Table 1.
Orthocoronavirus sequences analyzed in this study.
| Genus and published virus namea | Host species | Accession | Year | Sampling country |
|---|---|---|---|---|
| Alphacoronavirus | ||||
| Miniopterus bat coronavirus 1 | Miniopterus spp. | AY864196 | 2004 | Hong Kong |
| Bat coronavirus HKU7 | Miniopterus magnater | DQ249226 | 2005 | Hong Kong |
| Scotophilus bat coronavirus 512 | Scotophilus kuhlii | DQ648858 | 2005 | China |
| Bat coronavirus HKU2 | Rhinolophus sinicus | EF203064 | 2006 | China |
| Bat coronavirus 1B | Miniopterus pusillus | EU420137 | 2006 | China |
| Bat coronavirus 1A | Miniopterus magnater | EU420138 | 2005 | China |
| Bat coronavirus HKU8 | Miniopterus pusillus | EU420139 | 2005 | China |
| Bat coronavirus | Miniopterus schreibersii | GU190243 | 2008 | Bulgaria |
| Bat coronavirus | Miniopterus schreibersii | GU190244 | 2008 | Bulgaria |
| Miniopterus bat coronavirus/Kenya/KY33/2006 | Miniopterus inflatus | HQ728485 | 2006 | Kenya |
| Coronavirus BtCoV/KP256/Art_jam/PAN/2010 | Artibeus jamaicensis | JQ731784 | 2010 | Panama |
| Coronavirus BtCoV/KP565/Art_jam/PAN/2010 | Artibeus jamaicensis | JQ731786 | 2010 | Panama |
| Bat coronavirus | Miniopterus schreibersii | KF294269 | 2012 | China |
| Bat coronavirus | Miniopterus schreibersii | KF294270 | 2012 | China |
| Bat coronavirus | Miniopterus schreibersii | KF294271 | 2012 | China |
| Bat coronavirus | Miniopterus schreibersii | KF294275 | 2012 | China |
| Mystacina coronavirus New Zealand/2013 | Mystacina tuberculata | KF515987 | 2013 | New Zealand |
| Mystacina coronavirus New Zealand/2013 | Mystacina tuberculata | KF515988 | 2013 | New Zealand |
| Mystacina coronavirus New Zealand/2013 | Mystacina tuberculata | KF515989 | 2013 | New Zealand |
| Mystacina coronavirus New Zealand/2013 | Mystacina tuberculata | KF515990 | 2013 | New Zealand |
| Alphacoronavirus BtCoV/MSTM2/Min_nat/RSA/2010 | Miniopterus cf. natalensis | KF843851 | 2010 | South Africa |
| Alphacoronavirus BtCoV/VH_NC2/Neo_cap/RSA/2012 | Neoromicia cf. capensis | KF843854 | 2010 | South Africa |
| Alphacoronavirus BtCoV/GrNC1/Neo_cap/RSA/2012 | Neoromicia cf. capensis | KF843855 | 2010 | South Africa |
| Alphacoronavirus BtCoV/GrNC2/Neo_cap/RSA/2012 | Neoromicia cf. capensis | KF843856 | 2010 | South Africa |
| BtRf-AlphaCoV/HuB2013 | Rhinolophus ferrumequinum | KJ473807 | 2013 | China |
| BtMs-AlphaCoV/GS2013 | Myotis sp. | KJ473810 | 2013 | China |
| 229E-related bat coronavirus | Hipposideros abae | KT253270 | 2010 | Ghana |
| 229E-related bat coronavirus | Hipposideros abae | KT253272 | 2010 | Ghana |
| 229E-related bat coronavirus | Hipposideros cf. ruber | KT253273 | 2010 | Ghana |
| 229E-related bat coronavirus | Hipposideros abae | KT253274 | 2010 | Ghana |
| 229E-related bat coronavirus | Hipposideros cf. ruber | KT253297 | 2011 | Ghana |
| 229E-related bat coronavirus | Hipposideros cf. ruber | KT253298 | 2011 | Ghana |
| Bat coronavirus MsBtCoV/4039 | Miniopterus schreibersii | KU343194 | 2012 | China |
| Bat coronavirus HpBtCoV/3723 | Hipposideros pomona | KU343196 | 2012 | China |
| Bat coronavirus RaBtCoV/4307-1 | Rhinolophus affinis | KU343197 | 2013 | China |
| Bat coronavirus | Myotis siligorensis | KY770850 | 2013 | China |
| Bat coronavirus | Myotis davidii | KY770851 | 2013 | China |
| Bat coronavirus | Hipposideros armiger | KY770852 | 2013 | China |
| Bat coronavirus | Rhinolophus pearsonii | KY770853 | 2013 | China |
| Bat coronavirus | Rhinolophus macrotis | KY770854 | 2013 | China |
| Bat coronavirus | Myotis davidii | KY770856 | 2013 | China |
| Bat coronavirus | Ia io | KY770857 | 2013 | China |
| Alphacoronavirus sp. | Neoromicia capensis | MF593271 | 2013 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG193605 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG193610 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG193611 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG193616 | 2016 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG205585 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG205586 | 2014 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG205590 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG205592 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG205598 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG205599 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG252860 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG252863 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG252866 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG252870 | 2016 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG252871 | 2016 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG252874 | 2016 | South Africa |
| Bat alphacoronavirus | Neoromicia nanus | MG252875 | 2016 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310222 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310232 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310235 | 2015 | South Africa |
| Bat alphacoronavirus | Miniopterus natalensis | MG310236 | 2016 | South Africa |
| Bat alphacoronavirus | Miniopterus natalensis | MG310239 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310241 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310242 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310246 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310247 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310253 | 2014 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG310257 | 2014 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG817491 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG817498 | 2015 | South Africa |
| Bat alphacoronavirus | Neoromicia capensis | MG817499 | 2015 | South Africa |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687934 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687937 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687938 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687941 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687942 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687943 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687944 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687945 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687946 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687948 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687954 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687955 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687956 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687957 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687958 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687960 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687961 | 2014 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687965 | 2015 | Vietnam |
| Alphacoronavirus sp. | Scotophilus kuhlii | MH687966 | 2015 | Vietnam |
| Bat coronavirus | Pipistrellus pipistrellus | MH921428 | 2016 | China |
| Bat coronavirus | Pipistrellus pipistrellus | MH921429 | 2016 | China |
| Coronavirus BtSk-AlphaCoV/GX2018B | Scotophilus kuhlii | MK211370 | 2017 | China |
| Coronavirus BtSk-AlphaCoV/GX2018D | Scotophilus kuhlii | MK211372 | 2017 | China |
| Chalinolobus morio alphacoronavirus | Chalinolobus morio | MN602059 | 2016 | Australia |
| Chalinolobus morio alphacoronavirus | Chalinolobus morio | MN602060 | 2016 | Australia |
| Miniopterus pusillus bat coronavirus | Miniopterus pusillus | MN611518 | 2018 | China |
| Scotophilus kuhlii bat coronavirus 512-related |
Scotophilus kuhlii |
MN611521 |
2018 |
China |
| Betacoronavirus | ||||
| Bat SARS coronavirusc | Rhinolophus pearsoni | DQ071615 | 2004 | China |
| Bat coronavirus/133/2005 | Tylonycteris pachypus | DQ648794 | 2005 | China |
| Bat coronavirus HKU5 | Pipistrellus abramus | EF065512 | 2006 | China |
| Bat coronavirus HKU9 |
Rousettus leschenaulti |
HM211100 |
2006 |
China |
| Gammacoronavirus | ||||
| Infectious bronchitis virus | Gallus gallus | FJ904719 | 1991 | USA |
| Infectious bronchitis virus | Gallus gallus | FJ904721 | 1972 | USA |
| Turkey coronavirus | Meleagris gallopavo | GQ427173 | 2003 | USA |
| Turkey coronavirus | Meleagris gallopavo | GQ427175 | 1994 | USA |
| Turkey coronavirus | Meleagris gallopavo | GQ427176 | 1998 | USA |
| Infectious bronchitis virus | Gallus gallus | GQ504724 | 1941 | USA |
| Infectious bronchitis virus | Gallus gallus | GU393336 | 1954 | USA |
| Duck coronavirus | Duckf | JF705860 | 2004 | China |
| Infectious bronchitis virus |
Gallus gallus |
JF828980 |
2010 |
China |
| Deltacoronavirus | ||||
| Bulbul coronavirus HKU11 | Pycnonotus jocosus | FJ376619 | 2007 | China |
| Thrush coronavirus HKU12 | Turdus hortulorum | FJ376621 | 2007 | China |
| Munia coronavirus HKU13 | Lonshura striata | FJ376622 | 2007 | China |
| White-eye coronavirus HKU16 | Zosterops sp. | JQ065044 | 2007 | China |
| Sparrow coronavirus HKU17 | Passer montanus | JQ065045 | 2007 | China |
| Magpie robin coronavirus HKU18 | Copsychus saularis | JQ065046 | 2007 | China |
| Night-heron coronavirus HKU19 | Nycticorax nycticorax | JQ065047 | 2007 | China |
| Wigeon coronavirus HKU20 | Anas Penelope | JQ065048 | 2008 | China |
| Common-moorhen coronavirus HKU21 | Gallinula chloropus | JQ065049 | 2007 | China |
a
Species, strain/isolate names are in Supplemental Table S2.