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Dromedary Sequencing Data Details Diversity, Dispersal of MERS Coronavirus

NEW YORK (GenomeWeb) – A study appearing online today in Science suggests a form of Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV) that was behind a recent outbreak in Korea involved a recombinant MERS-CoV lineage circulating in some dromedary camels from Saudi Arabia.

Researchers from Saudi Arabia, China, Australia, and Egypt collected samples from more than 1,300 dromedary camels in Saudi Arabia over almost a year, starting in the spring of 2014. Using isolates from the roughly one quarter of camels that carried either MERS-CoV or other coronaviruses, they sequenced the genomes of 67 MERS-CoVs and more than two dozen other coronaviruses.

The team's analyses of these and other sequences suggest Saudi Arabian camels carry five main MERS-CoV lineages, all of which have been detected in human infections since 2012. One of these, called lineage 5, became more prominent in camels late last year, subsequently spreading to humans in the Middle East and Korea.

"Several MERS-CoV lineages were present in camels," the authors of the study wrote, "including a recombinant lineage that has been dominant since December 2014 and subsequently led to the human outbreaks in 2015."  

Since the first human MERS-CoV cases were confirmed in 2012, the virus has caused 1,300 confirmed infections worldwide and killed hundreds of people, mainly in Saudi Arabia and, more recently, in Korea.

In an effort to explore the roots of such human outbreaks, the researchers collected rectal or nasal swab samples from 1,309 camels at farms, slaughterhouses, and markets in the Saudi Arabian cities of Jeddah, Riyadh, and Taif between May 2014 and the following April.

Through RT-PCR testing, they identified CoV sequences in just over 25 percent of the animals tested, with most positive samples stemming from camel nasal samples collected at markets where dromedary camels from Saudi Arabia come in contact with camels from Sudan, Somalia, and elsewhere.

Even so, the Saudi Arabian camels had slightly higher CoV-positive rates than camels from other parts of the world. And the team saw a spike in CoV-positive nasal swab samples in late 2014 and early 2015, particularly in juvenile camels and calves.

But MERS-CoV — a betacoronavirus group C virus — wasn't the only coronavirus carried by the camels. Camel samples also contained a camelid alpha-CoV resembling a common cold-causing human coronavirus 229E, as well as a camel beta-1-HKU23-CoVs belonging to betacoronavirus group A.

Indeed, nearly 57 percent of camel nasal swabs that tested positive for MERS-CoV also contained camelid alpha-CoV sequences.

To examine relationships between these viruses, the researchers generated whole-genome sequences for 67 MERS-CoVs, 25 camelid alpha-CoV isolates, and a single camel beta-1-HKU23-CoV, isolated from 79 nasal swabs.

Using the newly sequenced MERS-CoV genomes, along with more than 100 MERS-CoV sequences obtained from public databases, the team performed a phylogenetic analysis that uncovered five main MERS-CoV lineages.

MERS-CoV from humans and camels turned up in each of the lineages, suggesting the virus may move from camels to humans relatively easily.

The Saudi Arabian camel isolates collected for the study mainly clustered in lineages 3, 4, and 5, though MERS-CoVs from lineage 5 — the lineage linked to human cases in South Korea and in Riyadh, Saudi Arabia — appeared to predominate in the Saudi Arabian camel samples collected this year.

The available sequences suggested these lineage 5 viruses likely sprung up through recombination between MERS-CoVs from lineages 3 and 4 sometime at the end of 2013 or during the first few months of 2014. 

In a related paper published online today in Science, a team from the Netherlands, Germany, and elsewhere described progress being made in developing a vaccine that decreases MERS-CoV RNA levels released by infected dromedary camels.