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The first isolation and whole genome characterization of Porcine Deltacoronavirus from pigs in Peru
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  • Juan More-Bayona,
  • Mercy Ramírez,
  • Ben Hause,
  • 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
Kansas State Univ
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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 positives to Porcine Deltacoronavirus with a cycle threshold (Ct) between 9-14, revealing a high viral load, while tested negatives 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. 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.

Peer review status:IN REVISION

04 Jun 2020Submitted to Transboundary and Emerging Diseases
04 Jun 2020Assigned to Editor
04 Jun 2020Submission Checks Completed
05 Jun 2020Reviewer(s) Assigned
26 Jul 2020Review(s) Completed, Editorial Evaluation Pending
26 Jul 2020Editorial Decision: Revise Major