Apparently the 2 starred (red stars in the figure) virus genomes are from the same 60-year old male patient [1,2,3; ] but the original variant, EMC/2012, was sequenced from material after 6 rounds of cell culture  while the Bisha_1 variant was not ; it was subjected to deep sequencing directly after nucleic acid preparation using an original respiratory sample aliquot (nasopharyngeal swab).
Given that cell culture passage seems to be related to the positioning of EMC/2012 in Clade A versus Bisha_1 in Clade B (indicated by a pale blue line), does this mean there is no Clade A (dark blue vertical bar) and that it's just an artefact??
Probably not. Why? Because the Jordan-N3/2012 virus that is also found in Clade A and it also originates from a human specimen collected in 2012. It is listed as having been sequenced from a bronchial sample. There is no mention of cell culture on its GenBank record - which does not mean there was no culture. But when that sample was passaged through culture and sequenced (N3/2012 MG167; sequence not shown in this tree) it remained 99.95% identical to the original sequence; just 2 nucleotide differences out of 30,028nt. 1 difference in the spike gene and 1 Open Reading Frame 1a). These are unlikely to be enough to switch its clade but I'm realigning with this sequence included just to be sure about that!
I thought that was kinda interesting.
NB. There may be some concern over the specimen labelling used to identify samples for sequencing of EMC/2012 or Bisha_1. I'm attempting to sort our by following this up with the lead author.
- Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Cotten et al. Lancet 2012;382:1993-2002
- 60-year old man from Bisha who died in a Jeddah hospital (EMC/2012 variant)
Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia. Zaki et al. N Engl J Med 2012; 367:1814-1820
- Genomic workup on EMC/2012
Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans. van Boheemen. mBio 2002; 3(6): e00473-12