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We have designed a Bioinformatics activity that uses tools to identify the origins and mutations in the novel SARS-CoV2 strains.
We have designed a Bioinformatics activity that can be used in a Microbiology, Genetics or Evolution lab class. This learning activity uses tools to identify the origins and mutations in the novel SARS-CoV2 strains.To study the origins of the SARS-CoV2 strain, students are given the spike protein sequences from the human, pangolin and bat coronavirus strains. Using global and local alignments, students create phylogenetic trees in BLAST to identify regions in the protein that show evidence of genetic recombination. Domains in the protein that have undergone recombination are identified using the Conserved Domain Database.
Following this activity, students are divided into groups. Each group is given the spike protein sequences from various coronavirus strains including the emerging variants as identified by the Centers for Disease Control. Using the multiple sequence alignment tool, CLUSTAL omega, students locate the mutations in the emerging variants. Students are expected to identify the kind of mutations and its effects on the emerging variants. Both these activities help students understand the origins of the novel coronavirus strains and the role mutations play in the emerging variants.
- Arora_MicrobrewExpandedformatASMCUE2021.pptx(PPTX | 31 MB)
- AroraG_MicrobrewAbridgedFormatASMCUE2021.pptx(PPTX | 30 MB)
- GeneticVariation1_Subsequences.xlsx(XLSX | 9 KB)
- Group1Spike.fasta(FASTA | 11 KB)
- Group2Spike.fasta(FASTA | 11 KB)
- Group3Spike.fasta(FASTA | 11 KB)
- ORF1ab.txt(TXT | 21 KB)
- Spike.Txt(TXT | 4 KB)
- License terms
Cite this work
Researchers should cite this work as follows:
- Arora, G. (2021). Using Bioinformatics Activities to understand the Past and Present of SARS-CoV2. Genome Solver, QUBES Educational Resources. doi:10.25334/85AH-FF43
This resource has materials that were presented at the American Society of Microbiology Conference of Undergraduate Educators. The presentation date was June 30th., 2021