The Distribution of COVID 19 based on Phylogeny Construction in Silico Sequences SARS-CoV-2 RNA at Genbank NCBI

Authors

  • Revolson Alexius MEGE Department of Biology Faculty of Mathematics and Natural Sciences, Manado State University, Tondano, Minahasa, North Sulawesi, Indonesia
  • Herry Sinyo SUMAMPOUW Department of Biology Education, Faculty of Mathematics and Natural Sciences, Manado State University, Tondano, Minahasa, North Sulawesi, Indonesia
  • Dewa Nyoman OKA Department of Biology Education, Faculty of Mathematics and Natural Sciences, IKIP Saraswati Tabanan, Bali, Indonesia
  • Nonny MANAMPIRING Department of Biology Faculty of Mathematics and Natural Sciences, Manado State University, Tondano, Minahasa, North Sulawesi, Indonesia
  • Yermia Semuel MOKOSULI Bioactivity and Molecular Biology Laboratory, Department of Biology, Faculty of Mathematics and Natural Sciences, Manado State University, Tondano, Minahasa, North Sulawesi, Indonesia

Keywords:

SARS Covid-19 gene, Genbank, NCBI, Spread

Abstract

The Covid-19 pandemic, due to severe acute respiratory coronavirus (SARS-CoV-2) virus, has an effect on human civilization today. With high fatality infections, SARS Covid-19 has influenced the global economic, socio-cultural, and even political order. This study aims to construct the phylogeny of the SARS corona virus that causes Covid-19 in various countries in the world by using the SARS Covid-19 gene database from the NCBI GenBank. The results of this study can trace the origin of SARS Covid-19, which is then called SARS-CoV-2, the gene characteristics, and the evolutionary relationship of these genes to various countries in the world. This research uses in silico method with gene sequence sources from the NCBI GenBank (www.ncbi.nih.gov). A total of 433 SARS Covid-19 sequences reported by 21 countries as of April 2rd, 2020 were the subject of the study. Sequences representing each country were analyzed using the MEGA 7.0 program. The results showed that the phylogeny trees formed were obtained by 2 main monophyletic groups. The first major monophyletic group consisted of 11 nodes, with 19 SARS-CoV-2 gene sequences from 23 countries. The second major monophyletic group consisted of 5 nodes with 5 countries of origin of SARS-CoV sequence 19. The spread of Covid-19 from the epicenter in Wuhan, China to the world has taken place randomly. This has happened because of the migration of people from the Chinese epicenter. The location of the countries adjacent to China did not determine the closest phylogenic relationship. The number of phylogenetic nodes formed showed mutases which caused very high variations of the SARS CoV 2 RNA gene sequence. The results of this study reinforce that efforts to limit the spread of human viruses to humans must be done. The presence of sequences from China in the 2 main monophyletic groups confirms that this virus originated in the Chinese epicenter.

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

Data COVID-19, Available at: https://www.covid19.go.id, accessed April 2020.

China National Center for Bioinformation, Available at: https://bigd.big.ac.cn/ncov/about?lang=en, accessed April 2020.

J Cui, F Li and ZL Shi. Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 2019; 17, 181-92.

K Subbaram, H Kannan and MK Gatasheh. Emerging developments on pathogenicity, molecular virulence, epidemiology and clinical symptoms of current middle east respiratory syndrome coronavirus (MERS-CoV). Hayati. J. Biosci. 2017; 24, 53-6.

Y Chen, Q Liu and D Guo. Emerging coronaviruses: Genome structure, replication, and pathogenesis. J. Med. Virol. 2020; 92, 418-23.

L Gao, J Qi, H Wei, Y Sun and B Hao. Molecular phylogeny of coronaviruses including human SARS-CoV. Chinese Sci. Bull. 2003; 48, 1170-4.

Y Gao, T Li and L Luo. Phylogenetic study of 2019-nCoV by using alignment-free method. Ic. 2019.

ZW Ye, S Yuan, KS Yuen, SY Fung, CP Chan and DY Jin. Zoonotic origins of human coronaviruses. Int. J. Biol. Sci. 2020; 16, 1686-97.

BG Hall. Building phylogenetic trees from molecular data with MEGA. Mol. Biol. Evol. 2013; 30, 1229-35.

S Kumar, G Stecher and K Tamura. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016; 33, 1870-4.

National Center for Biotechnology Information, Available at: https://www.ncbi.nlm.nih.gov/ genbank/sars-cov-2-seqs, accessed March 2020.

Downloads

Published

2020-08-30

How to Cite

MEGE, R. A. ., SUMAMPOUW, H. S. ., OKA, D. N. ., MANAMPIRING, N. ., & MOKOSULI, Y. S. . (2020). The Distribution of COVID 19 based on Phylogeny Construction in Silico Sequences SARS-CoV-2 RNA at Genbank NCBI. Walailak Journal of Science and Technology (WJST), 17(8), 893-902. Retrieved from http://wjst.wu.ac.th/index.php/wjst/article/view/9814