Sequencing supports novel coronavirus's tie to bat strains

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Nov 20, 2012 (CIDRAP News) – Complete genetic sequencing of a novel coronavrius isolated from a Saudi Arabian man who died in June supports earlier findings that the virus is most closely related to coronaviruses found in bats, according to a report published today in mBio.

An international team of authors reports that the novel virus, known as HCoV-EMC/2012, is most closely related to two species of Asian bats, one from Southeast Asia and one from Japan. The novel virus may be even more closely akin to a bat coronavirus found in the Netherlands in 2008, but not enough sequence data are available to establish that, the scientists say.

The novel coronavirus has been identified in three cases so far. The Saudi man, who died of a respiratory disease Jun 24 at age 60, was the index case-patient. His illness was publicly reported in September, at the same time that a second case was reported in a Qatari man who fell ill on Sep 3 and was flown to London for treatment, where he apparently remains hospitalized.

The third case was reported Nov 4 in another Saudi Arabian. Saudi officials said the man had been hospitalized in intensive care but was recovering and that he had no ties to the other two patients.

The senior author of the new report is Ron Fouchier, PhD, of Erasmus Medical Center in the Netherlands, who conducted initial analyses of the novel virus after the patient's Saudi doctor sent him clinical samples.

Before 2003, only two coronaviruses were known to infect humans, causing generally mild respiratory illnesses, the report notes. When SARS (severe acute respiratory syndrome) emerged in 2002 and was identified in 2003, it was traced to a then-new coronavirus. SARS spurred more research on such viruses, leading to the discovery of two additional human coronaviruses in 2004 and 2005.

Fouchier's team compared the HCoV-EMC/2012 genome with the genomes of other coronaviruses for which complete sequences are available. They determined that the amino acid sequence for the replicase gene of the new virus has 75% identity with the same gene in the bat coronavirus HKU4, found in lesser bamboo bats (Tylonycteris pachypus) in South and Southeast Asia.

Further, they found that the novel virus's replicase gene shares 77% similarity with its counterpart in the bat coronavirus HKU5, found in Japanese house bats (Pipistrellus abramas).

By convention, a virus is defined as a new species if its replicase gene is less than 90% the same as other strains in the same genus, the report says. Thus the authors propose that the novel virus is a new coronavirus species in the genus Betacoronavirus, making it the sixth coronavirus known to infect humans. But this awaits confirmation by the International Committee on Taxonomy of Viruses, they note.

They also report that the new virus may be even more closely related to a bat coronavirus identified in the Netherlands in 2008, judging from a partial sequence from that virus. The virus, called VM314/2008, was isolated from a Pipistrellus pipistrellus bat. A 332-nucleotide fragment of the virus's genome is 88% the same as the corresponding part of HCoV-EMC/2012, the report says.

This suggests that both viruses belong to the same species, but confirmation of this will require full sequencing of the Netherlands isolate's genome, the authors say.

They conclude, "It is tempting to speculate that HCoV-EMC/2012 emerged from bats—either indirectly or via an intermediate animal host, possibly Pipistrellus bats. This species is known to be present in the Kingdom of Saudi Arabia and neighboring countries."

The researchers also comment that the availability of the novel virus's genome sequence will facilitate the development of diagnostic tests that can be used to study the prevalence and clinical impact of infections in humans.

Van Boheemen S, de Graaf M, Lauber C, et al. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mBio 2012 Nov/Dec;3(6) [Abstract]

See also:

Nov 13 UK Health Protection Agency statement on sequencing of novel corona virus in London patient

Nov 5 CIDRAP News story "Saudi Arabia reports third novel coronavirus case"

Sep 28 CIDRAP News story "Scientists sequence new coronavirus, develop diagnostic tests"

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