key: cord-0699154-bphubv70 authors: Abe, T.; Arita, M. title: Genomic Surveillance in Japan of AY.29--A New Sub-lineage of SARS-CoV-2 Delta Variant with C5239T and T5514C Mutations date: 2021-09-22 journal: nan DOI: 10.1101/2021.09.20.21263869 sha: 8ff1e504b8365c2dcb5c0cd2138cb4ecd5e0d366 doc_id: 699154 cord_uid: bphubv70 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. Furthermore, the number of Delta variants imported from abroad during the Tokyo 2020 23 Olympics and Paralympics (held in August 2021) was extremely low. Therefore, the 24 epidemic of the new Delta variant is attributable to a newly occurring mutation in Japan. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread 27 rapidly across the globe since it was first reported in December 2019, and the 28 momentum of its spread has not diminished (1) . To address the trend of SARS-CoV-2 29 pandemic, genome sequencing has been performed on a global scale, and the results 30 have been publicized at the global initiative on sharing avian influenza data (GISAID) 31 (2). Currently, Delta variants (Phylogenetic Assignment of Named Global Outbreak 32 (PANGO) (3) lineage: B.1.617.2) are spread worldwide and predominant in many 33 countries including Japan after its first report in India in December 2020 (4, 5). In the present study, genomic surveillance was performed on the genomic 35 sequence data registered at GISAID to investigate the characteristics of the Delta 36 variants isolated in Japan. First, to investigate the diversity, haplotype networks from 37 genomic Delta single nucleotide variants (SNVs) were constructed using median joining 38 network analysis (6) with PopART version 1.7 (7) against 1,348 strains downloaded on 39 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2021. World Health Organization (WHO). 2021. Coronavirus Disease (COVID-2019 Situation Reports Global initiative on sharing all influenza data -from 101 vision to reality A dynamic nomenclature proposal for 103 SARS-CoV-2 lineages to assist genomic epidemiology World Health Organization (WHO). 2021. Tracking SARS-CoV-2 variants COVID-19 Cases & Deaths. Available at 109