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

Abstract

e 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.

Evolutionary dynamics of bovine coronaviruses: natural selection pattern of the spike gene implies adaptive evolution of the strains

“…Recently, the International Committee on Taxonomy of Viruses has proposed two subfamilies for the family Coronaviridae: subfamily Coronavirinae and subfamily Torovirinae. The former comprises three groups renamed as genera Alphacoronavirus, Betacoronavirus and Gammacoronavirus, respectively (de Groot et al, 2012) and with a novel (but yet to be approved) genus, provisionally named Deltacoronavirus (Woo et al, 2012). Four separate lineages (A through D), some of them encompassing multiple virus species, are commonly recognized within the genus Betacoronavirus.…”

Evolving views on enteric viral infections of equines: an appraisal of key pathogens

“…The later subfamily classified into four different genera viz. Alphacoronavirus, Betacoronavirus, Deltacoronavirus and Gammacoronavirus based on the serological and molecular differences (Woo et al, 2012). These are mainly associated with respiratory, neurologic, hepatic or gastrointestinal disorders in animals (Holmes, 2001).…”

“…These are mainly associated with respiratory, neurologic, hepatic or gastrointestinal disorders in animals (Holmes, 2001). The different animals reported to have Coronavirus mediated infections are swine, cattle, horse, dog, cat and avian species like chicken and turkey (Saif et al, 1991;White & Fenner, 1994;Studdert, 1996;Jamieson et al, 1998;Guy et al, 2000;Lai & Holmes, 2001;McIntosh, 2002;Strauss & Strauss, 2002;Ksiazek et al, 2003;Van der Hoek et al, 2004;Brian & Baric, 2005;Weiss & Navas-Martin, 2005;Decaro & Buonavoglia, 2008;Boileau & Kapil, 2010;Woo et al, 2012).…”

“…The group 2 is represented by human coronavirus strains (OC43 and HKU1), murine hepatitis virus, bovine coronavirus, porcine hemagglutinating encephalomyelitis virus, canine respiratory coronavirus (Erles et al, 2007), and bubaline coronavirus (Decaro et al, 2010). Viruses such as turkey coronavirus and infectious bronchitis virus are included in group 3 (Resta et al, 1985;Studdert, 1996;Davis et al, 2000;Guy et al, 2000;Lai & Holmes, 2001;McIntosh, 2002;Strauss & Strauss, 2002;Van der Hoek et al, 2004;Smith & Denison, 2012;Woo et al, 2012;Smith et al, 2013).…”

Genome Sequencing and Analysis of a Porcine Delta Coronavirus from Eastern China

“…The virus was first identified through a genomic sequence analysis of avian and pig isolates in Hong Kong in 2012 [2]. PDCoV was first detected in farmed pigs with diarrhea in the United States in early 2014 [3].…”