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London1 Novel CoV 2012 nsp12 Coronavirus Sequence
Recombinomics Commentary 01:00
September 26, 2012

HPA nsp12 Phylogenetic Tree

The above phylogenetic tree (generated by the UK Health Protection Agency - HPA) is of the partial sequence from the coronavirus polymerase gene (nsp12) from the Qatar case (49M) demonstrates the novel aspect of this cornonavirus (CoV).  The HPA used a 208 base pair fragment representing positions 15303-15510 of the closet match, Bat coronovirus HKU5-5, sequenced by researchers at The University of Hong Kong from an isolate from Guangdong Province.  The fragment had 35 differences (83% identity), in contrast to the Netherlands sequence from the index case (60M who died in Saudi Arabia), which had 1 difference (99.5% identity).

Thus, the coronavirus is clearly novel and does not match any public coronavirus sequence.

The HPA is to be commended for the rapid release of this important sequence.

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