J Virol. 2012 Apr;86(7):3995-4008. doi: 10.1128/JVI.06540-11. Epub 2012 Jan 25.
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.
Woo PC1, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY. 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.
Fig 1. From: 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.
Phylogenetic analysis of amino acid sequences of the 228-bp fragment (excluding primer sequences) of RNA-dependent RNA polymerase (RdRp) of CoVs identified from dead wild birds and pigs in the present study. The tree was constructed by the neighbor joining method using Kimura correction and bootstrap values calculated from 1,000 trees. The scale bar indicates the estimated number of substitutions per 20 amino acids. The eight genomes completely sequenced are shown in bold.
PEDV, porcine epidemic diarrhea virus (NC_003436);
Sc-BatCoV-512, Scotophilus bat coronavirus 512 (NC_009657);
TGEV, transmissible gastroenteritis virus (NC_002306);
FIPV, feline infectious peritonitis virus (AY994055);
CCoV, canine coronavirus (GQ477367);
PRCV, porcine respiratory coronavirus (DQ811787);
Rh-BatCoV-HKU2, Rhinolophus bat coronavirus HKU2 (EF203064);
Mi-BatCoV 1A, Miniopterus bat coronavirus 1A (NC_010437);
Mi-BatCoV 1B, Miniopterus bat coronavirus 1B (NC_010436);
Mi-BatCoV-HKU8, Miniopterus bat coronavirus HKU8 (NC_010438);
HCoV-229E, human coronavirus 229E (NC_002645);
HCoV-NL63, human coronavirus NL63 (NC_005831);
HCoV OC43, human coronavirus OC43 (NC_005147);
BCoV, bovine coronavirus (NC_003045);
AntelopeCoV, sable antelope CoV (EF424621);
GiCoV, giraffe coronavirus (EF424622);
ECoV, equine coronavirus (NC_010327);
PHEV, porcine hemagglutinating encephalomyelitis virus (NC_007732);
MHV, murine hepatitis virus (NC_001846);
RCoV, rat coronavirus (NC_012936);
HCoV-HKU1, human coronaviurs HKU1 (NC_006577);
Ty-BatCoV-HKU4, Tylonycteris bat coronavirus HKU4 (NC_009019);
Pi-BatCoV-HKU5, Pipistrellus bat coronavirus HKU5 (NC_009020);
SARS CoV, SARS-related human coronavirus (NC_004718);
SARSr-Rh-BatCoV HKU3, SARS-related Rhinolophus bat coronavirus HKU3 (DQ022305);
SARSr CoV CFB, SARS-related Chinese ferret badger coronavirus (AY545919);
SARSr-CiCoV, SARS-related palm civet coronavirus (AY304488);
Ro-BatCoV-HKU9, Rousettus bat coronavirus HKU9 (NC_009021);
IBV, infectious bronchitis virus (NC_001451);
IBV-partridge, partridge coronavirus (AY646283);
TCoV, turkey coronavirus (NC_010800);
IBV-peafowl, peafowl coronavirus (AY641576);
BWCoV-SW1, beluga whale coronavirus SW1 (NC_010646);
ALCCoV, Asian leopard cat coronavirus (EF584908);
BuCoV HKU11, bulbul coronavirus HKU11(FJ376619);
ThCoV HKU12, thrush coronavirus HKU12 (FJ376621);
MunCoV HKU13, munia coronavirus HKU13 (FJ376622);
PorCoV HKU15, porcine coronavirus HKU15;
WECoV HKU16, white-eye coronavirus HKU16;
SpCoV HKU17 (TrSp, tree sparrow), sparrow coronavirus HKU17
MRCoV HKU18 (OMR, oriental magpie robin), magpie robin coronavirus HKU18;
NHCoV HKU19 (BlCrNH, black-crowned night heron), night heron coronavirus HKU19;
WiCoV HKU20 (EuWi, Eurasian wigeon), wigeon coronavirus HKU20;
CMCoV HKU21, common moorhen (CM) coronavirus HKU21.
Mu, munia;
ChMu, chestnut munia; GbTh, gray-backed thrush;
ShBu, sooty-headed bulbul;
RwBu, red-whiskered bulbul;
ChBu, chestnut bulbul.
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.
Fig 1. From: 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.
Phylogenetic analysis of amino acid sequences of the 228-bp fragment (excluding primer sequences) of RNA-dependent RNA polymerase (RdRp) of CoVs identified from dead wild birds and pigs in the present study. The tree was constructed by the neighbor joining method using Kimura correction and bootstrap values calculated from 1,000 trees. The scale bar indicates the estimated number of substitutions per 20 amino acids. The eight genomes completely sequenced are shown in bold.
PEDV, porcine epidemic diarrhea virus (NC_003436);
Sc-BatCoV-512, Scotophilus bat coronavirus 512 (NC_009657);
TGEV, transmissible gastroenteritis virus (NC_002306);
FIPV, feline infectious peritonitis virus (AY994055);
CCoV, canine coronavirus (GQ477367);
PRCV, porcine respiratory coronavirus (DQ811787);
Rh-BatCoV-HKU2, Rhinolophus bat coronavirus HKU2 (EF203064);
Mi-BatCoV 1A, Miniopterus bat coronavirus 1A (NC_010437);
Mi-BatCoV 1B, Miniopterus bat coronavirus 1B (NC_010436);
Mi-BatCoV-HKU8, Miniopterus bat coronavirus HKU8 (NC_010438);
HCoV-229E, human coronavirus 229E (NC_002645);
HCoV-NL63, human coronavirus NL63 (NC_005831);
HCoV OC43, human coronavirus OC43 (NC_005147);
BCoV, bovine coronavirus (NC_003045);
AntelopeCoV, sable antelope CoV (EF424621);
GiCoV, giraffe coronavirus (EF424622);
ECoV, equine coronavirus (NC_010327);
PHEV, porcine hemagglutinating encephalomyelitis virus (NC_007732);
MHV, murine hepatitis virus (NC_001846);
RCoV, rat coronavirus (NC_012936);
HCoV-HKU1, human coronaviurs HKU1 (NC_006577);
Ty-BatCoV-HKU4, Tylonycteris bat coronavirus HKU4 (NC_009019);
Pi-BatCoV-HKU5, Pipistrellus bat coronavirus HKU5 (NC_009020);
SARS CoV, SARS-related human coronavirus (NC_004718);
SARSr-Rh-BatCoV HKU3, SARS-related Rhinolophus bat coronavirus HKU3 (DQ022305);
SARSr CoV CFB, SARS-related Chinese ferret badger coronavirus (AY545919);
SARSr-CiCoV, SARS-related palm civet coronavirus (AY304488);
Ro-BatCoV-HKU9, Rousettus bat coronavirus HKU9 (NC_009021);
IBV, infectious bronchitis virus (NC_001451);
IBV-partridge, partridge coronavirus (AY646283);
TCoV, turkey coronavirus (NC_010800);
IBV-peafowl, peafowl coronavirus (AY641576);
BWCoV-SW1, beluga whale coronavirus SW1 (NC_010646);
ALCCoV, Asian leopard cat coronavirus (EF584908);
BuCoV HKU11, bulbul coronavirus HKU11(FJ376619);
ThCoV HKU12, thrush coronavirus HKU12 (FJ376621);
MunCoV HKU13, munia coronavirus HKU13 (FJ376622);
PorCoV HKU15, porcine coronavirus HKU15;
WECoV HKU16, white-eye coronavirus HKU16;
SpCoV HKU17 (TrSp, tree sparrow), sparrow coronavirus HKU17
MRCoV HKU18 (OMR, oriental magpie robin), magpie robin coronavirus HKU18;
NHCoV HKU19 (BlCrNH, black-crowned night heron), night heron coronavirus HKU19;
WiCoV HKU20 (EuWi, Eurasian wigeon), wigeon coronavirus HKU20;
CMCoV HKU21, common moorhen (CM) coronavirus HKU21.
Mu, munia;
ChMu, chestnut munia; GbTh, gray-backed thrush;
ShBu, sooty-headed bulbul;
RwBu, red-whiskered bulbul;
ChBu, chestnut bulbul.
Fig
2. From: 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.
- DOI:
- 10.1128/JVI.06540-11
- [Indexed for MEDLINE]
- INTRODUCTION Coronaviruses (CoVs) are found in a wide variety of animals, in which they can cause respiratory, enteric, hepatic, and neurological diseases of varying severity. Based on genotypic and serological characterization, CoVs were traditionally divided into three distinct groups (3, 22, 54). Recently, the Coronavirus Study Group of the International Committee for Taxonomy of Viruses has proposed three genera, Alphacoronavirus, Betacoronavirus, and Gammacoronavirus, to replace the traditional CoV groups 1, 2, and 3. As a result of the unique mechanism of viral replication, CoVs have a high frequency of recombination (22). Their tendency for recombination and the inherently high mutation rates in RNA virus may allow them to adapt to new hosts and ecological niches (18, 47).The recent severe acute respiratory syndrome (SARS) epidemic, the discovery of SARS coronavirus (SARS-CoV), and the identification of SARS-CoV-like viruses from Himalayan palm civets and a raccoon dog from wild live markets in China have boosted interest in the discovery of novel CoVs in both humans and animals (5, 16, 33, 36, 39, 40, 46).A novel human CoV (HCoV) of the genus Alphacoronavirus, human coronavirus NL63 (HCoV-NL63), was reported independently by two groups in 2004 (12, 44).In 2005, we also described the discovery, complete genome sequence, clinical features, and molecular epidemiology of another novel HCoV, human coronavirus HKU1 (HCoV-HKU1), in the genus Betacoronavirus (24, 48, 50).As for animal CoVs, we and others have described the discovery of SARS-CoV-like viruses in horseshoe bats in Hong Kong Special Administrative Region (HKSAR) and other provinces of China (25, 30). Based on these findings, we conducted molecular surveillance studies to examine the diversity of CoVs in bats of our locality as well as of the Guangdong province of southern China, where the SARS epidemic originated and wet markets and game food restaurants serving bat dishes are commonly found. In these studies, at least nine other novel CoVs were discovered, including two novel subgroups in Betacoronavirus, subgroups C and D (26, 37, 45, 51). Other groups have also conducted molecular surveillance studies in bats and other animals, and additional novel CoVs were discovered and complete genomes sequenced (4, 6, 7, 9, 10, 13–15, 17, 21, 31, 32, 34, 43, 53).Birds are the reservoir of major emerging viruses, most notably, avian influenza viruses (29). Due to their flocking behavior and abilities to fly over long distances, birds have the potential to disseminate these emerging viruses efficiently among themselves and to other animals and humans. As for CoVs, the number of known CoVs in birds is relatively small compared to that in bats. Recently, we described the discovery of three novel CoVs in three families of birds, namedbulbul coronavirus HKU11 (BuCoV HKU11),thrush coronavirus HKU12 (ThCoV HKU12), andmunia coronavirus HKU13 (MunCoV HKU13) (49).These three CoVs formed a unique group of CoV, which probably represented a novel genus of CoV, Deltacoronavirus (8). We hypothesize that there are other previously unrecognized CoVs in this novel genus from mammals and other families of birds. To test this hypothesis, we carried out a territory-wide molecular epidemiology study in 3,137 mammals and 3,519 birds in HKSAR. Based on the results of comparative genome and phylogenetic analysis in the present study, we propose seven novel CoVs in Deltacoronavirus. Our model of bats and birds as the gene source of the four genera of coronaviruses is also discussed.N proteiini
Phylogenetic analyses of 3CLpro, RdRp, helicase (Hel), S, and N proteins of PorCoV HKU15, WECoV HKU16, SpCoV HKU17, MRCoV HKU18, NHCoV HKU19, WiCoV HKU20, and CMCoV HKU21. The trees were constructed by using the neighbor joining method using Kimura correction and bootstrap values calculated from 1,000 trees. Two hundred ninety-five, 892, 590, 802, and 249 amino acid positions in 3CLpro, RdRp, Hel, S, and N, respectively, were included in the analyses. The trees were midpoint rooted. For 3CLpro and S, the scale bar indicates the estimated number of substitutions per 10 amino acids. For RdRp and Hel, the scale bar indicates the estimated number of substitutions per 20 amino acids. For N, the scale bar indicates the estimated number of substitutions per 5 amino acids. Viruses characterized in this study are in bold. Virus name abbreviations are the same as those in the Fig. 1 legend.
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