An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

Eden, John-Sebastian; Rockett, Rebecca; Carter, Ian; Rahman, Hossinur; de Ligt, Joep; Hadfield, James; Storey, Matthew; Ren, Xiaoyun; Tulloch, Rachel; Basile, Kerri; Wells, Jessica; Byun, Roy; Gilroy, Nicky; O’Sullivan, Matthew V; Sintchenko, Vitali; Chen, Sharon C; Maddocks, Susan; Sorrell, Tania C; Holmes, Edward C; Dwyer, Dominic E; Kok, Jen

Of note, the genomes of all patients with a history of travel to Iran were part of a monophyletic group defined by three nucleotide substitutions (G1397A, T28688C, and G29742T) in the SARS-CoV-2 genome relative to the Wuhan prototype strain (Fig. 1B) . G1397A and T28688C both occur in coding regions with G1397A producing a non-synonymous change (V378I) in the ORF1ab-encoded non-structural protein 2 region. G29742T occurs in the 3 0 -UTR. In addition to the Australian and New Zealand strains, this clade also included a traveller who had returned to Canada from Iran (BC_37_0-2), providing further evidence of its likely link to the Iranian epidemic. Indeed, a search of all currently available GISAID sequences and metadata revealed no other complete genome sequences from patients with documented history of travel to or residence in Iran (as of 9 March 2020). A search of partial sequences identified two SARS-CoV-2 sequences which originated in Iran (413553/IRN/ Tehran15AW/2020-02-28 and 413554/IRN/Tehran9BE/2020-02-23) spanning a 363 nt region of the viral nucleoprotein (N). Although short in length, these two sequences covered one of the informative SNPs defining this clade-T28688C, and both Iranian strains matched the sequences from patients with travel histories to Iran and grouped by phylogenetic analysis (Supplementary Figs. S1 and S2).