pango-designation
Repository for suggesting new lineages that should be added to the current scheme (by cov-lineages)
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pango-designation | rt-from-frequency-dynamics | |
---|---|---|
209 | 38 | |
1,027 | 46 | |
0.1% | - | |
0.0 | 2.5 | |
8 days ago | 3 months ago | |
Jupyter Notebook | Mathematica | |
GNU General Public License v3.0 or later | - |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
pango-designation
Posts with mentions or reviews of pango-designation.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-10-15.
- Sequencing and Variants Update - [Dec 01, 2023]
- Sequencing and Variants Update - [Nov. 24, 2023]
- Sequencing and Variants Update - [Oct. 06]
- Sequencing and Variants Update - [Sep 29, 2023]
- Sequencing and Variants Update - [Sep. 15, 2023]
- Sequencing and Variants Update - [Sep. 08, 2023]
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Daily Notes - August 14, 2023
And don't miss this news as well as the link that goes to the discussion.
- Sequences and Variants Update - [July 28th]
rt-from-frequency-dynamics
Posts with mentions or reviews of rt-from-frequency-dynamics.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-15.
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2/16 Variant Graph Update
Although several XBB.1.5 descendants are growing marginally faster, all variants that aren't XBB+486P are on the decline nationwide. This includes CH.1.1, which has been the clear #2 VOC behind XBB.1 since ~October and which has gotten some press recently.
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California tops 12 million coronavirus cases as XBB.1.5 becomes dominant
State or national variant numbers can currently be best accessed at cov-spectrum; in this link by clicking on "show regions". Covariants provides an even easier-to-read version, but it only separates a few classes of variants and in 2-week intervals. And Bedford labs variant tracker provides a unique perspective of different variant growth, but currently does not separate by states and has irregular updating.
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What we know about Omicron subvariant XBB.1.5 spreading across the U.S.
With variant tracking the main place to follow is the pango-designation project on github (but please do not post there if you go). Cov-spectrum is great for following the epidemiology of variants, as well as bedford labs. And before that covariants, but they haven't kept up with cov-spectrum's development. All of it's very simple from a modelling perspective, but applying the gisaid data to the case data is massively enlightening.
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12/8 Variant Graph Update
Though they update even more infrequently, I really like the new Bedford labs graphs. These make it very clear just how complicated trying to model the next several months would be.
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Sequencing Update - Weekend Edition
For a national perspective you can see Trevor Bedford’s GitHub. https://github.com/blab/rt-from-frequency-dynamics/tree/master/results/pango-countries
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Japan's daily COVID-19 cases rise week-on-week for 17 straight days | NHK WORLD-JAPAN News
Bedford labs splits it up into specific case counts, and shows the same thing. Here we see that BA.5 cases just stopped declining and started rising. Unfortunately they update irregularly. I'm looking specifically at the third graph here, and what makes me not want to be certain is the dark gray dots that are rising rapidly at the right. These aren't on the legend but I believe mean "other".
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October 19 2022 4 PM CDPHE Update
Bedford labs this week has added several new graphs. This looks in detail at just the US at a lot of different lineages. This looks at many countries with fewer lineages. Note that they do not have XBB.1 (everything's grouped as XBB giving variable results) and their updates are very irregular.
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October 14 2022 4 PM CDPHE Update
4 Bedford labs variant tracker is following XBB now, but not XBB.1. This isn't very useful to see growth in many countries where XBB has been spreading for a bit and XBB.1 has just been introduced, though the r~0.19 (3.8-fold weekly growth) is probably pretty accurate for Singapore.
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The level of coronavirus in Eastern Mass. waste water just shot up
covariants, cov-spectrum, outbreak.info, blab
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The Omicron SARS-CoV-2 variant is more transmissible and less fatal than seasonal influenza
But my best source, when it's updated, is Bedford labs variant tracking project.
What are some alternatives?
When comparing pango-designation and rt-from-frequency-dynamics you can also consider the following projects:
pangolin - Software package for assigning SARS-CoV-2 genome sequences to global lineages.
CovidColoradoCharts - Charts from Colorado's COVID data
pangoLEARN - Store of the trained model for pangolin to access.
2020-rki-impf-archive
nitter - Alternative Twitter front-end
covid-19-excess-deaths-tracker - Source code and data for The Economist's covid-19 excess deaths tracker
privacy-redirect - A simple web extension that redirects Twitter, YouTube, Instagram & Google Maps requests to privacy friendly alternatives.
SARS-CoV-2_variant-reports - Informal summaries of notable SARS-CoV-2 lineages
pango-designation vs pangolin
rt-from-frequency-dynamics vs CovidColoradoCharts
pango-designation vs pangoLEARN
rt-from-frequency-dynamics vs 2020-rki-impf-archive
pango-designation vs nitter
pango-designation vs CovidColoradoCharts
pango-designation vs covid-19-excess-deaths-tracker
pango-designation vs privacy-redirect
pango-designation vs SARS-CoV-2_variant-reports