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Novel Beta2c Coronavirus Spike Q1020R & Q1020H
Recombinomics Commentary 22:00
March 11, 2013

The recent CDC early release MMWR and novel coronavirus alert cited the recent cluster in the UK which demonstrated clear human to human transmission, including a mild case (30F) that recovered without treatment of hospitalization.  Moreover, this cluster may have involved a fourth family member who infected the mild case, raising additional concerns that the virus was adapting to humans and transmitting in humans more efficiently.

The Health Protection Agency (HPA) recently released the full sequences from the index case (60M), England 2, which was closely related to the sequence, EMC/2012, from the first confirmed case (60M) and England 1, from the second case (49M), which was identical to England/Qatar/2012.  The sequences from these three cases created a consensus sequence for the human cases, which was used to demonstrate the high level of identity.  England 1 had only 21 differences plus a 6 BP deletion, while England 2 had 26 difference with the 30,118 BP consensus sequence.  Thus, both sequences were greater than 99.9% identical to the consensus, while EMC/2012 was just under 99.8% (with 70 differences).

The sequence of the spike protein (S) is of interest because that sequence determines receptor binding.  At the protein level, England 2 had only one difference with the consensus (Q1020R), while England 1 had only two differences (L506F and Q1020H).  The EMC/2012 S protein sequence matched the consensus.  The change at position 1020 in England 1 and England 2 raises concerns that changes at this position represent adaptation to humans. England 2 was  from the idenx cases of a confirmed cluster, while 13 health care workers who had contact with the Qatar case developed mild symptoms (although all tested negative)
Thus far England 2 represents the only sequence from a confirmed cluster. 

Release of sequences, including the region encoding the S gene,  from the Jordan ICU and Riyadh familial clusters would be useful.

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