COVID-19 Evolves in Human Hosts

10 Pages Posted: 24 Apr 2020 Last revised: 11 Aug 2020

See all articles by Yanni Li

Yanni Li

Xidian University - School of Computer Science and Technology

Bing Liu

Peking University

Zhi Wang

Xidian University - School of Computer Science and Technology

Jiangtao Cui

Xidian University

Kaicheng Yao

Xidian University

Pengfan Lv

Xidian University - School of Computer Science and Technology

Yulong Shen

Xidian University

Yueshen Xu

Xidian University

Yuanfang Guan

University of Michigan at Ann Arbor - Department of Computational Medicine and Bioinformatics

Xiaoke Ma

Xidian University - School of Computer Science and Technology

Date Written: March 20, 2020

Abstract

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 HA-MLCS for the big sequence data (with sequence length over 10^3) 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.

Note: Funding: Yanni Li’s work was supported by the National Natural Science Foundation of China (No. 61472296).

Conflict of Interest: We declare no competing interest.

Keywords: COVID-19; Big Sequence Data; Multiple Longest Common Subsequences (MLCS); Similarity; Evolutionary Tree

Suggested Citation

Li, Yanni and Liu, Bing and Wang, Zhi and Cui, Jiangtao and Yao, Kaicheng and Lv, Pengfan and Shen, Yulong and Xu, Yueshen and Guan, Yuanfang and Ma, Xiaoke, COVID-19 Evolves in Human Hosts (March 20, 2020). Available at SSRN: https://ssrn.com/abstract=3562070 or http://dx.doi.org/10.2139/ssrn.3562070

Yanni Li (Contact Author)

Xidian University - School of Computer Science and Technology ( email )

Xi'an, Shaanxi 710126
China

Bing Liu

Peking University ( email )

No. 38 Xueyuan Road
Haidian District
Beijing, Beijing 100871
China

Zhi Wang

Xidian University - School of Computer Science and Technology ( email )

Xi'an, Shaanxi 710126
China

Jiangtao Cui

Xidian University ( email )

Xi'an Chang'an two hundred ten National Road
Xian, Shaanxi Province
China

Kaicheng Yao

Xidian University ( email )

Xi'an Chang'an two hundred ten National Road
Xian, Shaanxi Province
China

Pengfan Lv

Xidian University - School of Computer Science and Technology ( email )

Xi'an, Shaanxi 710126
China

Yulong Shen

Xidian University ( email )

Xi'an Chang'an two hundred ten National Road
Xian, Shaanxi Province
China

Yueshen Xu

Xidian University ( email )

Xi'an Chang'an two hundred ten National Road
Xian, Shaanxi Province
China

Yuanfang Guan

University of Michigan at Ann Arbor - Department of Computational Medicine and Bioinformatics ( email )

Ann Arbor, MI 48109
United States

Xiaoke Ma

Xidian University - School of Computer Science and Technology ( email )

Xi'an, Shaanxi 710126
China

Do you have negative results from your research you’d like to share?

Paper statistics

Downloads
518
Abstract Views
3,200
Rank
99,604
PlumX Metrics