We have recently conducted a selection pressure analysis on SARS-CoV-2 spike glycoprotein sequences. The analysis revealed not even a single site showing evidence of purifying selection but episodic diversifying selection on three sites. Out of these three sites, two sites are potentially relevant (Fig. 3).

Fig. 3 Structure of Spike Glycoprotein (PDB ID: 6VXX) of SARS-CoV-2. The detected residues under positive selection are shown in red color.

The analysis was performed using Hyphy [1] on the Datamonkey server [2]. BUSTED [3], MEME [4], and FUBAR [5] methods were used. MEME [4] and FUBAR [5] found 3 and 5 sites respectively under positive selection. However, BUSTED [3] did not found any evidence of selection on the tested branches of the phylogeny.

These spike glycoproteins are being analyzed further. Additionally, we are analyzing spike glycoproteins of SARS-CoV for comparison between SARS-CoV and SARS-CoV-2 spike glycoproteins.

References

1. Pond, S. L. K., & Muse, S. V. (2005). HyPhy: hypothesis testing using phylogenies. In Statistical methods in molecular evolution (pp. 125-181). Springer, New York, NY.
2. Weaver, S., Shank, S. D., Spielman, S. J., Li, M., Muse, S. V., & Kosakovsky Pond, S. L. (2018). Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Molecular biology and evolution, 35(3), 773-777.
3. Murrell, B., Weaver, S., Smith, M. D., Wertheim, J. O., Murrell, S., Aylward, A., … & Scheffler, K. (2015). Gene-wide identification of episodic selection. Molecular biology and evolution, 32(5), 1365-1371.
4. Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Pond, S. L. K. (2012). Detecting individual sites subject to episodic diversifying selection. PLoS genetics, 8(7).
5. Murrell, B., Moola, S., Mabona, A., Weighill, T., Sheward, D., Kosakovsky Pond, S. L., & Scheffler, K. (2013). FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Molecular biology and evolution, 30(5), 1196-1205.