COVID variants

Variants of concern. Summary from the US Centre for Disease Control. 

Royal Australian College of General Practitioners

  • "Current COVID vaccines could be ineffective by next year: epidemiologists"

    • https://www1.racgp.org.au/newsgp/clinical/current-covid-vaccines-could-be-ineffective-by-nex  31March2021

      • "Two-thirds of epidemiologists who took part in a recent global survey have predicted it will be less than a year before SARS-CoV-2 mutates to such an extent that the majority of first generation COVID vaccines are rendered ineffective and new or modified candidates are required."

      • "Variants of concern have already emerged in South Africa, the US, India and Brazil, and Yale University’s Associate Professor Gregg Gonsalves said the fact that millions of people around the world are still contracting the disease means new mutations will arise every day."

      • There is some concern that the AstraZeneca vaccine shows much less protection against the South African strain [B.1.351], but it was quite a small study that did not examine whether there was still protection against severe disease.'

"What are the Indian, Brazil, South Africa and UK variants?"  24/Apr/21

  • https://www.bbc.com/news/health-55659820 

    • "These strains of Covid-19 may be more contagious and dodge immunity to some extent.

      • The UK or Kent variant (also known as B.1.1.7) now dominant in much of Britain, has spread to more than 50 countries and appears to be mutating again

      • The South Africa variant (B.1.351) has found in at least 20 other countries, including the UK

      • The Brazil variant (also known as P.1) has now been found in the UK 

      • The Indian variant B.1.617 has some potentially important mutations (E484QL452R and P681R) that might help it escape some immunity, which is why experts are urgently studying it."

        • The title of the L452R paper , is "Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation"

          • "We identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged around May 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020 to January 29, 2021"

        • Anne de Gheest's 30/Apr/21 Epidemiological update spends some time on the Indian variant. http://puzzlefinancialadvice.com.au/2021/COVID/Anne_de_Gheest_Epidemiological_COVID_update_210430.pdf   I don't think we really know how dangerous the Indian variant is just yet at this time 4/May/21. (not enough research on it yet)  Clearly Ann de Gheest is worried about it..... worried about the Indian variant getting into the USA. And Anne does point out that this variant has over 2 months, become dominant in India. (7min6sec into that video update).

        • More about the Indian delta variant here    

"With Rise In Variants, Scientists Warn Of Evolutionary Arms Race Between Virus And Vaccines" 14/Apr/21

  • https://www.wbur.org/commonhealth/2021/04/14/more-infectious-coronavirus-variants-overtake-massachusetts

    • The original coronavirus is being overtaken in Massachusetts by newer and more infectious variants. The Broad Institute of MIT and Harvard regularly sequences the genomes of coronaviruses taken from COVID-19 patients and, lately, the analyses have been showing more of these variants than the original or "wild-type" strain, which contains no major mutations.

    • In the past few weeks and as of last night in particular, we are seeing over 50% of the cases we are sequencing at the Broad being variants of concern,” Bronwyn MacInnis, a genomicist at the Broad Institute, said at a state legislative hearing on Tuesday. “A large proportion of those being the B.1.1.7 variant first identified in the U.K., but also P.1, the variant first identified in Brazil.”

    • Barouch mentioned several concerning variants including the P.1 strain first identified in Brazil and domestic mutations that have emerged in California and New York, noting these variants “also have the property of being able to partially evade antibodies, and therefore raise the specter as to whether they may reduce vaccine efficacy.”

    • Scientists point to the rapid spread of these variants in their countries of origin and around the world as one line of evidence that they’re more infectious than the original coronavirus strain. In Brazil, the P.1 variant quickly became dominant in the country and surged into nearby nations. In the United Kingdom, the prevalence of B.1.1.7 rapidly overtook other coronavirus variants in multiple parts of the country.  

Which variant has most immune evasion properties?

  • Eric Topol's summary.   25/Apr/21

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Eric Topol's summary of results of testing of vaccines vs variants.      25/Apr/21  ->

Topol_vaccine_vs_variants_210513.jpg

7/May/2021  https://twitter.com/EricTopol/status/1390707410407358464

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Below, from Anne de Gheest's 30/Apr/21 COVID Epidemiological update, you can see how fast this new Indian variant became dominant in India - even out-competing the UK variant B.1.1.7 which is also in India.  That is a very bad sign, suggesting (to me at least) perhaps that this Indian might rapidly become the globally dominant variant

Indian_variant_in_India_210507.png

15/May/25 Variants in the USA & UK  https://twitter.com/EricTopol/status/1392524120122748933 

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On the Australian chart, the light green variant showing up at the bottom is variant: 20A/S:154K   which is also better known as B.1.617.1 

You can find the mapping of COVID variant names here

https://covariants.org/variants/20A.S.154K 

The dark pink section above B.1.617.2 is the Brazilian variant P.1

Much of this Aussie data will be from sequencing of infections in hotel quarantine

3/June/21  Mix of variants in California. The 3 to watch are Indian variant (pink), UK variant (blue), Brazilian variant (light blue)

Californian_mix_of_variants_210603.jpg

https://twitter.com/EricTopol/status/1402384202805374978  9/June/21

Comparig South African to Brazil variant

The following is a very important article.

The following 16/June/21 article is a very useful summary of how effective each vaccine is against each major variant (except the Brazilian variant Gamma). I commend this article to you.

https://twitter.com/EricTopol/status/1407526454594703361    23/June/21

https://www.youtube.com/watch?v=GM5dpZsjM1c  Anne de Gheest COVID Epidemiology Update. 25/June/21

  • South America is dominated by the Gamma Variant - previously known as the Brazilian P.1 variant.   In South America, they have mainly been relying on the Chinese vaccines.

  • At the 2min45sec point in this presentation Anne says that in Argentina, neither Sputnik nor Sinopharm nor AstraZeneca has proved to be a effective against the Gamma variant. This is the first time I have heard an authoritative assessment of that. I had expected that this might be the case because:

Anne_de_Gheest_AstraZeneca_not_good_re_G

Anne de Gheest's latest COVID clinical update   25/June/21 https://www.youtube.com/watch?v=77skcFyRWXE

  • The latest vaccine vs variants matrix  

  • Also the very dangerous Gamma (P.1) variant from Brazil is growing in the USA   

  • A useful summary of comparative transmissibility by variant provided below.

  • New variants emerging including mutant variant of Delta.    

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Anne_de_Gheest_Clinical_upd_P1-Gamma_var
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New variant cousin (AY.3) of delta (B.1.617.2)  rapidly replacing B.1.617.2 in USA. Must have advantages vs B1.617.2

This is really interesting https://outbreak.info/location-reports?loc=USA&selected=B.1.1.7&selected=B.1.617.2&selected=P.1

This chart is indicating that in the USA, variant AY.3 seems like it is well on the way to replacing the delta COVID variant.

 

What is AY.3 ? https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html It appears that AY.3 is a variant derived from delta.  Delta Plus is also known as AY.1. Looks like WHO is classifying AY.3 still as part of the delta family. https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

 

This web page https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant perhaps gives us a little extra information. I think it is saying that AY.3 is a close relative of Delta Plus. My guess is that, noting the rapid rise of AY.3 in the USA, rapidly replacing (it seems) B.1.617.2 (the primary delta variant), it won't be long before AY.3 has its own name - and will be famous. :) :) '

"Delta plus" variant See also: Variants of SARS-CoV-2 § Delta (lineage B.1.617.2) Delta with K417N corresponds to lineages AY.1 and AY.2[40] and has been nicknamed "Delta plus" or "Nepal variant". It has the K417N mutation[41] which is also present in the Beta variant.[42] The exchange at position 417 is a lysine-to-asparagine substitution.[43] As of 15 July 2021, the AY.3 variant accounted for approximately 21% of cases in the United States.[44]'

 

In summary, that chart (see below) is pretty interesting - and for me, pretty alarming ... because it says to me that delta now has a nastier cousin coming to visit us real soon .... It would be interesting to know which member of the delta family is causing all this current lockdown in NSW (at July 2021)

AY.3 rapid_spread_in_USA_210730.JPG