Strains of SARS-CoV-2 causing COVID-19

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

Updated: June 1, 2021

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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. Several new variants emerged in the fall of 2020 and are described below.
  • Genes in the SARS-CoV-2 genome are shown in Figure 1.
Figure 1
SARS-CoV-2 Genome showing region producing spike protein
SARS-CoV-2 Genome. The dark brown section in the picture has genetic instructions to build the Spike protein, which then allows the virus to attach to human cells during infection. This section of the genome serves as a key region for monitoring mutations.
Source: US Centers for Disease Control

Emerging Strains Across the Globe

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 South Africa strain (Variant B.1.351) as of April 28, 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
Descriptive text is not available for this image
Emerging SARS-CoV-2 Variant Cases in the United States as of May 8, 2021.
Source: US Centers for Disease Control
*The data shows the estimated biweekly prevalence of the most common SARS-CoV-2 lineages circulating in the United States, based on >40,000 sequences collected through CDC’s national genomic surveillance since Dec 20, 2020 and grouped in2-weekintervals. Data are subject to change over time and will be updated as more data become available. Variant proportions in djusted using statistical weighting to correct for the non-random sampling of sequencing data over time and across statesand to providemore representative national estimates.

United Kingdom (UK) variant – B.1.1.7

  • 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.[1],[2]
  • Early reports found no evidence to suggest that the variant has any impact on the severity of disease or vaccine efficacy.[3],[4],[5]

South Africa variant – B.1.351

  • 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.[6] 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[7], but clinical efficacy is yet to be determined.

Brazil variant – P.1

  • 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.

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References

  1. 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...]
  2. 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]
  3. 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]
  4. 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]
  5. Weisblum Y, Schmidt F, Zhang F, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020;9.  [PMID:33112236]
  6. 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]
  7. 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]
  8. Baric RS. Emergence of a Highly Fit SARS-CoV-2 Variant. N Engl J Med. 2020;383(27):2684-2686.  [PMID:33326716]
  9. 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]
  10. Plante JA, Liu Y, Liu J, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2020.  [PMID:33106671]
  11. 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]
  12. 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...]
Last updated: June 1, 2021