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French MERS-CoV Sequences Identical To England2
Recombinomics Commentary 19:30
May 30, 2013

Confirmatory sequence analysis of the RdRp and N gene segments was done directly on RNA extracted from the bronchoalveolar lavage specimen from patient 1 and sputum specimen from patient 2. The sequences from both patients were identical. The RdRp sequences showed the C→T polymorphism at position 15196, which distinguishes all available sequences from that of the EMC/2012 isolate.5 For the N gene, sequences were identical to that of the EMC isolate and did not show the short deletion (nucleotides 29736–29741) nor any of the polymorphisms recorded at positions 29714 (A→T) and 29723 (G→T) in the England/Qatar/2012 sequence, nor that found at position 29811 (C→T) in the Jordan-N3/2012 sequence (appendix).5,15,17 These results definitively establish that both patients were infected with MERS-CoV.

The above comments from the Lancet paper on nosocomial MERS-CoV transmission in France describe the sequences from the two cases in France.  The RdRp region is 182 BP in length and both sequences from France were identical to the England1/2012 sequence (from the Qatari resident who developed MERS-CoV symptoms while performing Umrah in Saudi Arabia in 2012, the Essen sequence (from the Qatari diagnosed in Germany) and England2/2013 (from the England resident who developed MERS-CoV symptoms while performing Umrah in Saudi Arabia in 2013).  These sequences had zero difference with the consensus sequence, while the EMC/2012 and Jordan-N3/2012 each had one difference.  In contrast the closest bat sequence (from Romania) had 20 differences.

Similarly, the N gene region, which represented 240 BP, for the two cases from France was identical with England2.  This region diverges from all animal sequences, but the first 62 positions are identical in all seven human sequences, but have 7 differences with the most closely related bat sequence.

Thus, all human sequences are closely related to each other, and easily distinguished from all bat sequences, which are decades or centuries away from the human sequences.  The eighth human sequence, from the first case in Riyadh represents other regions but is identical to the consensus sequence for those regions.

The two sets of sequences from the French cases increases the number of public human sequences to eight and all are virtually identical to the consensus (identities of 99.6% or higher) strongly supporting human transmission, which appears to be evolving toward greater efficiency as seen by the large hospital clusters in eastern Saudi Arabia as well as the export of MERS-CoV via infected patients traveling via commercial airline from the Middle East to England, France, Tunisia, or Morocco.

These hospital clusters and exports, coupled with the high case fatality rate, signal sustained community transmission in the Middle East.

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