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Jeddah MERS Sub-Clade Sustained Transmission
Recombinomics Commentary 23:30
May 17, 2014

MERS Phylogenetic Tree

The above MERS phylogenetic tree posted by Andrew Rambaut at his website helps visualize the clonal expansion of the novel Jeddah MERS sub-clade.  All eight sequences (six nearly full sequences from cases from four hospitals in Jeddah and Mecca generated by Christian Drosten, (C8826 and C9055) collected on April 12 and April 14 from hospital A and C, respectively, as well as Mecca (C9355) collected on April 15.  The three earlier sequences were from two hospitals ((C7149 and C7770 from hospital A collected on April 3 and 7, respectively as well as C7569 from hospital B collected on April 5), 1 complete sequence s generated by the CDC from a Jeddah export case in Orlando, Florida USA, Florida/USA-2_Saudi Arabia_2014, and 1 partial sequence generated by the CDC from another Jeddah export case in Athens, Greece, Spike and N gene sequences, Greece-Saudi Arabia_2014, are all located on the same branch (blue shading).

This branch has no camel sequences because all of the human sequences have a change in the Spike gene (Q833R) and orf8b gene (L6Q) which has never been reported in any camel sequence or any MERS sequence that was not from the Jeddah sub-clade which is defined by 11 polymorphisms.  In addition to the eight sequences on the tree, 25 more Spike gene sequences with the two spike gene markers have been generated from patients in Jeddah.  Thus, there have been 33 full are partial sequences generated from cases linked to Jeddah or Mecca and all 33 belong to the same sub-clade.

These data highlight the need for sequences from pilgrims in Mecca and Medina.  The latest Jeddah exports are cases in the Netherlands who developed symptoms while in Medina (70M) and Mecca (73F).  The presence of the Jeddah sub-clade in Mecca raises concerns that it has spread to both Mecca and Medina and producing symptomatic exports, which have largely tested negative by PCR.

However, today’s presser on a casual contact (in Illinois) of the confirmed cases in Munster, Indiana (who was infected with a MERS sub-clade similar to prior cases in Riyadh) and the suggestion of additional cases in contacts in Indiana, raises concerns that the PCR data is largely false due to limitations in collection of optimal samples, and that serum testing of these suspect contacts will confirm many more exports from pilgrims infected in Jeddah, Mecca, or Medina.

The above phylogenetic tree supports clonal expansion and sustained transmission which is not limited to hospital settings and instead represents sustained transmission.

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