Cluster HK1 is most closely related to genomes of patients traveling from the Philippines, while cluster HK2 is most closely related to those from Kazakhstan. However, there are important differences between our locally-acquired clusters and these imported cases. All the genomes from cases imported from the Philippines did not contain nsp3 A85V or NP A12G that define cluster HK1, while those from Kazakhstan lack the mutation C28269T that define cluster HK2. Hence, our results suggest that there is a missing link between these locally-acquired cases in Hong Kong and those cases from the Philippines or Kazakhstan. Further investigations are required to investigate the source of this outbreak in Hong Kong.
