key: cord-0839012-tvlz9pob authors: Li, Ganwu; Chen, Qi; Harmon, Karen M.; Yoon, Kyoung-Jin; Schwartz, Kent J.; Hoogland, Marlin J.; Gauger, Phillip C.; Main, Rodger G.; Zhang, Jianqiang title: Full-Length Genome Sequence of Porcine Deltacoronavirus Strain USA/IA/2014/8734 date: 2014-04-10 journal: Genome Announc DOI: 10.1128/genomea.00278-14 sha: 4ebdb50f487a8f6c2421e3e3281b053990cb4fac doc_id: 839012 cord_uid: tvlz9pob Porcine deltacoronavirus (PDCoV) was detected in feces from diarrheic sows during an epidemic of acute and transmissible diarrhea. No transmissible gastroenteritis virus or porcine epidemic diarrhea virus was detected. The PDCoV USA/IA/2014/8734 from the herd was sequenced for full-length genomic RNA to further characterize PDCoV in U.S. swine. positive-sense RNA viruses belonging to the order Nidovirales and the family Coronaviridae. Three genera, Alphacoronavirus, Betacoronavirus, and Gammacoronavirus, were proposed to replace the traditional group 1, 2, and 3 coronaviruses (1-3). The fourth genus, Deltacoronavirus, has recently been described by a research group in Hong Kong (4, 5) . By use of a molecular tool, they detected deltacoronaviruses in various species, including at least nine avian CoVs and two porcine CoVs (HKU-15-44 and HKU-15-155). In late February of 2014, we received a submission for diagnostic investigation from a 2,500-sow herd in Iowa with a history of acute severe diarrhea. The epidemic started in one breeding barn and progressed throughout the breeding and gestation barns over a 7-day period. Acute diarrhea started in the farrowing rooms (sows and piglets) approximately 8 to 9 days after the initial onset of clinical signs in the breeding barn. Viral enteritis was suspected based on clinical impression and gross and microscopic lesions. Molecular testing did not detect porcine epidemic diarrhea virus, transmissible gastroenteritis virus, or porcine rotaviruses. Bacterial culture yielded mixed and inconsistent populations of expected flora with no significant pathogens consistently identified. Unexpectedly, all fecal samples tested positive for porcine deltacoronavirus (PDCoV) by a pan-Coronaviridae PCR (6) followed by sequencing confirmation of PCR amplicons, as well as by a PDCoV-specific real-time reverse transcription (RT)-PCR assay with cycle threshold (C T ) values ranging from 14 to 19. Since the full-length genomic sequences of PDCoV in U.S. swine have not been previously reported, complete genomic sequencing of PDCoV (USA/IA/2014/8734) was attempted using next-generation sequencing technology on an Illumina MiSeq platform following the procedures established in our laboratory (7) . Sequences were mapped to all known coronaviruses and de novo assembled and then analyzed using the DNAStar Lasergene 11 Core Suite. The The PDCoV USA/IA/2014/8734 sequence data will facilitate future research on the epidemiology and evolutionary biology of PDCoVs in U.S. swine. Further study remains to be conducted to determine the clinical significance of PDCoV. Nucleotide sequence accession number. The complete genome sequence of PDCoV strain USA/IA/2014/8734 has been deposited in GenBank under the accession number KJ567050. Heterologous gene expression from transmissible gastroenteritis virus replicon particles Coronavirus genomics and bioinformatics analysis Coronavirus diversity, phylogeny and interspecies jumping 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 Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States This study was supported by Iowa State University Veterinary Diagnostic Laboratory.We thank Wendy Stensland, Amy Chriswell, Derek Dunn, and Sarah Abate for technical assistance in casework.