  Today, we are all threatened by an unprecedented pandemic: COVID-19. How
different is it from other coronaviruses? Will it be attenuated or become more
virulent? Which animals may be its original host? In this study, we collected
and analyzed nearly thirty thousand publicly available complete genome
sequences for COVID-19 virus from 79 different countries, the previously known
flu-causing coronaviruses (HCov-229E, HCov-OC43, HCov-NL63 and HCov-HKU1) and
the lethal, pathogenic viruses, SARS, MERS, Victoria, Lassa, Yamagata, Ebola,
and Dengue. We found strong similarities between the current circulating
COVID-19 and SARS and MERS, as well as COVID-19 in rhinolophines and pangolins.
On the contrary, COVID-19 shares little similarity with the flu-causing
coronaviruses and the other known viruses. Strikingly, we observed that the
divergence of COVID-19 strains isolated from human hosts has steadily increased
from December 2019 to May 2020, suggesting COVID-19 is actively evolving in
human hosts. In this paper, we first propose a novel MLCS algorithm NP-MLCS1
for the big sequence analysis, which can calculate the common model for
COVID-19 complete genome sequences to provide important information for vaccine
and antibody development. Geographic and time-course analysis of the evolution
trees of the human COVID-19 reveals possible evolutional paths among strains
from 79 countries. This finding has important implications to the management of
COVID-19 and the development of vaccines and medications.
