#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

#India is another country where #SARS_CoV_2 BA.2 is rapidly replacing #Delta & #Omicron BA.1. The pace of sharing sequences by India is very slow, median days from collection to deposition is 69 days according to GISAID. Genome sequencing among the states is not always fair.🧵 In the state of #Telangana #India, #Omicron BA.1 in the most recent dates are exclusively from #Hyderabad. Except for a couple cases, BA.2 positive samples were collected outside of Hyderabad. The last sequence from this state is from Jan 6, 2022.

Since India announced the ‘E484Q & L452R’ #DoubleMutant , I was curious about the emergence of the ‘E484Q and L452R’ mutations. When I analyzed all publicly available #SARSCoV2 sequences, the first ever case was reported in Maharashtra, India in a sample collected on 12/5/2020. In India, the Double Mutants are primarily found in Lineage B.1; USA- B.1.427 and B.1.429; Sweden-L.3. Outside of India only 46 sequences of double mutant were found, UK-22, USA-12 (mostly California), Sweden-5, Canada -3, 1 in Singapore, Germany, Australia and New Zealand each.

Risk of a second wave of #SARSCoV2 infections in #Nepal is high due to the recent surge/second wave of #COVID19 cases in #India. Because of open borders and free movement of citizens, it is just a matter of time before we see a significant surge in cases in Nepal. Currently, India stands at 3.14% active cases, mostly concentrated in a few states. Some of these states in India are hubs for workers from western Nepal. Temporary workers may soon return home in part due to fear of previous lockdown experience or rise in COVID cases etc.