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