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.

Patrick C Y Woo1 Susanna K P Lau Carol S F Lam Candy C Y Lau Alan K L Tsang John H N Lau Ru Bai Jade L L Teng Chris C C Tsang Ming Wang Bo-Jian Zheng Kwok-Hung Chan Kwok-Yung Yuen
Affiliations 1 institutions
  1. Department of Microbiology, The University of Hong Kong, Hong Kong, and Guangzhou Center for Disease Control and Prevention, Guangzhou, China.

Abstract

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.

Supporting text Virus Host Location
Animals 1948 Base Sequence 52 Bird Diseases 23 Birds 212 Cats 120 Chiroptera 371 Coronaviridae 13 Coronaviridae Infections 4 Coronavirus 92 Dogs 176 Evolution, Molecular 176 Genome, Viral 317 Haplorhini 7 Humans 1440 Mammals 92 Molecular Sequence Data 160 Phylogeny 805 Rodentia 51 Swine 258 Viral Proteins 152

Evidence records

10 total
Zoonotic Surveillance
9 records · 2 evidence types
Evidence type
7 records
OVE11492
Key finding

Porcine coronavirus HKU15 was detected in pigs through molecular epidemiology sampling.

Virus
Host
Location
Not specified
Supporting text

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.

Method
molecular epidemiology sampling | genome sequencing
OVE11493
Key finding

White-eye coronavirus HKU16 was detected in birds through molecular epidemiology sampling.

Virus
Host
Location
Not specified
Supporting text

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.

Method
molecular epidemiology sampling | genome sequencing
OVE11494
Key finding

Sparrow coronavirus HKU17 was detected in birds through molecular epidemiology sampling.

Virus
Host
Location
Not specified
Supporting text

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.

Method
molecular epidemiology sampling | genome sequencing
OVE11495
Key finding

Magpie robin coronavirus HKU18 was detected in birds through molecular epidemiology sampling.

Virus
Host
Location
Not specified
Supporting text

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.

Method
molecular epidemiology sampling | genome sequencing
OVE11496
Key finding

Night heron coronavirus HKU19 was detected in birds through molecular epidemiology sampling.

Virus
Host
Location
Not specified
Supporting text

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.

Method
molecular epidemiology sampling | genome sequencing
OVE11497
Key finding

Wigeon coronavirus HKU20 was detected in birds through molecular epidemiology sampling.

Virus
Host
Location
Not specified
Supporting text

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.

Method
molecular epidemiology sampling | genome sequencing
OVE11498
Key finding

Common moorhen coronavirus HKU21 was detected in birds through molecular epidemiology sampling.

Virus
Host
Location
Not specified
Supporting text

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.

Method
molecular epidemiology sampling | genome sequencing
Evidence type
2 records
OVE11500
Key finding

Bats are proposed as ecological gene sources and natural hosts for Alphacoronaviruses and Betacoronaviruses, supporting their reservoir role.

Virus
Host
Location
Not specified
Supporting text

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.

Method
comparative genome analysis | molecular epidemiology studies
OVE11501
Key finding

Birds are proposed as ecological gene sources and natural hosts for Gammacoronaviruses and Deltacoronaviruses, supporting their reservoir role.

Virus
Host
Location
Not specified
Supporting text

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.

Method
comparative genome analysis | molecular epidemiology studies
Genomic Evolution
1 records · 1 evidence types
Evidence type
1 records
OVE11499
Key finding

Molecular clock analysis estimated that the most recent common ancestor of all coronaviruses dates to around 8100 BC, with separate divergence times for Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus genera.

Virus
Host
Not specified
Location
Not specified
Supporting text

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.

Analysis methods
molecular clock analysis | phylogenetic analysis