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Mashup Score: 31Pathogen phylogenetics for decision making - 3 year(s) ago
Trevor Bedford (@trvrb) Fred Hutchinson Cancer Center / Howard Hughes Medical Institute 23 Aug 2022 From Trees to Public Health Policy Module International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology Slides at:…
Source: bedford.ioCategories: Healthcare Professionals, Latest HeadlinesTweet
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Mashup Score: 23SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers - 3 year(s) ago
Accurately estimating relative transmission rates of SARS-CoV-2 Variant of Concern and Variant of Interest viruses remains a scientific and public health priority. Recent studies have used the sample proportions of different variants from sequence data to describe variant frequency dynamics and relative transmission rates, but frequencies alone cannot capture the rich epidemiological…
Source: bedford.ioCategories: Healthcare Professionals, Latest HeadlinesTweet-
We can assess variant-specific Rt using method developed by @marlinfiggins (https://t.co/Uq7Nl2mI2R), where we observe current Rt for BA.2.12.1 of ~1.0, compared to Rt of BA.4 of ~1.2 and BA.5 of ~1.5. 7/12 https://t.co/e91i6r8uNA
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Mashup Score: 14Continuing SARS-CoV-2 evolution under population immune pressure - 3 year(s) ago
Trevor Bedford (@trvrb) Fred Hutchinson Cancer Center / Howard Hughes Medical Institute 6 Apr 2022 Vaccines and Related Biological Products Advisory Committee Meeting FDA Slides at: bedford.io/talks Continuing SARS-CoV-2 evolution under population immune pressure Trevor Bedford (@trvrb) Fred…
Source: bedford.ioCategories: Infectious Disease, Latest HeadlinesTweet-
Today, I presented to @US_FDA VRBPAC with an overview of SARS-CoV-2 evolution up to this point and a brief perspective for what to expect going forward. Slides are here: https://t.co/QnzOctVCSN and my slot in the full recording is viewable here: https://t.co/n5rlgOvtEg. 1/13
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Mashup Score: 4Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E - 4 year(s) ago
Seasonal coronaviruses (OC43, 229E, NL63 and HKU1) are endemic to the human population, regularly infecting and reinfecting humans while typically causing asymptomatic to mild respiratory infections. It is not known to what extent reinfection by these viruses is due to waning immune memory or antigenic drift of the viruses. Here, we address the influence of antigenic drift on immune…
Source: bedford.ioCategories: Healthcare Professionals, Latest HeadlinesTweet-
@BillHanage @iddux @ENirenberg @baym @maryebushman Seasonal coronavirus OC43 and 229E have similar rates of adaptive evolution as flu B viruses (https://t.co/CGeN6dQJsP). SARS-CoV-2 has much more going on in terms of evolution at S1. Figures from https://t.co/1BlsrKINhq. https://t.co/QBSmAIRO3Z
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Mashup Score: 74SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers - 4 year(s) ago
Accurately estimating relative transmission rates of SARS-CoV-2 Variant of Concern and Variant of Interest viruses remains a scientific and public health priority. Recent studies have used the sample proportions of different variants from sequence data to describe variant frequency dynamics and relative transmission rates, but frequencies alone cannot capture the rich epidemiological…
Source: bedford.ioCategories: Healthcare Professionals, Latest HeadlinesTweet-
If we partition @CDCgov cases between Delta and Omicron using @GISAID sequence data following approach by @marlinfiggins (https://t.co/Uq7Nl2mI2R) we can see clear Omicron epidemics. 3/9 https://t.co/Y41HPdJIhB
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Mashup Score: 140Multistrain models - 4 year(s) ago
Two-strain SIR model, cross-immunity through polarizing immunity
Source: bedford.ioCategories: Infectious Disease, Latest HeadlinesTweet-
We can model this as a two-strain SIRS model with polarizing immunity (https://t.co/IZDvoi4qG1). Here, β1 is transmission rate of strain 1, β2 is transmission rate of strain 2, γ is recovery rate, ω is rate of immune waning and σ is cross-immunity. 4/15 https://t.co/qfF1XOfbHh
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Mashup Score: 9SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers - 4 year(s) ago
Accurately estimating relative transmission rates of SARS-CoV-2 Variant of Concern and Variant of Interest viruses remains a scientific and public health priority. Recent studies have used the sample proportions of different variants from sequence data to describe variant frequency dynamics and relative transmission rates, but frequencies alone cannot capture the rich epidemiological…
Source: bedford.ioCategories: Healthcare Professionals, Latest HeadlinesTweet-
We've observed that the "fixed growth" model is more robust during initial spread while variant is still rare and so we've switched to this model for primary analysis. Full details on model differences are available in the technical report at https://t.co/Uq7Nl2mI2R. 8/10
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Mashup Score: 14
Despite the appearance of variant SARS-CoV-2 viruses with altered receptor-binding or antigenic phenotypes, traditional methods for detecting adaptive evolution from sequence data do not pick up strong signals of positive selection. Here, we present a new method for identifying adaptive evolution on short evolutionary time scales with densely-sampled populations. We apply this method to…
Source: bedford.ioCategories: Hem/Oncs, Latest HeadlinesTweet-
RT @trvrb: To this end, @KateKistler revised analysis from https://t.co/1BlsrKINhq to reconstruct a tree of 20k SARS-CoV-2 genomes, infer d…
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Mashup Score: 81Cryptic transmission of SARS-CoV-2 in Washington State - 4 year(s) ago
Cryptic transmission of SARS-CoV-2 in Washington State Bedford T, Greninger AL, Roychoudhury P, Lea M Starita, Famulare M, Huang M, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Peter D Han, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ,…
Source: bedford.ioCategories: Healthcare Professionals, Latest HeadlinesTweet-
We did this previously for early data in Washington State to infer the introduction time and rate of exponential growth when community transmission was first identified in Feb/Mar 2020 (Figure 2B of https://t.co/ryQawSDXVi). 12/16 https://t.co/LsSja3HzWL
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Mashup Score: 14
Despite the appearance of variant SARS-CoV-2 viruses with altered receptor-binding or antigenic phenotypes, traditional methods for detecting adaptive evolution from sequence data do not pick up strong signals of positive selection. Here, we present a new method for identifying adaptive evolution on short evolutionary time scales with densely-sampled populations. We apply this method to…
Source: bedford.ioCategories: Healthcare Professionals, Latest HeadlinesTweet-
To this end, @KateKistler revised analysis from https://t.co/1BlsrKINhq to reconstruct a tree of 20k SARS-CoV-2 genomes, infer date and country of internal nodes and use these inferences to estimate vaccination coverage at internal nodes in the tree from @OurWorldInData. 12/19
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I was invited by @VandammeAm and other organizers of the #VEME2022 Virus Evolution and Molecular Epidemiology Workshop to present my perspective on applying pathogen phylogenetics for decision making. Slides from my talk are available here: https://t.co/dcRz1LSpbP.