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COVID-19

Where Did You Come From, Where Did You Go?


Author(s)

Stefanie H. Chen
Department of Biological Sciences
North Carolina State University
slchen2@ncsu.edu
Carlos C. Goller
Department of Biological Sciences
North Carolina State University
ccgoller@ncsu.edu
Melissa C. Srougi
Department of Molecular Biomedical Sciences
North Carolina State University
mcsrougi@ncsu.edu

Abstract

In this directed case study, students assume the role of investigators for the Centers for Disease Control and Prevention (CDC) as they examine and compare different DNA sequences from human patients infected with SARS-CoV-2, the coronavirus that causes COVID-19. The case focuses on the evolution and spread of SARS-CoV-2 during the world pandemic by tracking changes in its genomic code. Students use freely available bioinformatics tools (NCBI, BLAST, Nextstrain) to analyze the relatedness of various coronavirus strains against a consensus SARS-CoV-2 genome. Students generate DNA sequence alignments with related sequences and explore a phylogenetic tree. Finally, students apply these tools to viral sequences obtained from infected “patients” to decipher where they contracted the virus. Through these activities, students learn about sequencing tools and technology, and how they can be applied to epidemiology. This case was developed for use in an introductory biology or genetics course but could be adapted for upper-level molecular biology or biochemistry courses.


Objectives

  • Utilize NCBI BLAST to perform sequence alignments.
  • Interpret BLAST results to identify similar sequences based on probability scores (E value).
  • Interpret a phylogenetic tree of coronavirus sequence divergence.
  • Explain how the coronavirus is spread and provide recommendations on how to dampen disease transmission from infected patients.

Keywords

COVID-19; SARS-CoV-2; coronavirus; BLAST; sequence; phylogeny; high-throughput; sequence alignment;

Topical Areas

N/A, Policy issues

Educational Level

Undergraduate lower division, Undergraduate upper division

Format

PDF

Type / Methods

Directed

Language

English

Subject Headings

Bioinformatics  |   Biology (General)  |   Epidemiology  |   Evolutionary Biology  |   Molecular Biology  |  


Date Posted

05/05/2020

Teaching Notes

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Teaching notes are intended to help teachers select and adopt a case. They typically include a summary of the case, teaching objectives, information about the intended audience, details about how the case may be taught, and a list of references and resources.

Supplemental Materials

Below are three data files that were generated on May 4, 2020 (see teaching notes for details), and a simple text file of viral sequences for use with BLAST.

  
  covid19_blast_NC045512_may2020.csv
  
  covid19_blast_patient1_may2020.csv
  
  covid19_blast_patient2_may2020.csv
  
  covid19_blast_sequences.txt

Answer Key

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Comments


Theresa landon
tlandon@rjuhsd.us

Granite Bay High School, RJUHSD
Rocklin
05/07/2020
For part three, now one of the top five results is from India.

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