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MERS KSA Export To Munster Indiana Raises SARS Concerns
Recombinomics Commentary 10:45
May 3, 2014

There is one isolate of the virus that was collected recently from a patient in Saudi Arabia that was sequenced and reported and there had not been changes in the virus that suggested any kind of mutation. Based on the sequence of one viral isolate recently, we haven't seen changes. We will continue to monitor the situation. As you know with viral outbreaks, that's something that is very important to keep a look out on. With the SARS virus 11 years ago, we do believe there was a change in the virus that led to more explosive transmission. We will continue to look at that but we don't have data to confirm that has happened.

The above comments from the May 2 CDC presser on the first confirmed MERS case in the United States (Munster, Indiana - a suburb of Chicago, Illinois) cite the emergence of a SARS-CoV with a genetic change (29 nt deletion which was not in the S gene) that was found in cases from the Metropole Hotel, who were infected on Feb 20-21, 2003.  This 29 nt deletion was found in almost all subsequent sequences indicating that the explosion in SARS-CoV cases were largely due to this novel sub-clade.

There is data to support a similar emergence of MERS in Jeddah, Saudi Arabia.  As happened in 2003, sequencers have begun to make sequences public by posting early results on the website.  Three nearly complete sequences have been released on the Virology Institute in Bonn, Germany website from early April collections (C7149 and C7770 from hospital A on April 3 and 7, respectively as well as C7569 from hospital B on April 5).  Although the samples came from two different hospitals, all three sequences were virtually identical. 

They contained 9 polymorphisms that were in all 3 Jeddah sequences, but not in any other published sequence, signaling the emergence of a novel sub-clade in Jeddah.  Moreover, the partial sequence of the S gene from 25 additional Jeddah patients were said to be identical, raising concerns that all of the Jeddah sequences were from the same sub-clade, especially if the S sequence included positions 23804 and 23953, which are 2 of the 9 unique polymorphisms (and A23953G generates Q833R).  Therefore, the identification of the S gene positions sequenced would be useful.

Comments have been made that the receptor binding domain is not unique, but the novel Jeddah sub-clade has 4 genetic changes that produce protein sequence changes in 3 genes (ORF1a, S, ORF8b) as well as a 10th change (G28941C) that is only found in an Al Hasa sub-clade (AH19, AH24, AH25, AH26) involved in human to human transmission. That change produces non-synonymous changes in ORF8b (K60N) and the N gene (D126H), which is also in HKU-1 a human beta 2a coronavirus.

Prior to the Indiana case, there were 6 MERS exports from Jeddah to five countries (Jordan, Malaysia, Greece, United Arab Emirates, and Egypt).  Release of these sequences of the websites of the sequencers would be useful.

The Indiana case flew out of Riyadh, and comments suggested the health care worker was stationed in Riyadh, where there has also been a recent increase in reported MERS cases.  Therefore the release of those sequences by the US CDC would also be useful.

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