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

The Australian strains of SARS-CoV-2 were dispersed across the global SARS-CoV-2 phylogeny (Fig. 1A) . The first four cases of COVID-19 disease in NSW occurred between 24 and 26 January 2020, and these were closely related with 1-2 single nucleotide polymorphisms (SNPs) difference to the dominant variant circulating in Wuhan at the time (prototype strain MN908947/SARS-CoV-2/Wuhan-Hu-1). As the four patients identified in this period had recently returned from China, this region was the likely source of infection. From 1 February 2020, travel to Australia from mainland China was restricted to returning Australian residents and their children, who were placed in home quarantine for 14 days. Despite the intensive testing of such returning travellers, no further cases of COVID-19 were detected in NSW until 28 February 2020, when SARS-COV-2 was detected in an individual returning from Iran (NSW05). A close contact of this individual also tested positive (NSW14) providing the first evidence of local transmission within NSW. This was followed by further Iran travel-linked cases in NSW (NSW06, NSW11, NSW12, and NSW13) and New Zealand (NZ01).