Chelsea Rose Campbell

CSC 448 Bioinformatic Algoritms Project


GOAL

This is a weekly analysis of COVID-19 and the coronavirus, incorporating real data generated by leading scientists and institutions.


Week 1

A review of some current available resources.

The GISAID Initiative

The GISAID Initiative (previously known as a Global Initiative on Sharing All Influenza Data) promotes the sharing of data related to human and animal viruses with the purpose of helping researchers comprehend how viruses behave. GISAID fights any restrictions that prevent the spreading of data before it is published formally. The data accumulated in GISAID is available internationally to anyone (who follows GISAID guidelines) for free.

COVID-19 Efforts

Currently, the number of hCoV-19 genome sequences being made available on GISAID is rapidly increasing as laboratories all around the world are sharing their findings regarding this pressing, new virus.

Folding@home

Folding@home is a project that studies and stimulates various protein dynamics, like the way proteins move in diseases and the folding of protein. It provides a platform for citizen scientists to volunteer and bring their ideas and findings together.

COVID-19 Efforts

With the understanding that viruses use proteins to suppress the immune system and reproduce, Folding@home is attempting to comprehend how these viral proteins function and develop therapeutics to stop them to contribute to the fight against the coronavirus. Folding@home specializes in using computer simulations to understand the numerous moving parts in a protein. Using these simulations, they were able to locate a site in Ebola proteins that is potentially druggable. They hope to have similar findings with coronavirus proteins.

Nextstrain

Nextstrain combines constantly-updated public data and powerful analytic and visualization technologies to provide real-time graphics that display pathogen genome data. Their goal is to increase the understanding of epidemics and improve the response to outbreaks.

COVID-19 Efforts

They are obtaining and displaying data of nCoV genomes as soon as they are shared. Then, they are providing up-to-date analyses and situation reports. They have customizable and filterable graphs, charts and animations that show data regarding the specifics about nCoV’s phylogeny, transmissions, and diversity. There are written reports to explain the data displayed in these visuals. These efforts help scientists and researchers understand how COVID-19 behaves to facilitate their studies of the virus.

ASM’s Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal

This is a study published by the American Society for Microbiology in their Microbiology Resource Announcements. It shows and analyzes a complete genome sequence obtained for a SARS-CoV-2 strain isolated from a patient from Nepal with COVID-19. This 32-year-old man had returned to Nepal from a trip to Wuhan, China. The report explains the process in which the patient was diagnosed and how the genome sequence was obtained. It covers background information about SARS-CoV-2 such as its geographical origins and phylogeny. Pattens in the genome are analyzed and compared to other types of genomes. Any mutations in the genome are identified and discussed. It provides a table with the gene-specific and probe sequences used.

COVID-19 Analysis: The Galaxy Project

This resource provides tools and digital infrastructure to enable the public to virually analyze SARS-CoV-2 data. They have features to conduct three of the best practices for analyzing this virus: Genomics, Evolution, and Cheminformatics. These analyses are available to expand the research that is occurring and spread awareness and knowledge about the SARS-CoV-2 virus. Each of these analysis sections are constantly updated as new data is shared. More information about what these three practices entail is as follows:

  • Genomics: Assembly and intra-host variation
    • Assembly
    • MRCA timing
    • Variation analysis
    • Selection and recombination
  • Evolution: Sites under selection
    • Natural Selection Analysis
    • Analysis
    • Visualizations
    • Observable Notebooks
  • Cheminformatics: Screening of the main protease
    • Compound enumeration
    • Generation of 3D conformations
    • Docking
    • Scoring
    • Selection of compounds for synthesis

Week 2