Figure 2

Bayesian-inferred phylogeny of all 21 new sequences

Combined with the published genomes (EMC/2012 [GenBank number {"type":"entrez-nucleotide","attrs":{"text":"JX869059","term_id":"409052551","term_text":"JX869059"}}JX869059], Jordan-N3 [{"type":"entrez-nucleotide","attrs":{"text":"KC776174","term_id":"469569405","term_text":"KC776174"}}KC776174], Munich/AbuDhabi [{"type":"entrez-nucleotide","attrs":{"text":"KF192507","term_id":"511262662","term_text":"KF192507"}}KF192507], England-Qatar_2012 [{"type":"entrez-nucleotide","attrs":{"text":"KC667074","term_id":"453061240","term_text":"KC667074"}}KC667074], Al-Hasa_1_2013 [{"type":"entrez-nucleotide","attrs":{"text":"KF186567","term_id":"511261302","term_text":"KF186567"}}KF186567], Al-Hasa_2_2013 [{"type":"entrez-nucleotide","attrs":{"text":"KF186566","term_id":"511261290","term_text":"KF186566"}}KF186566], Al-Hasa_3_2013 [{"type":"entrez-nucleotide","attrs":{"text":"KF186565","term_id":"511261314","term_text":"KF186565"}}KF186565], Al-Hasa_4_2013 [{"type":"entrez-nucleotide","attrs":{"text":"KF186564","term_id":"511261278","term_text":"KF186564"}}KF186564], and England2-HPA [no number available]). The single letter patient codes from Assiri and colleagues¹⁶ are given where appropriate. Clade A, clade B, and the Al-Hasa cluster are marked with vertical bars. Aminoacid changes along the internal branches were established though likelihood-based ancestral state reconstruction. These are shown above the branches and colour-coded by ORF. The scale bar below the phylogeny shows the genetic distance, in substitutions per site, from the arbitrary midpoint root. Bayesian posterior probabilities for each clade are given above the relevant node. MERS-CoV=Middle East respiratory syndrome coronavirus. ORF=open reading frame.