3dgiordano / sars-cov-2-variants

This project tries to give a glimpse of the different variants of SAR-CoV-2 in the world.

SARS-CoV-2-Variants

This project tries to give a glimpse of the different variants of SAR-CoV-2 in the world.

Website: https://3dgiordano.github.io/SARS-CoV-2-Variants/

Naming:

The naming system used is a mix between the names denominated by WHO, the Pango Lineage system and some Nextstrain Clade names.

The project use the denomination of:

• WHO/CDC/ECDC/PHE Variants of Concern (VOC)
• WHO/CDC/ECDC Variants of Interest (VOI)
• WHO Alerts for Further Monitoring (AFM)
• CDC Variants Being Monitored (VBM)
• ECDC Variants Under Monitoring (VUM)
• PHE Variants Under Investigation (VUI)

If a major variant is detected, the WHO name is used. If it is some other variant to consider not yet considered by WHO, its Pango lineage is used. Otherwise, the first letters of the Pango lineage are used. If the variant is in WHO/CDC/ECDC VOI, VOC, AFM or VUM, the label is included.

For more information about lineages names and classifications

• WHO - Tracking SARS-CoV-2 variants https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
• CDC - SARS-CoV-2 Variant Classifications and Definitions https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html
• ECDC - SARS-CoV-2 variants of concern https://www.ecdc.europa.eu/en/covid-19/variants-concern
• PHE - COVID-19 (SARS-CoV-2) variants https://www.gov.uk/government/collections/new-sars-cov-2-variant

About:

The project, site, published data, and graphics are free and open source. A work in progress project created by @3dgiordano. They can access the source code and data in their GitHub project https://github.com/3dgiordano/SARS-CoV-2-Variants.

Inspiration ideas

If it inspires, it is worth not to miss the opportunity to cite the people and their work.

Charts

The visualization idea is inspired by the work of Emma B. Hodcroft @hodcroftlab

Emma B. Hodcroft. 2021. "CoVariants: SARS-CoV-2 Mutations and Variants of Interest." https://covariants.org/

Color scheme

The color palette was mainly based on the color palette used by the project Our World in Data Grapher

Genomic data sources:

outbreak.info

Julia L. Mullen, Ginger Tsueng, Alaa Abdel Latif, Manar Alkuzweny, Marco Cano, Emily Haag, Jerry Zhou, Mark Zeller, Emory Hufbauer, Nate Matteson, Kristian G. Andersen, Chunlei Wu, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes, and the Center for Viral Systems Biology outbreak.info. Available online: https://outbreak.info/ (2020)

GISAID Initiative

Elbe, S., and Buckland-Merrett, G. (2017) Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges, 1:33-46. DOI: 10.1002/gch2.1018 PMCID: 31565258; Shu, Y., McCauley, J. (2017) GISAID: Global initiative on sharing all influenza data – from vision to reality. EuroSurveillance, 22(13) DOI: 10.2807/1560-7917.ES.2017.22.13.30494 PMCID: PMC5388101 data license: https://www.gisaid.org/registration/terms-of-use/

External projects that use our data

poreCov

poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer https://www.frontiersin.org/articles/10.3389/fgene.2021.711437/full

https://github.com/replikation/poreCov

VOCAL

VOCAL: Variant Of Concern ALert and prioritization https://github.com/rki-mf1/vocal

sars-cov-2-variants's Issues

Overlapping of graph date intervals (cases.html)

The cases.html page depicts a line plot of average covid cases for a 2 week period correctly from the date period "2023-01-02 to 2023-01-15" onwards.

However, in the date periods preceding "2023-01-02 to 2023-01-15", there seems to be an overlap in dates.

For example, after the date period "2022-12-19 to 2023-01-01", the next time period is "2022-12-26 to 2023-01-08" instead of "2023-01-02 to 2023-01-15".

For your reference, in the image above, all the points encircled in purple are the overlapping dates.

Question: What means VOC-SUM?

Hi @3dgiordano ,

thanks for this repo!

I've discovered some VOC-SUM types in the variants.csv (all WHO). Do you know what it means?
Couldn't find something on WHO website

Thanks :)