====== SARS-CoV-2 Variants of Interest ======
**SARS-CoV-2 variants of interest** (or **variants of concern**) are evolutionary offshoots in the [[:SARS-CoV-2]] [[:phylogenetic tree]] that are at least temporarily evolutionarily stable due to outcompeting other strains in their immediate [[:geography]].

While there is no guarantee that SARS-CoV-2 variants are correctly identified or defined, these are resources with descriptions and definitions:
  * [[https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-classifications.html|CDC: SARS-CoV-2 Variant Classifications and Definitions]]

See also
  * [[SARS-CoV-2:Surveillance and Testing]]

===== Online Resources =====
  * [[https://cov-lineages.org/|CoV-Lineages.org]] Pango Lineages: Latest epidemiological lineages of SARS-CoV-2.
  * [[https://covariants.org/|CoVariants.org]] draws data from [[:GISAID]].
  * [[https://covid.cdc.gov/covid-data-tracker/#variant-proportions|CDC COVID Tracker Variant Proportions]].
    * This page is a little misleading in terms of whether it is more surveillance or modeling. Read the description and judge for yourself, and perhaps check other sources.
  * [[https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-case-data-2-july-2021|UK Health Security Agency]] Variants: distribution of case data
  * [[https://cov-spectrum.org/explore/Hong%20Kong/AllSamples/Past6M/variants?aaMutations=S%3AI1221T&pangoLineage=BA.2|CoV-Spectrum.com]] Shows proportions of SARS-CoV viruses/strains by nation.

===== General Research on SARS-CoV-2 Variants =====

^             Variants of Concern (VOC)                 ^^^^^^^ 
^ WHO Label ^  Pango lineages  ^  GISAID clade  ^  Nextstrain clade  ^  Additional amino acid changes monitored  ^  Earliest documented samples  ^  Date of designation  ^
| Alpha |  B.1.1.7   | GRY | 20I (V1) | +S:484K and +S:452R | [[:United Kingdom]] (Sep, 2020) | Dec 18, 2020 |
| Beta |   B.1.351  | GH/501Y.V2 | 20H (V2) | +S:L18F | [[:South Africa]] (May, 2020) | Dec 18, 2020 |
| Gamma | P.1 |  GR/501Y.V3  | 20J (V3)  | +S:681H | [[:Brazil]] (Nov, 2020) | Jan 11, 2021 |
| Delta | B.1.617.2 |  G/478K.V1 | 21A | +S:417N | [[:India]] (Oct, 2020) | Apr 4, 2021 |
| Omicron | B.1.1.529 | GR/484A | 21K | - | Multiple nations (Nov, 2021) | Nov 24, 2021 |
| Lambda | C.37 | GR/452Q.V1 | 21G | - | [[:Peru]] (Dec, 2020) | June 14, 2021 |
| Mu | B.1.631 | GH | 21H | - | [[:Colombia]] (Jan, 2021) | Aug 30, 2021 |

==== Potential Consequences of SARS-CoV-2 Mutation ====
Early during the pandemic, research indicated no evidence across over 15,000 SARS-CoV-2 genomes isolated from patients worldwide that mutations led to increased transmissibility.((May 21, 2021 | van Dorp et al | [[:Nature Communications]] | [[https://www.biorxiv.org/content/10.1101/2020.05.21.108506v1|doi: 10.1038/s41467-020-19818-2]])) In Congress, Dr. [[:Anthony Fauci]] notes that all RNA viruses mutate, "but that doesn't mean they change," suggesting that evolution of the virus was not likely to change vaccine efficacy.((Published June 26, 2020 | House Energy & Commerce Committee | [[https://ugetube.com/watch/anthony-fauci-grilled-by-rep-kurt-shrader-over-covid-19-vaccine_OPZTqigtn3vdilU.html|Anthony Fauci grilled by Rep. Kurt Shrader over Covid-19 vaccine]]))

==== Reproduction Numbers (R_t) ====
  * Dec 11, 2021 - Figgins and Bedford (preprint): SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers.((December 11, 2021 | Figgins & Bedford | preprint | [[https://www.medrxiv.org/content/10.1101/2021.12.09.21267544v1.full-text|doi.org/10.1101/2021.12.09.21267544]]))

===== List of SARS-CoV-2 Variants of Interest =====
The [[:Greek alphabet]] is being used to name SARS-CoV-2 variants of interest.

==== Alpha Variant (B.1.1.7) ====
The alpha strain (UK variant) has 19 nonynonymous mutations across its genome including 8 substitutions or deletions in the [[:spike protein]]. These changes in the spike protein result in enhanced fitness and transmission.((March 9, 2021 | Liu et al | preprint | [[https://www.biorxiv.org/content/10.1101/2021.03.08.434499v1|doi.org/10.1101/2021.03.08.434499]]))

==== Beta Variant (501Y.V2/B.1.351) ====

==== Gamma (P.1) Variant ====

==== Delta Variant (B.1.617.2) ====
The delta strain appears to have emerged from India, and may have been an (immune) escape variant.((July 15, 2021 | [[:Mathew Crawford]] | [[:Rounding the Earth]] | [[https://roundingtheearth.substack.com/p/variant-roulette-evolution-and-immunity|Variant Roulette (Evolution and Immunity Escape)]])) Early data from the UK indicated that delta was far less lethal and that vaccines were far less effective against it.((June 22, 2021 | [[:Mathew Crawford]] | [[:Rounding The Earth]] | [[https://roundingtheearth.substack.com/p/are-uks-vaccinated-dying-more-from|Are UK's Vaccinated Dying More from the Delta Variant?]])) ((June 26, 2021 | [[:Mathew Crawford]] | [[:Rounding the Earth]] | [[https://roundingtheearth.substack.com/p/are-uks-vaccinated-dying-more-from-5e3|Are UK's Vaccinated Dying More from the Delta Variant? Part 2]])) However, case fatality rates around the world seem to remain unchanged despite delta taking over the lion's share of cases.

  * Claim: The reproductive number of delta is substantially higher than for prior variants (5.08 vs. 2.79).((October 7, 2021 | Liu & Rocklov | [[:Journal of Travel Medicine]] | [[https://academic.oup.com/jtm/article/28/7/taab124/6346388|doi.org/10.1093/jtm/taab124]]))
    * The study tests over a small number of locales, and without respect to vaccine interaction, which might influence R given evidence that delta was an escape variant.


==== Lambda Variant ====
Came from Peru.


==== Omicron (B.1.1.529) ====
Initially named a "variant of concern" by the [[:World Health Organization|WHO]], [[SARS-CoV-2:Omicron|Omicron]] appears to be a "cousin" of SARS-CoV-2, not part of the variant lineage.

===== Evolutionary Origins of SARS-CoV-2 Variants =====
Debate over the manner and emergence of some SARS-CoV-2 variants has been tenuous during the COVID-19 pandemic.

==== Caused by Mass Vaccination ====

An Emergency Room doctor told financial [[:YouTube|YouTuber]] [[:Gregory Mannarino]] on air that he believes "all variants are likely caused by the vaccine."((Mannarino, G. [Gregory Mannarino]. (2021, November 26). //ALERT ALERT! Banks WARN On New Variant, AND AN ER DOCTOR COMES FORWARD TO TELL THE TRUTH! Mannarino [Video].// YouTube. https://www.youtube.com/watch?v=4nPcF1o09EI))

Niesen et al: vaccination dampens antigen mutational variance https://www.medrxiv.org/content/10.1101/2021.07.01.21259833v1

[[:Bret Weinstein]], talking to [[:Joe Rogan]], [[https://www.youtube.com/watch?v=gmy8znrLPc0 | explains]] that Geert van den Bosch predicted that the vaccines would cause variants through evolutionary pressure. And here we are.

=== Vaccine Resistance ===
Wang et al: Mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. https://pubmed.ncbi.nlm.nih.gov/34873910/