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MERS-Related Coronavirus Characterized From Ugandan Bat Samples

NEW YORK (GenomeWeb) – A new study adds support to the notion that insect-eating bats may have been an evolutionary source of coronaviruses in the same lineage as the Middle East Respiratory coronavirus (MERS-CoV).

A team from Columbia University, the University of California at Davis, and elsewhere used PCR-based assays, targeted sequencing, and genome sequencing to profile viral material in samples from a Pipistrellus cf. hesperidus bat tested in Uganda in early 2013. The analyses uncovered a coronavirus that was almost 87 percent identical to MERS-CoV and shared some 91 percent of its sequences with a South African bat coronavirus known as NeoCoV.

As they reported in mBio today, the researchers dubbed the new MERS-related virus "PREDICT/PDF-2180," in a nod to the US Agency for International Development's PREDICT project, an effort focused on emerging pandemic threats. Their preliminary experiments suggest PREDICT/PDF-2180 cannot reproduce in African green monkey or human cells, apparently owing in part to divergence within a gene coding for a spike glycoprotein involved in receptor binding processes.

"In its current form, evolution notwithstanding, this virus is probably not going to be a threat to human health," first author Simon Anthony, an epidemiology researcher at Columbia's Mailman School of Public Health and the Columbia Center for Infection and Immunity, said in a statement.

When the MERS-CoV was first linked to respiratory infections and deaths in Saudi Arabia in 2012, early efforts to characterize the virus indicated that it was closely related to coronaviruses previously described in bats he and his co-authors noted. Although bats have been proposed as a possible reservoir for the virus, subsequent studies have highlighted dromedary camel roles in passing MERS-CoV to humans.

"While camels are thought to be important for the transmission of MERS-CoV," they wrote, "bats are widely considered to be the evolutionary source of the virus."

As part of a global virus surveillance survey, Anthony and his colleagues focused in on an apparent coronavirus identified in a southwestern Ugandan bat, using sequencing and consensus PCR assays to not only find and characterize viral particles in the bat's oral swab, rectal swab, and blood samples, but also to identify the bat's species.

From there, the researchers did Illumina sequencing on the virus, generating an almost-complete genome sequence for PREDICT/PDF-2180 that was compared with existing sequences for MERS-CoV and other coronaviruses. They noted that PREDICT/PDF-2180 and NeoCoV are closely related to one another, falling in a clade that's either basal or in a sister clade compared with MERS-CoV.

Some PREDICT/PDF-2180 genes shared very strong similarities to those MERS-CoV and NeoCoV. But the sequence identity between spike protein coding genes in PREDICT/PDF-2180 and MERS-CoV dropped off dramatically, prompting the team to take do several follow-up experiments to tease apart structure, binding, and other difference between the virulence spike proteins produced by the two viruses.

Ultimately, the authors concluded that PREDICT/PDF-2180 is unlikely to pose a zoonotic threat. "Recombination in the S1 subunit of the spike gene was identified as the primary mechanism driving variation in the spike phenotype and was likely one of the critical steps in the evolution and emergence of MERS-CoV in humans," they wrote.