MERS-CoVs: South African bats vs Saudi Arabian bats

The latest sign of MERS-CoV in an animal, the Taphozous perforatus bat, is based on a 181 basepair (bp) fragment amplified from the viral RNA collected from a bat's droppings. 

The sequence is not yet available on the public sequence database, GenBank, and I haven't asked Prof Lipkin et al. for it. In the meantime though, I've aligned the primers mentioned in the new Emerging Infectious Diseases article by Memish and et al., against a full genome of MERS-CoV (EMC, the Munich strain). Sorry the image doesn't come out perfectly-if you click on it it will expand to the size of your browser.

Click then expand browser for full size. The expected position of the Memish et al. Taphozous perforatus bat MERS-CoV sequence is shown as a grey box. Primer locations for the nested RT-PCR are shown as red (outer primers) and orange (inner primers; the sequence region depicted in the phylogenetic tree in the recent EID paper) boxes. The recent South African bat CoV relative of MERS-CoV is show in pink (not overlapping) and the same region of full length CoV genomes are shown in blue (MERS-CoV EMC Munich) and green (HKU5 bat CoV)

For fun (yeah, I should get out more) I wanted to see just how close the "Close Relative of Human Middle East Respiratory Syndrome Coronavirus in Bat, South Africa" was, as described from another recent EID paper, to the new bat CoV. '

Unfortunately, as you can see above, the two fragments don't overlap. So my fun is ruined! 
We do know from yesterdays article however, that the 181bp fragment was 100% identical to human MERS-CoV over this short span (about 0.6% of the length of the entire MERS-CoV EMC genome). 

As Prof Andrew Rambaut noted to Helen Branswell in the Vancouver Sun, we need a whole genome to get more information that will better place the T. perforatus into the clade of viruses that seem related to MERS-CoV.