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  on the Datamonkey server . BUSTED , MEME , and FUBAR  methods were used. MEME  and FUBAR  found 3 and 5 sites respectively under positive selection. However, BUSTED  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.
- 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.
- 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.
- 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.
- 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).
- 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.
Tutorial-II: Functional Divergence Analysis using DIVERGE 3.0 software
This is a continuation article of our previous post: Tutorial-I: Functional Divergence Analysis using DIVERGE 3.0 software. In our last tutorial, we explained Type-II functional divergence. In this article, we will explain the rest of the evolutionary analysis using DIVERGE 3.0 software . (more…)
Tutorial-I: Functional Divergence Analysis using DIVERGE 3.0 software
DIVERGE is a tool to detect functional divergence between member genes of a protein family based on (site-specific) shifted evolutionary rates after gene duplication or speciation . Since this tool contains several steps and offers a lot to discover, therefore, we are going to split its tutorial into parts. In this article, we will perform some initial steps in this software and will explain their significance. (more…)
Update: Selection analysis on spike glycoproteins of SARS-CoV
In our last article, we mentioned the selection pressure analysis of SARS-CoV-2 spike glycoproteins. Now, we have analyzed spike glycoprotein sequences of SARS-CoV. No single purifying selection site was found in SARS-CoV spike glycoproteins as was revealed from our last analysis of SARS-CoV-2 spike glycoproteins. (more…)