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Egypt MERS Recombinant Raises Surveillance Concerns
Recombinomics Commentary 22:00
September 19, 2013

The Kingdom of Saudi Arabia Ministry of Health (KSA-MoH) has recently released 45 MERS-CoV sequences.  Most were from patients in the Al Hasa outbreak (7 full sequences and 32 partial sequences from 9 additional patients), which were virtually identical to the earlier four sequences from Al Hasa.  Moreover, two of the recent sequences from other locations (Riyadh_2_2012 and Buraidah_1_2013) were also related to the Al Hasa sequences. 

However, the other four sequences had clear evidence of evolution via homologous recombination.  Two of the sequences (Bisha_1_2012  and Riyadh_1_2012) were virtually identical to each other (differed a 1 position) and had polymorphisms shared with England1 / UAE in the 5’ end and Al Hasa polymorphisms in the 3’ end.  A more complex pattern was seen in Hafr-Al-Batin_1_2013, which had clusters of polymorphism from four different parents.  The fourth sequence, Riyadh_3_2013, also has clear evidence of recombination with a cluster s of polymorphisms including four (T2456A, C3320T, T4847C, and T6332C) shared with EMC_12 / Jordan-N3 , which are downstream from the four Jordan-N3 / EMC-12 polymorphisms (A542G, T623C, T1514C, C1883A) found in Hafr-Al-Batin.

Riyadh_3_2013 also has a cluster of 7 polymorphisms found in England1 / UAE  (C11492T, A11534G, G19075A, C20848A, C22790T, T24299C, G24515C) with the first five of these polymorphisms also present in Riyadh_1 / Bisha_1.

Riyadh_3_2013 was from a sample collected on February 5, 2013, which corresponds to a patient (61F) who developed symptoms while traveling in Egypt, suggesting the sequences represents unreported MERS circulating in Egypt, which is supported by antibodies found in camels raised in Egypt for slaughter.

The Riyahd_3 sequence highlights the need for more aggressive MERS surveillance in countries adjacent to KSA.

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