The New Age of Virus Discovery: Genomic Analysis of a Novel Human Betacoronavirus Isolated from a Fatal Case of Pneumonia

Holmes, Kathryn V.; Dominguez, Samuel R.

What is the relationship between HCoV-EMC and known coronaviruses? According to the current classification by the International Committee on Taxonomy of Viruses, coronaviruses are in the order Nidovirales, family Coronaviridae, and subfamily Coronavirinae. There are at least 4 genera, alpha-, beta-, gamma-, and deltacoronaviruses, and the many virus species within each genus are grouped in multiple lineages called a, b, c, etc. The genome sequence revealed that HCoV-EMC is a betacoronavirus in lineage c, significantly different from SARS-CoV, a betacoronavirus in lineage b, and human betacoronaviruses OC43 and HKU1, which are placed in lineage a. The closest known relatives of HCoV-EMC in lineage c are two betacoronaviruses of Asian bats, but because HCoV-EMC and the bat viruses have only 75% to 77% amino acid identity in the 7 key conserved replicase domains used for phylogenetic analysis, HCoV-EMC is classified as a novel species within betacoronavirus lineage c (6) . The genomic analysis suggests that HCoV-EMC may be a zoonotic virus that spilled over to infect the 9 laboratory confirmed patients, either directly or indirectly, from an unknown reservoir, possibly a bat. This discovery justifies the recent worldwide surveillance of wildlife for coronavirus infection and the extensive genome sequencing and phylogenetic analysis that have been done since the SARS pandemic to identify potential risk to humans from zoonotic coronavirus infections.