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Hacking COVID-19 — Course 5

Tracing SARS-CoV-2's Evolution

Mikhail Rayko, Niema Moshiri, Vikram Sirupurapu, Sabeel Mansuri, and Pavel Pevzner

In this course, you will follow in the footsteps of the bioinformaticians investigating the COVID-19 outbreak by tracing the evolution of SARS-CoV-2. Whether you’re new to the world of computational biology, or you’re a bioinformatics expert seeking to learn about its applications in the COVID-19 pandemic, or somewhere in between, this course is for you! As you go through this journey, we will introduce and explain genomic concepts and give you many opportunities to practice your skills, and we will provide a series of problems with gradually increasing complexity. This fifth course will discuss the "Italy First" hypothesis of COVID-19 origins, and it will cover bioinformatics methods for rooting and dating a phylogenetic tree inferred from SARS-CoV-2 genome sequences.

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What's inside

Syllabus

Week 1

In Chapter 7, we will discuss how we can use rooted and dated phylogenetic trees to study the emergence of a virus, with the origins of COVID-19 as our primary inspiration, but with a real case study about HIV transmission as our focus.

Week 2

In Chapter 8, we will perform multiple sequence alignment, phylogenetic inference, tree rooting, and tree dating to investigate the "Italy First" hypothesis of COVID-19 origins.

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Teaches health concepts and methods that are in line with scientific understanding and the advice of the medical community

Covers unique perspectives and ideas that may add color to other topics and subjects

Takes a creative approach to an otherwise established topic, field, or subject

Examines x, which is highly relevant to y

Explores x, which is standard in industry y

Taught by x, who are recognized for their work in x

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Activities

Coming soon We're preparing activities for Hacking COVID-19 — Course 5: Tracing SARS-CoV-2's Evolution. These are activities you can do either before, during, or after a course.

Career center

Learners who complete Hacking COVID-19 — Course 5: Tracing SARS-CoV-2's Evolution will develop knowledge and skills that may be useful to these careers:

Bioinformatics Analyst

The global COVID-19 pandemic has put bioinformatics at the forefront of the fight against this virus. A Bioinformatics Analyst plays a crucial role in analyzing biological data, including viral genome sequences, to track the evolution and transmission of SARS-CoV-2. The 'Tracing SARS-CoV-2's Evolution' course from the University of California, San Diego, provides a solid foundation in bioinformatics methods, including phylogenetic analysis and tree rooting, which are essential for understanding viral evolution and guiding public health measures.

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Epidemiologist

Epidemiologists investigate the distribution and patterns of health events, including infectious diseases like COVID-19. The 'Tracing SARS-CoV-2's Evolution' course provides Epidemiologists with valuable insights into the evolution and spread of SARS-CoV-2, helping them develop effective strategies for disease surveillance, outbreak control, and pandemic preparedness.

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Computational Biologist

The 'Tracing SARS-CoV-2's Evolution' course covers essential bioinformatics techniques such as multiple sequence alignment, phylogenetic inference, and tree rooting, which are fundamental skills for Computational Biologists. This course empowers them to analyze and interpret genomic data, contribute to our understanding of viral evolution, and develop computational tools for virus surveillance and outbreak response.

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Research Scientist

Research Scientists play a vital role in advancing our knowledge of viral evolution, epidemiology, and public health. The 'Tracing SARS-CoV-2's Evolution' course provides Research Scientists with a comprehensive understanding of bioinformatics methods for studying viral genomics, empowering them to conduct cutting-edge research on COVID-19 and other infectious diseases.

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Virologist

Virologists are experts in the study of viruses, including their structure, replication, and evolution. The 'Tracing SARS-CoV-2's Evolution' course offers valuable insights into the molecular evolution of SARS-CoV-2, enabling Virologists to better understand the virus's behavior, develop antiviral therapies, and contribute to the development of vaccines and diagnostics.

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Public Health Analyst

Public Health Analysts play a critical role in protecting and improving the health of communities. The 'Tracing SARS-CoV-2's Evolution' course provides Public Health Analysts with a deeper understanding of the evolution and spread of COVID-19, empowering them to develop data-driven public health policies and interventions to mitigate the impact of the virus.

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Data Analyst

The 'Tracing SARS-CoV-2's Evolution' course equips Data Analysts with specialized skills in handling and analyzing biological data, including genomic sequences. This course provides a strong foundation in bioinformatics, enabling Data Analysts to contribute to research projects, develop predictive models, and support decision-making in the context of viral outbreaks.

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Biostatistician

Biostatisticians apply statistical methods to analyze and interpret biological data. The 'Tracing SARS-CoV-2's Evolution' course provides Biostatisticians with specialized knowledge in phylogenetic analysis and viral evolution, enabling them to contribute to research on COVID-19 epidemiology, vaccine effectiveness, and public health policy.

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Biomedical Engineer

Biomedical Engineers design and develop technologies for healthcare applications. The 'Tracing SARS-CoV-2's Evolution' course provides Biomedical Engineers with a foundation in bioinformatics, enabling them to contribute to the development of diagnostic tools, biosensors, and other technologies for virus detection and monitoring.

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Science Writer

Science Writers communicate complex scientific concepts to the public. The 'Tracing SARS-CoV-2's Evolution' course provides Science Writers with a comprehensive understanding of viral evolution and genomics, enabling them to accurately and effectively report on the latest scientific findings and their implications for public health.

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Healthcare Consultant

Healthcare Consultants provide guidance and recommendations to healthcare organizations on various aspects of healthcare delivery. The 'Tracing SARS-CoV-2's Evolution' course may be helpful for Healthcare Consultants who specialize in infectious disease management or pandemic preparedness, as it provides insights into the evolution and spread of COVID-19.

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Medical Writer

Medical Writers create and edit medical and scientific content for various purposes. The 'Tracing SARS-CoV-2's Evolution' course may be useful for Medical Writers who specialize in infectious diseases or virology, as it provides a comprehensive overview of the molecular evolution of SARS-CoV-2.

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Patent Attorney

Patent Attorneys specialize in the legal aspects of intellectual property, including patents for biotechnology and pharmaceutical inventions. The 'Tracing SARS-CoV-2's Evolution' course may be of interest to Patent Attorneys who handle cases related to viral genomics, diagnostics, or therapeutics.

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Science Teacher

Science Teachers educate students about scientific concepts and principles. While the 'Tracing SARS-CoV-2's Evolution' course is not directly related to K-12 science education, it may be of interest to Science Teachers who wish to incorporate current events and real-world examples into their lessons on genetics, evolution, or public health.

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Science Policy Advisor

Science Policy Advisors provide scientific expertise to policymakers and government agencies. The 'Tracing SARS-CoV-2's Evolution' course may be useful for Science Policy Advisors who work on issues related to pandemic preparedness, vaccine development, or global health.

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Reading list

We've selected 15 books that we think will supplement your learning. Use these to develop background knowledge, enrich your coursework, and gain a deeper understanding of the topics covered in Hacking COVID-19 — Course 5: Tracing SARS-CoV-2's Evolution.

Bioinformatics Algorithms