Exploring Diversity of COVID 19 Based on Substitution Distance
Background The number of COVID 19 infections worldwide has reached 10 million. COVID 19 caused by SARS CoV 2 is more contagious than SARS CoV 1. There is a dispute about the origin of COVID 19. Study results showed that all SARS CoV 2 sequences around the world share a common ancestor towards the end of 2019. Methods Virus sequences from COVID 19 samples at the early time should be less diversifiable than those from samples at the later time because there might be more mutations when the virus evolutes over time. The diversity of virus nucleotide sequences can be measured by the nucleotide substitution distance. To explore the diversity of SARS CoV 2, we use different nucleotide substitution models to calculate the distances of SARS CoV 2 samples from 3 different areas, China, Europe, and the USA. Then, we use these distances to infer the origin of COVID 19. Results It is known that COVID 19 originated in Wuhan China and then spread to Europe and the USA. By using different substitution models, the distances of SARS CoV 2 samples from these areas are significantly different. By ANOVA testing, the p value is less than 2.2e 16. The analyzed results in most substitution models show that China has the lowest diversity, followed by Europe and lastly by the USA. This outcome coincides with the virus transmission time order that SARS CoV 2 starts in China, then outbreaks in Europe and finally in the USA. Conclusion The magnitude of nucleotide substitution distance of SARS CoV 2 is closely related to the transmission time order of SARS CoV 2. This outcome reveals that the nucleotide substitution distance of SARS CoV 2 may be used to infer the origin of COVID 19.
Infection and drug resistance