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New Human Qatar Beta2c Coronavirus Sequence
Recombinomics Commentary 16:00
March 2, 2013

The Wellcome Trust has deposited a full beta2c sequence for the Qatar patient (49M) who has been hospitalized in the UK for the past 5 months.  The new sequence, designated Human betacoronavirus 2c England-Qatar/2012, is available at Genbank.  It exactly matches England1, which was a direct sequences generated by the Health Protection Agency (HPA) from the clinical sample.  The new sequence extends the front and back ends of the Egland1 sequence to create a full sequence of 30112 BP which starts and stops at the same positions as EMC/2012.  These extended regions exactly match the EMC/2012 sequence.  Thus, the new sequence independently confirms the HPA sequence, including the 6 BP deletion at positions 29737-29742.

The new sequence also adds confidence to the validity of the consensus sequence created by the earlier WGS (whole genome sequences) of EMC/2012, England1 and England2.  The consensus sequence can be used to demonstrate the strong conservation between the WGS of the three prior sequences as well as the partial sequences from the first case (45M) from Riyadh and the second case from Qatar (45M) who sought treatment in Germany leading to the Essen sequence.

The England1 (and the new Wellcome sequence) differ from the consensus at 21 positions, as well as the 6 BP deletion.  The England2 sequence has 26 single nucleotide polymorphisms (SNPs) for an identity of more than 99.9%.  The EMC/2012 sequence has 70 SNPs (excluding the insertion at position 30061, which is likely a sequencing error) for an identity of 99.8%. 

The identity of 99.9% for the two HPA sequences is striking, since one sequence was from a patient who developed symptoms in August, 2012, while the second sequence was from the 2013 index case for the UK cluster, who developed symptoms in January, 2013. 

This high level of identity supports transmission in humans and the human sequences (WGS and partial) are easily distinguished from all prior beta 2c sequences from bats in Europe, Africa, and Asia.

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