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Recombination In Qatar Beta2c Coronavirus Sequence
Recombinomics Commentary 00:45
March 3, 2013

The recent release of the whole genome sequence of the index case (60M) for UK cluster, England2, as well as the Wellcome Trust sequence for the first Qatari case (49M) which is designated as Human betacoronavirus 2c England-Qatar/2012 and exactly matches England1, allows for precise analysis of the human sequences.

The England2 sequence, in conjunction with the previous EMC/2012 and England1 sequences, define the consensus sequence for the novel human beta2c sub-clade.  Comparison of each sequence to the consensus demonstrates the stability and close relatedness of the human sequences, which have matches with the consensus in the 99.8-99.9% range.

The Wellcome Trust sequence confirms that England1 has only 21 differences with the consensus sequence of 30,118 BP, other than the 6 BP deletion in the N gene (positions 29737-29742).  The consensus sequence also demonstrates this conservation in the partial sequences from two additional cases.  The two sets of sequences generated for the Riyadh gym teacher (45M) exactly match the consensus.  This is also true for the first sequence (positions 15073-15254) for the Qatar case (45M) who was treated in Germany (in Essen).  However, the second sequence (positions 29598-29838), which does not have the 6 BP deletion, has one difference with the consensus, A29714T, which is one of the  21 differences the sequence from the first Qatari case.  Although this change is silent, the sharing of the A29714T polymorphism in both sequences from Qatari cases supports the infection of both cases in Qatar and raises the possibility of recombination

The second case had not left Qatar prior to symptoms, but the first case had developed mild symptoms while preforming Umrah in Saudi Arabia in August.  Those symptoms resolved after he returned to Qatar, and the symptoms reappeared two weeks later (and his condition then deteriorated and he was transported to the UK by air ambulance, where he has remained hospitalized for the past 5 months).

Thus, the match of A29714T in both Qatari sequences support infection of both in Qatar.  However, the presence of G29723T (which codes for H386Q) and the 6 BP deletion (which deletes S391 and I392 in the N gene) raises the possibilty that England1 is a recombinant.

A more complete sequence from the Essen case, as well as sequences from the Jordan (SARS-like) health care workers cluster, the Riyadh familial cluster, and the most recent Saudi case (61F), would be useful.

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