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

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

While all known cases linked to Iran are contained in this clade, it is important to note the presence of two Chinese strains sampled during mid-January 2020 from Hubei and Shandong provinces. It is expected that further Chinese strains would be identified within this clade, and across the entire diversity of SARS-CoV-2 as this is where the outbreak started, including for the outbreak in Iran itself. However, while we cannot completely discount that the cases in Australia and New Zealand came from other sources including China, our phylogenetic analyses, as well as epidemiological (recent travel to Iran) and clinical data (date of symptom onset), provide evidence that this clade of SARS-CoV-2 is linked to the Iranian epidemic, from where genomic data is currently lacking. Importantly, the seemingly multiple importations of very closely related viruses from Iran into Australia suggests that this diversity reflects the early stages of SARS-CoV-2 transmission within Iran.