihály Albert, Fruzsina Tóth, Gábor Reuter, and et al. 2025. "Multiple Co-Infecting Caliciviruses in Oral Fluid and Enteric Samples of Swine Detected by a Novel RT-qPCR Assay and a 3′RACE-PCR-NGS Method" Viruses 17, no. 2: 193. https://doi.org/10.3390/v17020193

APA Style

László, Z., Pankovics, P., Urbán, P., Herczeg, R., Balka, G., Igriczi, B., Cságola, A., Albert, M., Tóth, F., Reuter, G., & Boros, Á. (2025). Multiple Co-Infecting Caliciviruses in Oral Fluid and Enteric Samples of Swine Detected by a Novel RT-qPCR Assay and a 3′RACE-PCR-NGS Method. Viruses, 17(2), 193. https://doi.org/10.3390/v17020193

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