Information on Virus Variants

The information in this section comes from a summary on virus variants from the University of Washington Alliance for Pandemic Preparedness.

Naming Conventions: As the number of variants become more prevalent and widespread, it is important to move away from naming based on geographic origin. The problem is that there are multiple categorizations of these variants across research and public health organizations. Without going into a lot of detail on the naming conventions, here is a listing of the most referenced strains with their aliases:

  • Lineage B.1.1.7 (aka variant 20I/501.Y.V1 or VOC 202012/01) first identified in the UK
  • Lineage B.1.351 (aka variant 20H/501Y.V2) first identified in South Africa
  • P.1 variant (aka variant 20J/501Y.V3, branch from B.1.1.28 lineage) first identified in Brazil
  • CAL.20C variant first identified in southern California

Transmission

  • B.1.1.7 is found in 90% of samples across England, has a 25-40% higher attack rate, and 10-times higher affinity for the ACE2 receptor.
  • B.1.351 is the predominant strain now in South Africa, but has been found in the United States. It's estimated to be more transmissible, but less quantified than B.1.1.7.
  • P.1 variant is also estimated to be more transmissible and may lead to re-infection.
  • CAL.20C is showing increasing dominance in southern California, coinciding with the increased positivity in that region.

Implications for Re-Infection and Vaccine Efficacy: B.1.351 and P.1 mutations reduce neutralization by convalescent serum up to 10-fold, by most monoclonal antibodies and sera from vaccinated persons (6 to 8-fold). Cases of re-infection have been reported for all these variants. All vaccines approved or in Phase 3 trials have shown slight reduction in neutralization for the B.1.1.7 variant, and more so against the B.1.351 variant, although still over 50% efficacy.

Clinical Severity: Most of the data is on the B.1.1.7 variant out of the UK, which is conflicting, with some studies suggesting increased mortality, some finding no association and one showing equal likelihood of being asymptomatic.

Vaccines and Virus Variants

Below is a summary of the most recent information available on the effectiveness of vaccines on the emerging variants.

  • Serum samples from 20 participants in the Pfizer trial showed a reduction of 2/3 in neutralizing activity against the B.1.351 variant (South African origin) compared to the early strains and those from the UK and Brazil. (N Engl J Med, February 17)
  • Samples from participants in the Moderna trial showed a 6.4 fold reduction in neutralizing activity against the B.1.351 variant. (N Engl J Med, February 17)
  • Another good viewpoint written by the head of the CDC and NIAID reviews the 3 variants of concern (B.1.1.7, B.1.351 and P.1), current data on spread and risk for increasing cases of disease, concerns and steps to ensure that our current testing can detect disease caused by these variants, and steps to be taken to slow transmission. The authors feel strongly that current mitigation methods must be continued, including delaying travel. (JAMA Online First, February 17)
  • Sera from 20 participants who had received both doses of the Pfizer vaccine showed equivalent neutralization titers (differences of 4-fold or less) between the wild type and engineered variants that contained spike proteins from recently emerged variants, including those first described in the UK and South Africa. Neutralization geometric mean titers suggest small impacts of these mutations on neutralization by sera from vaccinated individuals. (Disclaimer: These engineered viruses do not contain all of the mutations present in the variants). (Nature Medicine, February 8)
  • SARS-CoV2 viral variants: capturing a moving target (JAMA, February 11)
  • SARS-CoV2 vaccines and the growing threat of viral variants (JAMA, January 28)—the authors point out several issues related to this problem, including issues with suboptimal immunity limiting the number or increasing the interval between doses, ability of vaccine-induced neutralizing antibodies to attack the virus, the loss of effectiveness of monoclonal antibodies against the variants, and then they propose an approach to the problem.
  • This pre-print article shows sera from patients who completed both doses of the Pfizer BioNTech vaccine had similar neutralizing geometric mean titers (GMTs) against SARS-CoV-2 engineered to contain the same mutations as the UK and South African variants, compared to the wild-type, although the GMTs against the South African variant were 19% lower. The authors note that the engineered viruses do not contain the full set of mutations present in the UK and South African variants. (bioRxiv, January 27)