Genomic Analysis of COVID-19 Virus Evolution --- Observation Asia

Observation---Asia

As of March 10, 2020, there are 1 sequenced virus in Cambodia, 28 sequenced viruses from Hong Kong, 2 from India, 6 from Iran, 11 from Japan, 13 from South Korea, 1 from Nepal, 7 from Taiwan, 1 from Vietnam, 11 from Singapore, 4 from Philippines, 2 from Thailand, and 3 from Malaysia.

South Korea, one of the worst impacted countries, has its cases mainly in two branches. One is mixed with other Asian countries, which was derived from a case in Sydney. The other ones are in a close cluster with viruses in Beijing.

Japan's 11 cases can be observed in 5 places in the graph. 3 are either the canonical form or its one-step variant. 3 of them are derived from a popular virus in Asia which was originated in Chongqing and Singapore. The only ones that show clustering are Japan_TY-WK501, 012 and 521. These three might show some sort of community infection. Overall, most of Japan's cases are at the end of the evolutionary chain. That may indicate that the infected patients are not propagating to others.

Taiwan's 7 cases include 2 cases (Taiwan4 and CGU1) of the canonical form, 1 case of minor variation (NTU02), 1 case in the European branch (NTU03, with a special story on Daily - March 9), and 2 cases (NTU01 and Taiwan3) are the same of viruses in Wuhan, and 1 in an 'Asia-Pacific' cluster that spread across 13 countries. Taiwan shows no evidence of follow-up variants that show the likelihood of strong patient quarantine without genomic evidence of internal community infection propagation.

Iran's 6 cases concentrate in one cluster. That cluster was directly derived from the canonical form. However, because Iran's viruses only report a small portion of the entire genomic sequence. It's not clear how to meaningfully interpret yet. More data will be needed for this country currently suffering an outbreak.

Singapore's cases are similar to Japan's. They are in different clusters, except five (Singapore 5, 7, 8, 9, 10) of them are in a single cluster which includes Korea, Sweden, Hong Kong, Italy, England, Guangdong, Wuhan, etc), and its branch virus of (Singapore 5, 9 & 10). Note that this multi-nation cluster was also the source of 5 cases of France.

Most of Hong Kong's data only has small segments that show no difference from the canonical form. It has three cases far away from the canonical form. Those three cases may represent they were infected while they travel in Europe or other places.

Cambodia's case is only one variant away from the canonical form.

Nepal's case is also not far away from the canonical form and has no further variants.

India's two cases are quite far away. One seems to be derived from a virus in South China. The other one was probably derived from Wuhan.

Thailand (Nonthaburi) are the original form of virus. Phillipines and Malaysia's sequencing are all too short to call. Vietnam's case is in the cluster heavily derived from Wuhan.