key: cord-0954923-z3221cfh authors: Wang, Leyi; Byrum, Beverly; Zhang, Yan title: Detection and Genetic Characterization of Deltacoronavirus in Pigs, Ohio, USA, 2014 date: 2014-07-03 journal: Emerg Infect Dis DOI: 10.3201/eid2007.140296 sha: 868afcaa176cdfdc50900313a5657583d5a74e9e doc_id: 954923 cord_uid: z3221cfh 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. indicating that mixed infection with PorCoV HKU15 and PEDV occurred in some pigs. On the basis of 2 complete genome sequences from GenBank, of PorCoV HKU15-44 and HKU15-155, we designed 16 pairs of primers to determine the whole genome of extracted RNA samples (OH1987) from Farm 1 ( Table 2 ). The genome of PorCoV HKU15 OH1987 comprised 25,422 nt (GenBank accession no. KJ462462). The genome organization and the transcription regulatory sequence motif 5′-ACACCA-3′ of PorCoV HKU15 OH1987 are the same as those reported for PorCoV HKU15-155 (1) . Similar to the BLAST search results of partial N and M fragments, the BLAST search of the whole genome of the PorCoV HKU15 OH1987 showed 99% nt identity to PorCoV HKU15-155. BLAST search of the spike gene of PorCoV HKU15 OH1987 showed 99% nt identity to PorCoV HKU15-44. These results confirmed that the coronavirus detected was a deltacoronavirus. Phylogenetic analysis of the complete genome of PorCoV HKU15 OH1987 showed that the OH1987 strain clustered with the other 2 PorCoVs, HKU15-155 and HKU15-44, and was distinct from the bird deltacoronaviruses ( Figure 1 ). In addition, the phylogenetic trees constructed by using the amino acid sequences of the spike glycoprotein and nucleocapsid protein showed that the OH1987 virus clustered with HKU15-155 and HKU15-44 ( Figure 2 ); this finding is in agreement with that in a previous study (1) . The OH1987 virus differs from HKU15-155 in the spike gene at nt 19469 and in the noncoding region at nt 25044; a 3-nt insertion is present at each location, making the whole-genome sequence of the OH1987 virus 6 nt longer than that of HKU15-155. The 2 insertion sites of the virus are identical to those of the HKU15-44 strain of porcine deltacoronavirus. However, the genome of OH1987 virus is 1 nt longer than that of HKU15-44 because of the insertion site at nt 25263, located in 3′ untranslated region. Of interest, strain OH1987 was most closely related to HKU15-155 when whole-genome sequence was used for phylogenetic analysis ( Figure 1 ), but strain OH1987 was more closely related to HKU15-44 when phylogenetic analysis of spike protein and nucleocapsid protein was performed ( Figure 2 ). On basis of the partial genome sequence, strain OH1987 was also closely related to a deltacoronavirus found in the Asian leopard cat (the whole-genome sequence is not available in GenBank). We detected a porcine deltacoronavirus in pigs in the United States. Although the genetic and phylogenetic analyses showed that the newly emergent strain, PorCoV HKU15 OH1987, was closely related to 2 strains from China, HKU15-155 and HKU15-44, in the genus Deltacoronavirus, when and how this virus was introduced into United States remain unknown. Further investigation is needed to determine whether infection with PorCoV HKU15 results in disease in pigs and if the virus was responsible for the clinical disease observed in outbreaks on the 5 Ohio farms in this study. In addition, surveillance should be conducted in other US states to define the distribution of the virus among the US pig population. Moreover, whole-genome sequence analysis should be performed for other strains from different locations to determine whether the virus was introduced into the United States by a single entry or by multiple entries. 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 Coronavirus genomics and bioinformatics analysis Interspecies transmission and emergence of novel viruses: lessons from bats and birds Transmissible gastroenteritis virus infection: a vanishing specter Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States New variant of porcine epidemic diarrhea virus, United States Bootstrap resampling (1,000 replications) was performed, and bootstrap values are indicated for each node. Reference sequences obtained from GenBank are indicated by strain name and accession number PEDV, virus and porcine epidemic diarrhea virus SARS, severe acute respiratory syndrome We acknowledge and appreciate the excellent technical help provided by Jason Herr and Kerri Lawrence.Dr Wang is a laboratory scientist at the Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture. His research interests include infectious diseases, molecular virology, and vaccine development.