World public health authorities alarmed about a new coronavirus related to viruses from bats

of the mBio study was fully sequenced within a few days by combining an optimized random amplification deep sequencing approach, which covered about 90 percent of the genome, with conventional Sanger sequencing to confirm these draft findings.

Phylogenetic analyses place the virus within the Betacoronavirus genus, where its closest fully sequenced relatives are viruses called BtCoV-HKU4 and BtCoV-HKU5, both of which were originally isolated in Asia from Lesser bamboo bats (Tylonycteris pachypus) and Japanese house bats (Pipistrellus abramus), respectively. HCoV-EMC/2012 bears only 77 percent sequence similarity with the BtCoV-HKU5 virus, however, making it distinct enough to be called a novel species of virus, says Fouchier.  A partial sequence from a virus that was isolated from a species of bat in the Netherlands appears to be a closer match with HCoV-EMC/2012, but without a full genome sequence the exact degree of relatedness is impossible to tell.

The release notes that based on the similarities the HCoV-EMC/2012 virus shares with viruses from bats, and taking into account a separate serological study carried out in Saudi Arabia that showed 2,400 hospital visitors had no antibodies to the virus, Fouchier feels confident saying the virus is new to humans. That source may well be bats, he says, since Pipistrellus bats are present in Saudi Arabia and neighboring countries.

The relatedness between the HCoV-EMC/2012 virus and the virus that infected the patient in the unnamed London hospital is interesting, says Fouchier, since they are similar enough to be the same species but different enough that they are probably not directly linked. “It is unlikely they would be infected from the same source. We really need to understand whether these viruses are coming from a single source or multiple sources” before more cases come to light, he says.

In addition to the insights it provides for identifying the source of the virus and linking cases of illness together, the genome sequence of the HCoV-EMC/2012 virus will also enable scientists to study the virus in more detail. By making synthetic copies of the virus genome, Fouchier says scientists can reconstruct the virus in the lab and study its properties to identify the sources of its virulence.

The genome sequence could also be pivotal to protecting public health.  “A well-annotated genome sequence is crucial to further the development of diagnostic methods and antivirals and vaccines that might be needed,” says Fouchier. Considering that three cases of disease from the virus have already been identified, he says, “we certainly need the diagnostics already.”

“Whether we would need antivirals and vaccines? Well, I certainly hope not,” says Fouchier.

— Read more in Sander van Boheemen et al., “Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans,” mBio 3, no. 6 (20 November 2012): e00473-12 (doi:10.1128/mBio.00473-12)