Sara and Rebecca will be presenting these papers:
Feb 8th: Phylogenomics Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and North America. Science. 2020 Oct 30;370(6516):564-570. doi: 10.1126/science.abc8169. Epub 2020 Sep 10. PMID: 32912998; PMCID: PMC7810038. Reviews: • Geoghegan JL, Holmes EC. The phylogenomics of evolving virus virulence. Nat Rev Genet. 2018 Dec;19(12):756-769. doi: 10.1038/ s41576-018-0055-5. PMID: 30305704; PMCID: PMC7096893. • Phylogeny for the faint of heart: a tutorial. Baldauf SL. Trends Genet. 2003 Jun;19(6):345-51.PMID: 12801728 **Nextstrain: https://www.fredhutch.org/en/research/diseases/coronavirus/understanding-nextstrain.html **Reuter’svisualization of the virus mutations: https://graphics.reuters.com/HEALTH-CORONAVIRUS/EVOLUTION/yxmpjqkdzvr/ Trevor Bedford’s website and data visualizations: https://bedford.io/
15 Comments
Rohan Babaria
2/5/2024 07:09:03 pm
In the paper they say that multiple independent 17747C is untenable- this raises questions with accuracy of sequencing technology using the RNA for alignment, as isn't it possible that similar issues happened for different loci analyzed.
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Huixian Qiu
2/5/2024 10:02:50 pm
How do we understand the word "fitness" in the context of virulence? Are experimental analysis of virulence determinants in different model organims (both in vitro and in vivo) usually consistent with each other?
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Kate Stack
2/6/2024 02:16:40 pm
In the "The phylogenomics of evolving virus virulence" review paper it states that virulence is often thought of as a fitness trade off involving transmissibility in addition to several other factors. Is it known if any of the sequenced variants in the "The emergence of SARS-CoV-2 in Europe and North America" paper had a particularly profound effect in swaying the disease course to favor a higher transmissibility? If so, was its virulence affected in response?
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2/6/2024 02:33:13 pm
What were the epidemiological parameters used in this study? Also, were these epidemiological parameters the same for looking at the establishment of SARS-CoV-2 in Europe and North America?
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Samuel Kivi
2/7/2024 03:58:48 pm
The article, "The phylogenomics of evolving virus virulence" was written before the COVID-19 pandemic. Since the initial outbreak of COVID-19, do you think that strains of the COVID-19 virus has mutated to become more virulent and transmissible, directly contrasting the "evolutionary trade-off" argument between virulence and transmissibility made in the article?
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Julia Carey
2/7/2024 07:50:15 pm
Could you help me understand what they mean by unsampled taxa/viruses and why it was included in the tree?
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Dianna Xie
2/8/2024 12:05:17 am
I was wondering why some people were infected and some resulted in long COVID, but others remained uninfected from the beginning to the end, even if they were in the same household. Is it because of the immune system or the virulence of the virus?
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Michelle Conte
2/8/2024 01:07:30 am
How does timing come into play when evaluating these phylogenetic inferences? Can examining genetic diversity of current strains help us predict future strains?
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Zoe Zwick
2/8/2024 09:39:30 am
In "The emergence of SARS-CoV-2 in Europe and North America", they mentioned that it was possible that the first outbreak in North America may have been in BC, Canada due to the greater number of genomes with clade-defining substitutions. Is it possible that there were perhaps other potential outbreak locations, but were undiagnosed or not sequenced, leading them to believe that the outbreak did start in Washington?
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Joely Swanson
2/8/2024 10:02:54 am
In the primary paper, it says that figure 4 is using a time-inhomogenous model. What does this mean?
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2/8/2024 10:05:56 am
In the article, "The emergence of SARS-CoV-2 in Europe and North America", the author talked about using phylogenetic inferences combine with genomic epidemiology approach to figure out when the SARS-CoV-2 unfolded in European and North American. Could this research model also be applied to future pandemics? And whether there is a better way to make the study's data more accurate.
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Perla Larios
2/8/2024 10:08:56 am
Most of the figures show the spread with the start day being late January, but Dr. Li discovered the spread in late december. How do you think this missing accounts/ data affect the overall calculations of the spread?
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Madeline Blum
2/8/2024 10:50:02 am
In "The emergence of SARS-CoV-2 in Europe and North America", the authors uses twitter posts as citation. Do you think it was relevant to use this as a source for this paper alongside the article it was referencing?
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Brooke Fuerstenau
2/8/2024 11:17:41 am
In "The Phylogenomics of Evolving Virus Virulence" article, they say that low-virulence infections have a greater chance of establishing transmission cycles in humans than viruses with higher mortality, why is this?
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Praneeth Venigalla
2/8/2024 02:52:57 pm
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