Abstract
Coronavirus HKU15 is a deltacoronavirus that was discovered in fecal samples of pigs in Hong Kong in 2012. Over the past three years, Coronavirus HKU15 has been widely detected in pigs in East/Southeast Asia and North America and has been associated with fatal outbreaks. In all such epidemiological studies, the virus was generally only detected in fecal/intestinal samples. In this molecular epidemiology study, we detected Coronavirus HKU15 in 9.6% of the nasopharyngeal samples obtained from 249 pigs in Hong Kong. Samples that tested positive were mostly collected during winter. Complete genome sequencing of the Coronavirus HKU15 in two nasopharyngeal samples revealed quasispecies in one of the samples. Two of the polymorphic sites involved indels, but the other two involved transition substitutions. Phylogenetic analysis showed that the two nasopharyngeal strains in the present study were most closely related to the strains PDCoV/CHJXNI2/2015 from Jiangxi, China, and CH/Sichuan/S27/2012 from Sichuan, China. The outbreak strains in the United States possessed highly similar genome sequences and were clustered monophyletically, whereas the Asian strains were more diverse and paraphyletic. The detection of Coronavirus HKU15 in respiratory tracts of pigs implies that in addition to enteric infections, Coronavirus HKU15 may be able to cause respiratory infections in pigs and that in addition to fecal-oral transmission, the virus could possibly spread through the respiratory route. The presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of Coronavirus HKU15 infection. Quasispecies were unprecedentedly observed in the 5′-untranslated region of coronavirus genomes.Emerging Microbes & Infections (2017) 6, e53; doi:10.1038/emi.2017.37; published online 21 June 2017
Highlights
Coronaviruses (CoVs) are found in a wide variety of animals, in which they can lead to enteric, hepatic, neurological and respiratory illnesses of differing severity
DNA sequencing showed that seven sequence variants were detected among the 24 positive samples, and pairwise alignment showed that these seven sequence variants possessed 98.7%–100% sequence identity to the corresponding region in the RNAdependent RNA polymerase (RdRp) gene of Coronavirus HKU15 strain HKU15-155 that we previously found in fecal samples of pigs in Hong Kong[3] (Supplementary Figure S1)
Coronavirus HKU15 has been widely detected in various locations around the Pacific Ocean, including Canada,[7] China,[12,13,16,17] Hong Kong,[3] Laos,[22,23] Mexico,[19] South Korea,[5,21] Thailand,[20,23] Vietnam[23] and the United States,[6,7,8,9,10,11,14,15,18,19] the virus has principally been found in fecal or intestinal specimens
Summary
Coronaviruses (CoVs) are found in a wide variety of animals, in which they can lead to enteric, hepatic, neurological and respiratory illnesses of differing severity. On the basis of genotypic and serological characterization, CoVs were traditionally divided into three distinct groups. In 2009, the Coronavirus Study Group of the International Committee for Taxonomy of Viruses replaced the traditional CoV groups 1, 2 and 3 with three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, respectively.[1] In the same year, we discovered three novel CoVs in avian cloacal swabs.[2] These CoVs formed a distinct novel CoV genus, named Deltacoronavirus.[1] Subsequently, in a large epidemiological study, we discovered seven additional deltacoronaviruses.[3] Interestingly, one of these deltacoronaviruses, which was originally named porcine CoV HKU15, was found in fecal samples of pigs in Hong Kong, and it is the only mammalian deltacoronavirus.[3] In 2016, the Coronavirus Study Group of the International Committee for Taxonomy of Viruses rectified the species name for this virus to Coronavirus HKU15.4
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