Strains of SARS-CoV-2 causing COVID-19

William M. Detmer, MD, supported by the Unbound Medicine Team

Updated: February 16, 2022

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SARS-CoV-2 Variant Strains

  • SARS-CoV-2, the virus that causes COVID-19, is constantly changing – like all viruses.
  • Genetic variations occur over time and can lead to the emergence of new variants – some may be more transmissible, deadly, or resistent to current vaccines.
  • Multiple SARS-CoV-2 variants are circulating globally. The omicron variant emerged in the fall of 2021 and is described below.
Coronavirus Variants in the United States
Coronavirus Variants in the United States
Graph shows the percentage of analyzed positive Covid test for each variant since March 2020 in the United States.
Source: GISAID and Our World in Data.

Emerging Strains: Omicron

Figure 2
Variant Strains of SARS-CoV-2 Globally
Emerging SARS-CoV-2 Variant Cases reported across the globe. Pictured here are cases of the Omicron variant (B.1.1.529) as of January 31, 2021.
Because of differences in detection and reporting, variants are likely present in some countries that have not yet reported them. The lack of reporting of a variant in a country does not indicate the variant is absent in that country.
Source: US Centers for Disease Control, WHO Variant Tracker.

SARS-CoV-2 Variants in the United States

Figure 3
Nowcast models of variants in the United States
Nowcast models of variants in the United States as of February 12, 2022. For several months before December 2021, the SARS-CoV-2 Delta variant (B.1.617.2) dominated. In the weeks since December 2, 2021 the Omicron variant (B.1.1.529 BA.2) has rapidly taken over as the dominant strain.
Source: US Centers for Disease Control and Prevention.

Omicron variant – B.1.1.519 and BA.2

  • On November 24, 2021, a new variant of SARS-CoV-2, B.1.1.529, was reported to the World Health Organization (WHO). This new variant was first detected in specimens collected on November 11, 2021 in Botswana and on November 14, 2021 in South Africa.
  • On November 30, 2021, the U.S. government SARS-CoV-2 Interagency Group (SIG) classified Omicron as a Variant of Concern (VOC). This classification was based on the following:
    • Detection of cases attributed to Omicron in multiple countries, including among those without travel history.
    • Transmission and replacement of the Delta variant in South Africa.
    • The number and locations of substitutions in the spike protein.
    • Available data for other variants with fewer substitutions in the spike protein that indicate a reduction in neutralization by sera from vaccinated or convalescent individuals.
    • Available data for other variants with fewer substitutions in the spike protein that indicate reduced susceptibility to certain monoclonal antibody treatments.
  • Omicron is believed to be far more contagious (spreading much quicker) – 70 times faster than any previous variants in the bronchi (lung airways), but to be less able to penetrate deep lung tissue, leading scientists to consider this reason as the cause of reduction in the risk of severe disease requiring hospitalisation, when compared to previously identified variants of concernThe average number of new cases spawned by each infection estimated to be 2 -- twice what it was when the Delta variant was circulating in South Africa[1]

Frequently asked questions[2]

  • How easily does Omicron spread? The Omicron variant spreads more easily than the original SARS-CoV-2 virus and the Delta variant. Anyone with Omicron infection can spread the virus to others, even if they are vaccinated or don’t have symptoms.
  • Will Omicron cause more severe illness? More data are needed to know if Omicron infections, and especially reinfections and breakthrough infections in people who are fully vaccinated, cause more severe illness or death than infection with other variants.
  • Will vaccines work against Omicron? Current vaccines are expected to protect against severe illness, hospitalizations, and deaths due to infection with the Omicron variant. However, breakthrough infections in people who are fully vaccinated will occur. With other variants, like Delta, vaccines have remained effective at preventing severe illness, hospitalizations, and death. The recent emergence of Omicron further emphasizes the importance of vaccination and boosters.
  • Will treatments work against Omicron? Scientists are working to determine how well existing treatments for COVID-19 work. Based on the changed genetic make-up of Omicron, some treatments are likely to remain effective while others may be less effective.

Delta variant – B.1.617.2

  • This SARS-CoV-2 variant – also known as 20A/S:478K was first detected in India in late 2020.
  • Carries a number of spike protein mutations including L452R
  • Because of increased transmission, it has become the dominant variant in the US and other countries.
  • May be less susceptable to neutralization by monoclonal antibodies
  • Neutralization by post-vaccination sera may be reduced in this variant.[3]

United Kingdom (UK) variant – B.1.1.7 (Alpha)

  • This SARS-CoV-2 variant – also known as 20I/501Y.V1 Variant of Concern [VOC] 202012/01 – emerged in the UK during September 2020.
    • Variant has a mutation in the receptor binding domain (RBD) of the spike protein at position 501, where the amino acid asparagine (N) has been replaced with tyrosine (Y). The shorthand for this mutation is N501Y. This variant also has several other mutations including a 69/70 deletion and mutation in the P681H region.
  • Detected in numerous countries, including the United States (US) at the end of December 2020.
  • Variant is associated with increased transmissibility (i.e., more efficient and rapid transmission).
  • In January 2021, UK scientists reported evidence that suggests the B.1.1.7 variant may be associated with an increased risk of death compared with other variants.[4],[5]
  • Early reports found no evidence to suggest that the variant has any impact on the severity of disease or vaccine efficacy.[6],[7]

South Africa variant – B.1.351 (Beta)

  • This SARS-CoV-2 variant – also known as 20H/501Y.V2 – shares some mutations with B.1.1.7 but emerged independently in October 2020 in South Africa.
    • Variant has multiple mutations in the spike protein, including K417N, E484K, N501Y. Unlike the B.1.1.7 lineage detected in the UK, this variant does not contain the deletion at 69/70.
  • Detected in multiple countries outside of South Africa, including Zambia in late December 2020 and the US at the end of January 2021.
  • Currently there is no evidence to suggest that this variant has any impact on disease severity.
  • However, preliminary studies of current vaccines suggest they may be less effective against this strain.
    • Oxford/AstraZeneca vaccine has been shown to be only 22% effective against mild-moderate COVID-19 caused by this strain.[8] For this reason, South Africa has discontinued use of this vaccine.
    • mRNA vaccines (Pfizer and Moderna) have been shown to induce significant neutralizing antibodies against B.1.351[9], but clinical efficacy is yet to be determined.[3]

Brazil variant – P.1 (Gamma)

  • This SARS-CoV-2 variant was first was identified in four travelers from Brazil, who were tested during routine screening at Haneda airport outside Tokyo, Japan.
  • Variant has 17 unique mutations, including three in the receptor binding domain of the spike protein.
  • Variant mutations may affect its transmissibility and antigenic profile.
    • A recent study reported on a cluster of cases in Manaus, the largest city in the Amazon region, in which the P.1 variant was identified in 42% of the specimens sequenced from late December. In this region, it is estimated that approximately 75% of the population had been infected with SARS-CoV2 as of October 2020. However, since mid-December the region has observed a surge in cases. The emergence of this variant raises concerns of a potential increase in transmissibility or propensity for SARS-CoV-2 re-infection of individuals.
  • Detected in the US at the end of January 2021.[3]

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See Also

References

  1. Callaway E, Ledford H. How bad is Omicron? What scientists know so far. Nature. 2021.  [PMID:34857948]
  2. Omicron Variant: What You Need to Know. US Centers for Disease Control and Prevention. [https://www.cdc.gov/coronavirus/2019-ncov/variants/omicron-variant.html]
  3. Liu J, Liu Y, Xia H, et al. BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants. Nature. 2021.  [PMID:34111888]
  4. Horby P, Huntley C, Davies N, et al. NERVTAG note on B.1.1.7 severity. SAGE meeting report. January 21, 2021. [https://www.gov.uk/government/publications/nervtag-paper-on-covid-19-varia...]
  5. Challen R, Brooks-Pollock E, Read JM, et al. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ. 2021;372:n579.  [PMID:33687922]
  6. Wu K, Werner AP, Moliva JI, et al. MRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. bioRxiv. 2021.  [PMID:33501442]
  7. Xie X, Zou J, Fontes-Garfias CR, et al. Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera. bioRxiv. 2021.  [PMID:33442691]
  8. Madhi SA, Baillie V, Cutland CL, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. N Engl J Med. 2021.  [PMID:33725432]
  9. Stamatatos L, Czartoski J, Wan YH, et al. MRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection. Science. 2021.  [PMID:33766944]
  10. Baric RS. Emergence of a Highly Fit SARS-CoV-2 Variant. N Engl J Med. 2020;383(27):2684-2686.  [PMID:33326716]
  11. Deng X, Garcia-Knight MA, Khalid MM, et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell. 2021;184(13):3426-3437.e8.  [PMID:33991487]
  12. Emary KRW, Golubchik T, Aley PK, et al. Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial. Lancet. 2021.  [PMID:33798499]
  13. Plante JA, Liu Y, Liu J, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2020.  [PMID:33106671]
  14. Sabino EC, Buss LF, Carvalho MPS, et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Lancet. 2021;397(10273):452-455.  [PMID:33515491]
  15. South Africa suspends use of AstraZeneca’s COVID-19 vaccine after it fails to clearly stop virus variant. Science News. February 8, 2021. [https://www.sciencemag.org/news/2021/02/south-africa-suspends-use-astrazen...]
  16. Weisblum Y, Schmidt F, Zhang F, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020;9.  [PMID:33112236]
Last updated: February 16, 2022