Open Access Peer-reviewed Research Article

Phylogenetic analyses and genomic variation of the 2019-nCoV

Main Article Content

Faiz Ul Haq corresponding author
Sidrah Saleem
Muhammad Imran
Ayesha Ghazal
Kashif Ahmad
Muhammad Roman
Saeed Ur Rahman
Sami Ullah
Iftekhar Ahmad
Habibah Mehmood
Wajahat Ullah

Abstract

There is a rising global concern about the SARS CoV-2 as a public health threat. Complete genome sequence have been released by the worldwide scientific community for understanding the molecular characteristics and evolutionary origin of this virus. Aim of the current context is to present phylogenetic relationship and genomic variation of 2019-nCoV. Based on availability of genomic information, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Middle East respiratory syndrome, severe acute respiratory syndrome and Bat coronavirus. The phylogenetic tree analysis suggested that SARS CoV-2 significantly clustered with bat SARS like coronavirus genome, however structural analysis revealed mutation in Spike Glycoprotein and nucleocapsid protein. However our phylogenetic and genomic analysis suggests that bats can be the reservoir for this virus. Lack of forest might be the fact in association of bats with human environment. It is also difficult to study on bats due to absence of proper reagent and availability of few species for research. We confirm high sequence similarity (>99%) among sequenced SARS CoV-2 genomes, and 96% genome identity with the bat coronavirus, confirming the notion of a zoonotic origin of SARS CoV-2.

Keywords
SARS-CoV-2, coronavirus, CLUSTAL analysis, genomic variation

Article Details

How to Cite
Haq, F., Saleem, S., Imran, M., Ghazal, A., Ahmad, K., Roman, M., Rahman, S., Ullah, S., Ahmad, I., Mehmood, H., & Ullah, W. (2020). Phylogenetic analyses and genomic variation of the 2019-nCoV. Journal of Pharmaceutical and Biopharmaceutical Research, 2(1), 126-130. https://doi.org/10.25082/JPBR.2020.01.004

References

  1. Cui J, Li F and Shi ZL. Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology, 2019, 17(3):181-192. https://doi.org/10.1038/s41579-018-0118-9
  2. Schoeman D and Fielding BC. Coronavirus envelope protein: current knowledge. Virology Journal, 2019, 16(1): 69. https://doi.org/10.1186/s12985-019-1182-0
  3. Hu B, Ge X, Wang LF, et al. Bat origin of human coronaviruses. Virology Journal. 2015, 12(1): 221. https://doi.org/10.1186/s12985-015-0422-1
  4. Benvenuto D, Giovanetti M, Ciccozzi A, et al. The 2019- new coronavirus epidemic: evidence for virus evolution. Journal of Medical Virology, 2020, 92(4): 455-459. https://doi.org/10.1002/jmv.25688
  5. Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet, 2020, 395(10224): 565-574. https://doi.org/10.1016/S0140-6736(20)30251-8
  6. Haq FU, Roman M, Ahmad K, et al. Artemisia annua: trials are needed for COVID-19. Phytotherapy Research. 2020.
  7. Khan MU, Muazzam A, Farooq H, et al. Interferon- : treatment option against COVID-19. Geriatric Care, 2020, 6(3): 65-66. https://doi.org/10.4081/gc.2020.9093
  8. Aljofan M and Gaipov A. COVID-19 Treatment: The Race Against Time. Electronic Journal of General Medicine, 2020, 17(6): em227. https://doi.org/10.29333/ejgm/7890
  9. Jeanmougin F, Thompson JD, Gouy M, et al. Multiple sequence alignment with CLUSTAL X. Trends in Biochemical Sciences, 1998, 23(10): 403-405. https://doi.org/10.1016/S0968-0004(98)01285-7
  10. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. Journal of Molecular Biology, 1990, 215(3): 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  11. Kumar S, Stecher G, Li M, et al. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 2018, 35(6): 1547-1549. https://doi.org/10.1093/molbev/msy096
  12. Tamura K and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 1993, 10(3): 512-526. https://doi.org/10.1093/oxfordjournals.molbev.a040023
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985, 39(4): 783- 791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  14. Ronquist F and H¨ulsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 2003, 19: 1572-1574. https://doi.org/10.1093/bioinformatics/btg180
  15. Yan Y, Harris AJ and Xingjin H. S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Molecular Phylogenetics and Evolution, 2010, 56: 848-850. https://doi.org/10.1016/j.ympev.2010.04.011
  16. Yu Y, Harris AJ, Blair C, et al. RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Molecular phylogenetics and evolution, 2015, 87: 46-49. https://doi.org/10.1016/j.ympev.2015.03.008
  17. York A. Novel coronavirus takes flight from bats? Nature Reviews Microbiology, 2020, 18: 191. https://doi.org/10.1038/s41579-020-0336-9
  18. Haider N, Yavlinsky A, Simons D, et al. Passengers’ destinations from China: low risk of Novel Coronavirus (2019- nCoV) transmission into Africa and South America. Epidemiology & Infection, 2020, 148(41): 1–7. https://doi.org/10.1017/S0950268820000424
  19. Ceraolo C and Giorgi FM. Genomic variance of the 2019- nCoV coronavirus. Journal of Medical Virology. 2020, 92(5): 522-528. https://doi.org/10.1002/jmv.25700
  20. Zhou P, Yang XL, Wang XG, et al. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. BioRxiv, 2020. https://doi.org/10.1101/2020.01.22.914952
  21. Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet, 2020, 395(10224): 565-574. https://doi.org/10.1016/S0140-6736(20)30251-8
  22. Banerjee A, Kulcsar K, Misra V, et al. Bats and coronaviruses. Viruses. 2019, 11(1): 41. https://doi.org/10.3390/v11010041
  23. Schountz T. Immunology of bats and their viruses: challenges and opportunities. Viruses, 2014, 6(12): 4880-4901. https://doi.org/10.3390/v6124880
  24. Ji W, Wang W, Zhao X, et al. Homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human. Journal of Medical Virology, 2020, 92(4): 433-440. https://doi.org/10.1002/jmv.25682
  25. Chakraborty S, Nag D, Mazumder TH, et al. Codon usage pattern and prediction of gene expression level in Bungarus species. Gene, 2016, 604: 48-60. https://doi.org/10.1016/j.gene.2016.11.023