Thread by @BijayaKDhakal

#Japan is experiencing a 6th wave of #SARSCoV2 #COVID19 pandemic. This wave is primarily driven by #Omicron BA.1.1, a sublineage of BA.1 with Spike protein R346K mutation, replacing #Delta sublineage AY.29. AY.29 is a Japanese lineage of Delta. Cases of BA.2 are also reported.🧵

BA.2 is primarily found in international travelers in #Japan. 152 cases of BA.2 have been sequenced, 133 of which are travel related. About 50% of cases have travel history to the #Philippines and 33% to #India. The graphs (1 & 2) shows travelers imported variants to Japan. 2/n

When travel related cases are removed from the analysis, it is primarily #Omicron BA.1.1 that is driving the present surge in #Japan. Although 19 likely community cases (no travel annotation) of BA.2 are reported in early January, no significant rise in BA.2 cases noted. 3/n

Based on the arrival description on #Japan government site, every passenger arriving at the airport is tested, which is likely key to understanding what variants are imported by the travelers. This has help identify P.1/#Gamma & also #Delta AY.1. 4/n
niid.go.jp/niid/en/2019-n…

I definitely have to thank the #Japan government for sharing the data with all the details and also GISAID for the incredible community of scientists that are hosting all the data to make this analysis possible. 5/5