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First isolation and whole genome characterization of Porcine Deltacoronavirus from pigs in Peru
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  • Juan More-Bayona,
  • Mercy Ramírez,
  • Ben Hause,
  • Eric Nelson,
  • Hermelinda Rivera
Juan More-Bayona
Universidad Nacional Mayor de San Marcos
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Mercy Ramírez
Universidad Nacional Mayor de San Marcos
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Ben Hause
Cambridge Technologies Worthington Minnesota USA 56187
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Eric Nelson
South Dakota State University Department of Veterinary and Biomedical Sciences
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Hermelinda Rivera
Universidad Nacional Mayor de San Marcos
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Abstract

Porcine Deltacoronavirus is a newly emergent enteric pathogen affecting swine farms worldwide. It has been detected in several countries in Europe, Asia and North America; yet, it has not been reported in South America. In November 2019, an enteric disease outbreak in a pig farm located in San Martin, Peru; was reported along with submission of three intestinal samples from pigs who succumbed to the disease. Samples were processed for molecular detection by qRT-PCR, viral isolation and further sequencing analysis. A taqman-based RT-PCR was performed to differentiate among the most relevant swine enteric coronaviruses described to date. All samples were positive to Porcine Deltacoronavirus with a cycle threshold (Ct) value between 9-14, revealing a high viral load, while testing negative to Porcine Epidemic diarrhea and Transmissible Gastroenteritis viruses. Following detection, viral isolation was performed using PK-15 and Vero cell lines. After 5 days of inoculation, no cytopathic effect was observed. A second blind passage allowed the observation of cytopathic effect on PK-15 cells, while it remained absent in Vero cells. A fluorescence test using an anti-N monoclonal antibody confirmed viral replication. One sample was processed for whole genome sequencing (NGS). In short, raw reads were imported into CLC genomics and assembled de novo. Out of 479k reads generated from the sample, 436k assembled into a 25501 bp contig which was 99.5% identical to a reference Porcine Deltacoronavirus strain from US within the North American phylogroup. Yet, there are relevant differences at the nucleotide and amino acid levels compared to previously described Porcine Deltacoronavirus strains. Altogether, our findings represent the first report of Porcine Deltacoronavirus in South America, its genomic characterization, which provides information of its evolutionary origin. Thus, this study offers new insights into the molecular epidemiology of Porcine Deltacoronavirus infections in the swine industry.
11 Nov 2021Submitted to Transboundary and Emerging Diseases
11 Nov 2021Submission Checks Completed
11 Nov 2021Assigned to Editor
16 Nov 2021Reviewer(s) Assigned
28 Nov 2021Review(s) Completed, Editorial Evaluation Pending
30 Nov 2021Editorial Decision: Revise Major
16 Feb 20221st Revision Received
16 Feb 2022Submission Checks Completed
16 Feb 2022Assigned to Editor
17 Feb 2022Reviewer(s) Assigned
18 Feb 2022Review(s) Completed, Editorial Evaluation Pending
18 Feb 2022Editorial Decision: Accept
15 Mar 2022Published in Transboundary and Emerging Diseases. 10.1111/tbed.14489