Variants

Intro

  • Global database of GISAID which collects the genomic sequencing around the world.
  • The virus was predicted to undergo just 2 to 3 mutations in an year but it underwent as many as 17 mutations in one go.
  • We have already seen that these heavily immunocompromised patients harbour virus much longer time and keep excreting. This is what it gives a good opportunity for the virus to evolve into variants.

Attenuation probability

Viruses don’t always become attenuated (less virulent). When they do, it’s because there is an evolutionary selection pressure driving it. No such pressure exists for SARS-CoV-2.

An example of this type of selection pressure would be a virus that is so virulent, it kills its host before it can be transmitted to another one. A virus is essentially a machine programmed to make more viruses. To do that, it needs to be spread to new hosts. So variants that are so virulent they kill a host before that host can pass it along, that is under negative selection pressure. The more virulent viruses won’t be passed on. But attenuated variants will. They are under positive selection.

For SARS-CoV-2, this has never been an issue. This virus can be transmitted to a new host before an infected person develops symptoms. Even those who die from COVID are most contagious before they become severely ill. (source: Angela Rasmussen)

Victoria

  • Original is called: Victoria.
  • R number was 2.5

20J/501Y.V3 or P.1

  • Manaus, Brazil. Later: British Columbia in Canada.
  • 2-2.5 times more transmissible and proving to be lethal. more likely to cause serious illness in young people (20-39 years being 2.7 times more likely to die).
  • vaccines work albeit some lowered efficacy
  • Brazil used Chinese Sinovac vaccine which has lesser protection against the mutants.

B.117 UK

  • VOC-202012/01, 20I/501Y.V1

Mutations

  • N501Y. Slight change in highly variable protein region here. One claim is that plasma therapy triggered it.
  • It has acquired another troublesome mutation E484 (found earlier in South Africa strain) which makes it adopted well to escape out from antibodies,cause re-infections and lessened vaccine efficacy.

Spread

  • R number of 4
  • Scientists speculate the B117 arose from one single source in an immunocompromised one where the virus underwent mutation.
  • In September, it first appeared from England.
  • By Nov it accounted for 28% of the virus moving around
  • Was circulating in the USA in mid Nov itself.
  • By Dec 9th,62% of the virus was this variant in London.
  • B117 variant “may be associated with higher degree of mortality” (30-40% increase in 60+ age group), in addition to 50-70% more transmissible.

Vaccination

  • See UK data under B 1.617

B.1.1.529 Omicron South Africa

  • Outcompeting Delta variant.
  • WHO skipped Nu and Xi while naming this :-).

501.V2, 20H/501Y.V2, B.1.351 lineage South Africa

  • spreading faster,tends to have high viral load and possibly more severe to young adults.
  • Mutations: N501Y E484K.
  • Preliminary data from South Africa suggests that the novel variant 501.V2 wasn’t recognised by antibodies in 21/44 serum samples collected from people infected in the first wave.

D614G and G614

  • D614 was the original Wuhan virus( China Virus)
  • G614 was a slight change that was noticed and scientists observed G614 had more transmissibility potential. Round about Feb 2020, new variant emerged in Europe.

L452R California B 1.429/427 ?

  • Resurfaced in Jan 2021

NY B 1.526

  • ability to escape from antibodies and vaccines.

B 1.617 Delta mahArAShTra

Mutations

  • Mutation L526R found in California makes it spread faster.
  • The E484Q mutation makes it behave like the African strain against which most vaccines have failed.

Subtypes

  • B 1.617.1
  • B 1.617.2
  • B 1.617.2.1 Aka Nepal, Delta plus - more mutation called K417 N in Spike protein
    • making it to be resistant to monoclonal antibodies.
  • most widespread
  • Lost E484Q.
  • B 1.617.3
  • The AY.4.2 (Delta Plus) variant, which is known to be 10-15% more transmissible than its predecessor, has increased to 11 folds in last two months in India.

Vaccines

  • COVAXIN and COVISHIELD have demonstrated early neutralizing efficacy against B 1.617
  • Pfizer and Moderna showing 7 fold reduction in antibodies that can neutralize the variant found in India(B 1.617.2) according to WHO’s weekly update.
  • Aggregate data from UK BioNTech/Pfizer and Oxford/AstraZeneca jabs.
    • 1 dose: 33 per cent protection against symptomatic infection from B.1.617.2, and 51 per cent against B.1.1.7.
    • 2 doses 81 per cent protection against the B.1.617.2, 87 per cent against the B.1.1.7 strain
  • Those who got infected with B 1.315 or P1 are still susceptible to get re-infected with the Delta variant.

Effects

  • R number of more than 6
  • The virus has about 40-50% more transmissibility than the B 117 UK variant.
  • causing more lung damages and weight loss.
  • Lesser numbers of asymptomatic cases.

B 1.618 bengAl

  • It has a mutation(E484K) that is notorious to cause escape to vaccines.

B 1.36 India

  • It has N440 mutation which might be the reason for some of the re- infections described.

N440K AP variant

  • Supposedly more infectious. But reports indicate that it’s been swamped by B 1.671.

Comparisons

  • B117 Alpha—29% faster
  • B1351 Beta—25%
  • P1 Gamma—38%
  • B16172 Delta—97%