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How Yale Genomic Epidemiologists Use Mutations to Track the COVID-19 Pandemic

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COVID-19 Genetics | Science News 2.1

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I want to answer your questions about the genetics of the novel coronavirus, SARS-CoV-2, which causes COVID-19. I'm a geneticist, and feel like this is the part of the science that I can try and help communicate. Leave your questions in the comments below, and we'll talk about them together this Friday at noon PST.

Well. I wanted this week’s 2-part science news video to be about a new CRISPR study, but instead, I just think it makes the most sense to talk about the genetics of COVID-19.

Let’s start with some basics. In their simplest form, viruses have two main parts: their genetic material, which could be DNA or RNA, and some kind of protein package that holds the genetic material. COVID-19 is an RNA virus. This means that the genetic material inside of it is stored as RNA, not DNA. And for COVID-19, that RNA is found within a nucleocapsid protein structure, which is inside of a lipid membrane envelope. That envelope is covered in spike proteins, which are what give the coronaviruses their name--they look a bit like a crown or corona.

To replicate, it must infect a host cell and hijack that cell’s replication and protein production machinery. Those spike proteins on the outside of the virus are what attach to receptors in the cells of your lungs, ACE2 receptors. The virus then fuses its membrane with the cell’s membrane and releases its RNA into the cell. This is where it takes advantage of that cell’s machinery to make more RNA and more of its capsid and envelope proteins.

But really, the virus’s RNA genome doesn’t need to contain too much information. It’s only about 30,000 bases long, and encodes for the proteins that it needs to make more virus. Once the new RNA and proteins are replicated they are assembled into new viruses, which then leave the cell to go infect more cells. There’s an awesome infographic from the NYTimes that goes over this that I’ve linked here:

Other Resources:
What is QPCR:
Using genetics to track how it spreads:

Using genetics to figure out where it came from:

A special thank you to my Patreon patrons. I'm pretty sure videos about this can't be monetized right now, so you are truly my heroes helping me to do what I do. This of course includes my helicases:
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Video produced by Helicase Media LLC (my new science production company!)
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Viral Genomes - Analysis of COVID 19 Genomics Data

Workshop for Georgetown University Medical School Students on analysis of genomic data from corona virus strains like SARS, MERS and SARS-COV-2. Multiple Sequence analysis, phylogenetics, phylogenetic tree, variant, spike glycoprotein.

Register for our upcoming program -
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Epidemiologist discusses how COVID-19 is spreading

Dr. Albert Ko, an epidemiologist at the Yale School of Public Health, explains the ways people can come in contact with the coronavirus.
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COVID19: Epidemiological curves

Data scientist Joe Brew shares his analysis of the data comparing the evolution of the epidemiological curves of COVID-19 as of March 13 in different countries.

More Information:
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COVID-19 Symposium: Epidemiology of SARS-CoV-2 Infection | Dr. Michael Levy

Dr. Michael Levy discusses the epidemiology of the SARS-CoV-2 Infection as part of Penn's first Coronavirus Outbreak Symposium.

#Coronavirus #COVID-19 #PennMedicine

How Yale Genomic Epidemiologists Use Mutations to Track the COVID-19 Pandemic

Learn more about the Yale School of Medicine's response to COVID-19, visit:

Dr. Nathan Grubaugh is an assistant professor of epidemiology at the Yale School of Public Health and uses genomic epidemiology to study viral outbreaks. His background has led him to studying the mutations in COVID-19 to track the spread of the virus.

Faculty across Yale, including at the School of Medicine, School of Nursing, School of Public Health, School of Engineering & Applied Science and Faculty of Arts and Sciences are actively engaged in research, innovation, and clinical efforts to combat COVID-19.

Attribution:




Tracking the spread and mutations of Coronavirus (COVID-19)

In this video, we speak to Dr Thushan de Silva, Senior Clinical Lecturer at the University of Sheffield and Honorary Consultant Physician in Infectious Diseases about why we would want to sequence the genome of coronavirus and how it is useful for tracking the spread and mutations of the virus.

To contact The Physiological Society:
pressoffice@physoc.org

Transcript:
As COVID-19 infects people around the world, it’s more important than ever to track the spread and evolution of the virus in order to guide and inform control strategies. But how do you track a virus?

Well, SARS-CoV-2 - the virus that causes COVID-19, behaves a little bit like a game of telephone – as the whispered sentence is passed from one person to the next, it might change ever-so-slightly! Data on SARS-CoV-2 show that it mutates at an average of about two mutations per month.. And we know this because scientists all around the world are collecting samples from patients with COVID-19 and sequencing the virus – reading its genetic code.

Leading the effort from The University of Sheffield is one of our Members, Dr Thushan de Silva. He’s a Senior Clinical Lecturer at the University of Sheffield and Honorary Consultant Physician in Infectious Diseases. He told us that as a virus travels within or between countries, it can mutate as it reacts to evolutionary pressure from localised populations. This can be due to immune responses or drugs active against the virus and can create slightly different strains. Over time, this could result in strains that are resistant to drugs, therefore it is important to track.

And even once we have a vaccine for COVID-19, continually sequencing the virus will still be vital in making sure that the vaccine is effective against all strains.

Dr. de Silva and his colleagues are part of a national effort to sequence the genomes of hundreds, perhaps thousands of samples each week over the next few months. In Sheffield alone, they’ve sequenced around 60 strains so far!

This data is then fed into a global database that can track the progression of the virus in real time! Rapid data sharing like this is key to understanding whether the virus is changing and how it is being transmitted.

COVID-19 Symposium: SARS-CoV-2 Genome Sequencing as a Window on the Epidemic | Dr. John Everett

Dr. John Everett explains the similarities and differences found during his analysis of SARS-CoV-2 genome sequencing within patients throughout the region

COVID-19: Sequencing the Genome

NYU Langone's Adriana Heguy, PhD, discusses her research sequencing the genome of COVID-19.

Yale School of Public Health Forum On Outbreak of Novel Coronavirus

February 6, 2020 - Winslow Auditorium, New Haven, CT
Saad Omer, director, Yale Institute of Global Health - Moderator
David Vlahov, professor, Yale School of Nursing
Gregg Gonsalves, assistant professor, Department of Epidemiology of Microbial Diseases, Yale School of Public Health.
Nathan Grubaugh, assistant professor, Department of Epidemiology of Microbial Diseases, Yale School of Public Health
Ellen Foxman, assistant professor, Laboratory Medicine and Immunobiology, Yale School of Medicine
Lisa Sanders, associate professor, General Medicine, Yale School of Medicine
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Genetic Sequences for the SARS-CoV-2 Coronavirus

John Cassel walks us through some of the genetic sequences for the SARS-CoV-2 virus. You can access the data yourself from the Wolfram Data Repository here:

The notebook materials are also available here:

Visit the hub for Wolfram resources related to novel coronavirus COVID-19:
and contribute to the official Wolfram Community forum:

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Stay up-to-date on the latest interest at Wolfram Research through our blog:

Genetic Factors Contributing to the Severity of COVID-19

Please join Dr. Casanova, who is now leading a project to identify the genes that predispose individuals to severe forms of COVID-19 in conversation with Russ Altman, a leading medical bioinformatics researcher and Editor of the Annual Review of Biomedical Data Science. Dr. Altman also hosts the radio show The Future of Everything.

Introduction to Genomic Epidemiology

This is the first lecture in the Infectious Disease Genomic Epidemiology 2017 workshop hosted by the Canadian Bioinformatics Workshops. This lecture is by William Hsiao from the BC Centre for Disease Control.

For tutorials and lecture slides for this workshop, please visit bioinformaticsdotca.github.io.

How it Begins by Kevin MacLeod is licensed under a Creative Commons Attribution license (
Source:
Artist:

Novel coronavirus not caused by a genetic mutation: Expert

Genome sequencing studies suggest that the novel coronavirus came from a single source in Wuhan around October to November 2019, says Paul Tambyah from NUS Yong Loo Lin School of Medicine.

COVID-19: Viral Genomes and Zoonotic Spillover

In this session of the COVID-19: Viral Genomes and Zoonotic Spillover, we discussed about the Origins and Pathogenesis of the Novel Coronavirus.

In the coming month, we will look at this in more details in the Bioinformatics for Infectious Diseases Program.

Register here:
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Public Health Masterclass in Genomics: Infectious Disease Genomics

University of Birmingham's Professor Nick Loman describes the vital role that genomics played in tackling the Ebola outbreak, and the future role of genomics in addressing acute microbial resistance. Recorded at a Health Education England West Midlands Public Health Practitioner Masterclass on 28th November 2017.

For more information about genomics in healthcare, visit

Oliver Pybus | Genomic Epidemiology of Zika Virus in the Americas

Pathogen genome sequences contain a remarkable amount of information about epidemiological processes. With appropriate analysis, they can reveal where and when an outbreak initiated, estimate transmission rates, quantify routes and rates of spatial spread, and inform studies of pathogenicity. Yet the contribution that genomics can make to infectious disease surveillance and outbreak control is only beginning to be appreciated by public health agencies. Faster, cheaper and more portable sequencing technologies mean that genomics can now take place alongside field epidemiology investigations. I will present recent results concerning the introduction, establishment, and evolution of Zika virus in the Americas, including findings from the ZiBRA project, a mobile lab that travelled across north-east Brazil in summer 2016 and generated Zika virus sequences using the Oxford Nanopore MinION device. Open sharing of data and protocols during the Zika virus epidemic facilitated the investigation of this new emerging virus.

Flongle, GridION, MinION, MinIT, PromethION, and VolTRAX are currently for research use only.

COVID-19 genomics follow pattern of naturally evolving organism

“When we look at genetic-sequence similarity and we compare it to others, we see that this particular virus not only made use of point mutation, or very small genetic mutations, but it also rearranges its genome a little bit,” Hengartner said. “And looking at the patterns and how it has been rearranged and point mutations, we are very confident to say that this follows what we would expect from a naturally emerging and evolving organism.”
LA-UR-20-22648

Jennifer Gardy - Genomic Epidemiology: Genome Sequencing as an Emerging Tool in Public Health Q&A

Jennifer Gardy speaks at the GBC Winter Symposium about Genomic Epidemiology: Genome Sequencing as an Emerging Tool in Public Health.
Q&A

Gundersen's successful COVID-19 genome sequencing effort ahead of 36 other states

Gundersen's successful COVID-19 genome sequencing effort ahead of 36 other states

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