Genomic Surveillance in Japan of AY.29--A New Sub-lineage of SARS-CoV-2 Delta Variant with C5239T and T5514C Mutations

In the present study, we report a new sub-lineage of the SARS-CoV-2 Delta variant called AY.29, which has C5239T and T5514C mutations. We investigated the monthly trend of AY.29 in Japan within 11,954 Delta variants downloaded on September 3, 2021. Among the total Japanese Delta variants, the AY.29 sub-lineage accounted for 88.4%. In terms of monthly changes, the sequences became predominant in June, and accounted for 93.2% and 94.2% of the reported sequences in July and August, respectively. Furthermore, the number of Delta variants imported from abroad during the Tokyo 2020 Olympics and Paralympics (held in August 2021) was extremely low. Therefore, the epidemic of the new Delta variant is attributable to a newly occurring mutation in Japan.