Jordan and Jeddah Beta2c Coronavirus Sequence Match

Recombinomics Commentary 19:30
March 26, 2013

NAMRU-3 has released a full sequence (30030 BP), Jordan-N3, from a bronchial wash from one of the fatal case linked to the SARS-like Jordan ICU cluster (collected in April, 2012).  Like EMC/2012, the sequence has 70 differences with the consensus sequence (defined by EMC/2012,England1, and England2) which is an identity of almost 99.8%. 

However, 37 of these 70 differences are shared with EMC/2012, defining two distinct sets of sequences (Jordan-N3 and EMC/2012 in one subclade and England1 and England2 in a second subclade).  Because of the similarities a fifth sequence would be required to create a true consensus because of the large number of positions which are shared by 2 or the 4 full sequences. A fifth sequence would help determine how much of the match between Jordan and Jeddah is due to an earlier sampling, and how much is due to sub-clade differences.

The relatedness between the Jordan and Jeddah sequences raises concerns that this Jeddah sequence is widespread.
 
The match between Jordan and Jeddah increases concerns regarding recent comments that mild cases in Saudi Arabia were concentrated inJeddah.  The Jordan ICU cluster was likely due to a patient who was treated last April, but that index case was not identified.  The match with EMC/2012 raises concerns that the Jordan cluster was also linked to the nCoV circulating in Saudi Arabia.
The match between the Jordan cluster and the first confirmed case in Saudi Arabia supports sustained transmission of this sub-clade.  Full sequences from the two partially sequenced cases would be useful.