Previously submitted to: JMIR Public Health and Surveillance (no longer under consideration since May 20, 2020)
Date Submitted: May 19, 2020
Warning: This is an author submission that is not peer-reviewed or edited. Preprints - unless they show as "accepted" - should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information.
Substitution Model Distance Analysis for SARS-CoV-2 in China, USA, and Europe
ABSTRACT
Background:
Coronavirus pandemic has been a wake-up call for the world. A dispute over the origin of SARS-CoV-2 has been raised. Study results showed that all SARS-CoV-2 sequences around the world sharing a common ancestor towards the end of 2019. Nevertheless, it is hard to reach conclusion regarding SARS-CoV-2 origin.
Objective:
In this study, we compare the divergence of SARS-CoV-2 sequences from the three areas, China, the USA, and Europe.
Methods:
We download SARS-CoV-2 sequences of China, USA, and Europe from the National Center for Biotechnology Information (NCBI). To investigate the diversity of these sequences from these three areas, we apply 17 different nucleotide substitution models to compare the diversity of these SARS-CoV-2 sequences. In the three groups of SARS-CoV-2 sequences, we calculate the pairwise nucleotide substitution distance of any two sequences in each group and then compare the distances in these three groups.
Results:
The analyzed results are consistent in most of the 17 substitution models. The outcomes from 14 substitution models show that China has the lowest diversity, followed by Europe and lastly by the USA. For the other 3 models, in one model, China has the lowest diversity, followed by the USA and lastly by Europe; in another model, USA has the lowest diversity, followed by China and lastly by Europe, and in the last one model, Europe has the lowest diversity, followed by China and lastly by the USA.
Conclusions:
In this study, we compare the diversity of SARS-CoV-2 samples from China, Europe, and the USA. Different substitution models were applied to analyze the data. Our outcome shows that China has the smallest mean distance value, followed by Europe and lastly by the USA, which consists with the virus transmission time order that SARS-CoV-2 starts in China, then outbreaks in Europe and finally in the USA.
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