Reference no: EM132573782

Coronaviruses use the spike (S) glycoprotein to bind to the host cell at the beginning of the infection process. The protein is responsible for membrane fusion in the severe acute respiratory syndrome-coronavirus (SARS-CoV) hence it is vital for virus entry and cell fusion. The target protein is also a major immunogen and a possible target for entry inhibitors.

Students are given a set of S glycoprotein nucleotide sequences (unaligned sequences) of multiple SARS-2-CoV-2 strains, an infectious agent causing COVID-19 disease from various origins. The nomenclature of the virus indicates the country of origin or region (for strains originated from PRC China) and the strains code. The sequences can be found in the file named small.set.s.protein.fasta in fasta format.

Perform a phylogenetic tree analysis using neighbor-joining method in MEGAX software with bootstrap replication of 50. Explain and discuss on the constructed phylogenetic tree. Include the method, parameters used and the output of the analysis with discussion.

Please include discussion of the following questions in your report:

-How many clades did you observe?

-Did you observe any clade that cluster SARS-CoV-2 strains based on geographical location?

-What are the genetic changes that common for the different clusters?