Subfamily: Orthocoronavirinae

Genus: Alphacoronavirus


Distinguishing features

Alphacoronaviruses form a distinct monophyletic group within the Orthocoronavirinae subfamily. They also have (i) a unique nsp1, distinct in size and sequence from the nsp1 of betacoronaviruses and without an apparent counterpart in either deltacoronaviruses or gammacoronaviruses (Connor and Roper 2007), and (ii) an accessory gene (designated ORF3 in most alphacoronavirus species, ORF3b in transmissible gastroenteritis virus and ORF3c in feline coronavirus/canine coronavirus) for a dispensable multi-spanning alphacoronavirus membrane protein (αmp) (Muller et al., 2010, Vlasova et al., 2011). For some alphacorona­viruses, αmp is the only accessory protein, but other alphacoronavirus genomes encode up to six accessory genes (e.g. certain coronaviruses in the species Alphacoronavirus 1) (Figure 1.Alphacoronavirus).

Alphacoronavirus genome organisation

Figure 1.Alphacoronavirus. Alphacoronavirus genome organization. Comparison of the 3′-terminal genomic regions downstream of ORF1b of alphacoronavirus representatives for members of different subgenera. ORFs are depicted as coloured boxes with red, S; blue, E; yellow, M and purple, N. ORFs for accessory proteins are depicted as coloured boxes in grey.


Alphacoronaviruses have been detected in a wide range of mammals. Members of the subgenera Colacovirus, Decacovirus, Duvinacovirus, Minuacovirus, Myotacovirus, Nyctacovirus, Pedacovirus, Rhinacovirus and Setracovirus are able to infect bats, while members of the subgenera Pedacovirus and Rhinacovirus can also cause enteric diseases in pigs (Pensaert and de Bouck 1978, Lau et al., 2007, Zhou et al., 2018). Two human coronaviruses are assigned to this genus, human coronavirus 229E and human coronavirus NL63, which belong to the subgenera Duvinacovirus and Setracovirus respectively (Tyrrell and Bynoe 1965, van der Hoek et al., 2004, Farsani et al., 2012). Lucheng Rn rat coronavirus (subgenus Luchacovirus), was discovered in brown rats (Wang et al., 2015). Mink coronavirus (subgenus Minacovirus), was found in the American mink (Mustela vison) (Vlasova et al., 2011). Common shrew coronavirus Tibet-2014 (subgenus Soracovirus) was found in common shrews (Wu et al., 2018). Suncus murinus coronavirus Xingguo-74 (subgenus Sunacovirus) was found in the Asian house shrew. In the subgenus Tegacovirus, members of the species Alphacoronavirus 1 infect multiple mammalian hosts, including dogs, cats and pigs (Whittaker et al., 2018).

Subgenus demarcation criteria

Details correspond to the family descriptions.

Species demarcation criteria

Details correspond to the family descriptions.