A Genetic Perspective of 2019-nCoV in Relation to Cross Species Transmission
Coronaviruses have caused two large scale pandemics severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) in last two decades. It was thought that SARS-related coronaviruses (SARSr-CoV) is mainly found in bats. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans. The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. Here we have taken an attempt to understand the genetic structure of 2019-nCoV and subsequent sequence analysis of multiple regions of its genome to identify unique motifs, receptor binding domain, hypervariable region which may direct some insight to future research for developing effective treatment against this novel coronavirus. We have identified unique motif in spike protein, multiple hypervariable regions, amino acids polymorphism in ORF8 and N protein. These may affect the conformation of the peptide and shed some light to cross species transmission, and subsequent host adaptation.
Keywords:Genomics, Sequence Analysis, 2019-nCoV
Ceraolo C, Giorgi FM. Genomic variance of the 2019?nCoV coronavirus. J Med Virol. 2020;92: 522–528. https://doi.org/10.1002/jmv.25700
Ji et al. Homologous recombination within the spike glycoprotein of the newly identified coronavirus 2019-nCoV may boost cross-species transmission from snake to human. https://doi.org/10.1002/fut.22099
Li X, Zai J, Zhao Q, et al. Evolutionary history, potential intermediate animal host, and cross?species analyses of SARS?CoV?2. J Med Virol. 2020; 1–10. https://doi.org/10.1002/jmv.25731
Li et al. Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species. Infection, Genetics and Evolution. 2020, Volume 82, https://doi.org/10.1016/j.meegid.2020.104285
Liu Z, Xiao X, Wei X, et al. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS?CoV?2. J Med Virol. 2020; 1–7. https://doi.org/10.1002/jmv.25726
Paraskevis et al. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infection, Genetics and Evolution, 2020, 79, 104212. https://doi.org/10.1016/j.meegid.2020.104212
Song et al. From SARS to MERS, Thrusting Coronaviruses into the Spotlight. Viruses 2019, 11(1), 59; https://doi.org/10.3390/v11010059
Wu et al. Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China. Cell Host & Microbe 27, March 11, 2020; https://doi.org/10.1016/j.chom.2020.02.001
Zhou et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 2020; Vol 579 https://doi.org/10.1038/s41586-020-2012-7
Copyright (c) 2020 Rimjhim Dasgupta
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Any non-commercial use, distribution, adaptation, and reproduction in any medium is permitted as long as the original work is properly cited. However, caution and responsibility are required when reusing as the articles on the preprint server are not peer-reviewed. Readers are advised to check for the availability of any updated or peer-reviewed version.