The impact and complete genome characterisation of viruses involved in outbreaks of gastroenteritis in a farrow-to-finish holding

Brnić, Dragan; Vlahović, Dunja; Gudan Kurilj, Andrea; Maltar-Strmečki, Nadica; Lojkić, Ivana; Kunić, Valentina; Jemeršić, Lorena; Bačani, Ivica; Kompes, Gordan; Beck, Relja; Mikuletič, Tina; Steyer, Andrej (2023) The impact and complete genome characterisation of viruses involved in outbreaks of gastroenteritis in a farrow-to-finish holding. Scientific Reports, 13 (1). ISSN 2045-2322

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Abstract

Viral enteric pathogens continuously burden intensive pig farming, causing gastrointestinal diseases of epidemic and endemic nature. The present study investigated two diarrhoea outbreaks on a large farrow-to-finish holding and subsequent circulation of outbreak-related enteric viruses. These viruses were characterised by whole genome sequencing, and statistical evaluation of the impact on specific production metrics was performed. The results provided evidence that the Porcine epidemic diarrhoea virus–swine enteric coronavirus (PEDV–SeCoV) S gene recombinant strain was responsible for the first outbreak, whilst Rotavirus A (RVA) in a mixed infection with Rotavirus B (RVB) and porcine kobuvirus (PKV) probably caused the second diarrhoea outbreak. Whole genome characterisation revealed a porcine origin of all viruses involved and significant heterogeneity of RVB strain, proposing four novel genotypes and changes in RVB VP1 genotype classification. The statistical evaluation confirmed only a minor disturbance in the number of weaned pigs per sow, with statistical forecasting showing positive trends. A follow-up study corroborated the endemicity of RVA and PKV, in contrast to PEDV–SeCoV. Punctual, comprehensive and timely investigation of diarrhoea outbreaks is a prerequisite for applying adequate pig health and biosecurity management. Calculating such outbreaks' impact on production metrics can potentially shape future decisions on management improvements.

Item Type:	Article
Uncontrolled Keywords:	PORCINE EPIDEMIC DIARRHEASWINE ENTERIC CORONAVIRUSHUNGARYSYSTEMFECESPIGSPCR
Subjects:	NATURAL SCIENCES > Physics NATURAL SCIENCES > Chemistry BIOMEDICINE AND HEALTHCARE > Public Health and Health Care BIOMEDICINE AND HEALTHCARE > Veterinary Medicine > Veterinary Public Health and Food Safety
Divisions:	Division of Physical Chemistry
Projects:	Project title Project leader Project code Project type Rotavirusi u ekosustavu Republike Hrvatske: molekularna epidemiologija i zoonotski potencijal-REco Dragan Brnić UIP-2017-05-8580 HRZZ UNSPECIFIED UNSPECIFIED D UNSPECIFIED
Depositing User:	Nadica Maltar Strmečki
Date Deposited:	06 Feb 2024 12:38
URI:	http://fulir.irb.hr/id/eprint/8511
DOI:	10.1038/s41598-023-45994-4

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