Sunday, September 30, 2012

Recombinomics: Human Betacoronavirus 2c EMC/12 - Human SARS CoV Match

September 28, 2012  

The Ron Fouchier Viroscience lab at the Erasmus Medical Centef has released the complete sequence (30118 BP) of an isolate, Human betacoronavirus 2c EMC/2012, from the recent fatal case (60M) from Saudi Arabia (at Genbank).  The lab is to be congratulated for its rapid release of this important sequence.

Earlier the Health Protection agency had released a 208 BP fragment from a case from Qatar (47M requiring an ECO machine for breathing), which was 99.5% identical to the above sequence, confirming the emergence of a novel human cornavirus from group 2c, which was most closely related to bat coronavirus sequences from isolates from Guangdong Province.  The full sequence was also most closely related to these group 2c bat isolates, which is incorporated in the name assigned to the isolate by the Fouchier lab.

The group 2c coronaviruses are distinct for the human SARS  CoV, which maps to group 2b.  However, coronavirus rapidly evolve via homologous recombination and portions of genes show regions of identity of high homology with coronavirus segments from other species or phylogenetic groups.

An example of this type of homology is seen for positions 14628-14656 which match to the polymerase gene in pp1a, where 28 of the 29 positions match human SARS CoV (see list here).

Correction:  The above match is with human HKU-1, which is from group 2a.  Example with human SARS Cov (group 2b) here (24/25 matches at positions 15475-15499).

The rapid evolution via recombination with sequence present in human SARS CoV raise concerns of human adaptation and species jumping of a novel coronavirus which produces severe and fatal disease in humans.

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