Wednesday, 18 September 2013

MERS-CoV genomes on GenBank...[UPDATE]

Click to enlarge. A scale schematic of the first
MERS-CoV genome, EMC/2012.
45 subgenomic (the smallest is 361 nucleotides [nt]) to full length genome (only 13; >30,000nt) sequences of the MERS-CoV have been released onto GenBank ahead of a Lancet Infectious Diseases paper arriving in days. The GenBank accession numbers range from KF600612 - KF600656 and repsenst human cases form 2012 & 2013. 

Usually (and hopefully soon), I would get the entire batch using a search of KF600612:KF600656[ACCN] at http://www.ncbi.nlm.nih.gov/nuccore. They seem to have to be downloaded manually for now.

The list of Middle East respiratory syndrome coronavirus sequences with their date of collection (DOC) includes:
  • KF600612, Riyadh_1_2012 ; 30,063nt
    DOC: 23-Oct-2012 
  • KF600613, Riyadh_3_2013; 30,064nt
    DOC: 05-Feb-2013
  • KF600614, Al-Hasa_10e_2013; 2,151nt
    DOC:02-May-2013
  • KF600615, Al-Hasa_14a_2013; 6,673nt
    DOC: 08-May-2013
  • KF600616, Al-Hasa_13b_2013; 3,787nt
    DOC: 07-May-2013
  • KF600617, Al-Hasa_22a_2013; 2,102nt
    DOC: 09-May-2013

Most are from cases in Al-Ahsa (adding to the previous 4), as well as from Riyadh, Buraidah and Hafr-Al-Batin

In case you read otherwise, there are no obvious signs of recombination among these viral sequences.

Thanks to @Sarah_E_Smith1 for announcing location on GenBank ahead of the Lancet paper.