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      Evaluation of a Porcine deltacoronavirus eradication program in a full-cycle pig farm in Peru

      case-report

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          Abstract

          Objective:

          In this case report, we report for first the time the presence of porcine deltacoronavirus (PDCoV) in Peru (October 2019) and Latin America, and we present a control and eradication program using feedback (exposure)/controlled homogenization in a pig farm.

          Materials and Methods:

          This farm is located in the eastern jungle of Peru. Initially, clinical signs that appeared to be infectious diarrhea were detected, but the disease rapidly progressed to green diarrhea, vomiting, and increased mortality in piglets. These symptoms were compatible with those produced by porcine epidemic diarrhea virus and transmissible gastroenteritis virus, but also with PDCoV. Because the disease could not be diagnosed by clinical signs and symptoms, analysis by real-time polymerase chain reaction was used. Implementation of a feedback/controlled homogenization program was quickly planned, accompanied by the closure of the farm, animal and farm health strategies, and its respective monitoring.

          Results:

          At the farm level, between 1 and 9 weeks after application of the program, the samples were positive for PDCoV, but at week 10, they were negative. At week 12, the weaned and fattening piglets gradually became populated as negative animals. In the follow-up before the opening of the farm, all the piglets were negative. In the final verification, gilts (week 35) entered the breeding area as replacements only after being tested negative for PDCoV.

          Conclusion:

          A rigorous feedback/controlled homogenization program and complementary measures led to eradicating PDCoV from the farm.

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          Most cited references21

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          Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus.

          Recently, we reported the discovery of three novel coronaviruses, bulbul coronavirus HKU11, thrush coronavirus HKU12, and munia coronavirus HKU13, which were identified as representatives of a novel genus, Deltacoronavirus, in the subfamily Coronavirinae. In this territory-wide molecular epidemiology study involving 3,137 mammals and 3,298 birds, we discovered seven additional novel deltacoronaviruses in pigs and birds, which we named porcine coronavirus HKU15, white-eye coronavirus HKU16, sparrow coronavirus HKU17, magpie robin coronavirus HKU18, night heron coronavirus HKU19, wigeon coronavirus HKU20, and common moorhen coronavirus HKU21. Complete genome sequencing and comparative genome analysis showed that the avian and mammalian deltacoronaviruses have similar genome characteristics and structures. They all have relatively small genomes (25.421 to 26.674 kb), the smallest among all coronaviruses. They all have a single papain-like protease domain in the nsp3 gene; an accessory gene, NS6 open reading frame (ORF), located between the M and N genes; and a variable number of accessory genes (up to four) downstream of the N gene. Moreover, they all have the same putative transcription regulatory sequence of ACACCA. Molecular clock analysis showed that the most recent common ancestor of all coronaviruses was estimated at approximately 8100 BC, and those of Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus were at approximately 2400 BC, 3300 BC, 2800 BC, and 3000 BC, respectively. From our studies, it appears that bats and birds, the warm blooded flying vertebrates, are ideal hosts for the coronavirus gene source, bats for Alphacoronavirus and Betacoronavirus and birds for Gammacoronavirus and Deltacoronavirus, to fuel coronavirus evolution and dissemination.
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            Coronavirus Genomics and Bioinformatics Analysis

            The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999–2002, with estimated substitution rate of 4×10−4 to 2×10−2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.
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              Detection and Genetic Characterization of Deltacoronavirus in Pigs, Ohio, USA, 2014

              In Ohio, United States, in early 2014, a deltacoronavirus was detected in feces and intestine samples from pigs with diarrheal disease. The complete genome sequence and phylogenetic analysis of the virus confirmed that the virus is closely related to a porcine deltacoronavirus (porcine coronavirus HKU15) reported in Hong Kong in 2012.
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                Author and article information

                Journal
                J Adv Vet Anim Res
                J Adv Vet Anim Res
                JAVAR
                Journal of Advanced Veterinary and Animal Research
                A periodical of the Network for the Veterinarians of Bangladesh (BDvetNET) (Bangladesh )
                2311-7710
                June 2021
                23 June 2021
                : 8
                : 2
                : 300-306
                Affiliations
                [1]Faculty of Veterinary Medicine and Animal Science, Universidad Nacional Micaela Bastidas de Apurímac, Abancay, Perú
                Author notes
                CorrespondenceJhonas Vicente-Huaman 072235@ 123456unamba.edu.pe Faculty of Veterinary Medicine and Animal Science, Universidad Nacional Micaela Bastidas de Apurímac, AbancayPerú
                Article
                10.5455/javar.2021.h515
                8280984
                34395601
                61cd2259-01da-42c5-b17d-96dda5a35d84
                Copyright: © Journal of Advanced Veterinary and Animal Research

                This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 License ( http://creativecommons.org/licenses/by/4.0)

                History
                : 29 March 2021
                : 25 April 2021
                : 27 April 2021
                Categories
                Case Report

                coronavirus,diarrhea,feedback,piglets,rt-pcr,viral exposure
                coronavirus, diarrhea, feedback, piglets, rt-pcr, viral exposure

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