Strains of SARS-CoV-2 causing COVID-19

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

Updated: February 22, 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

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] More studies are needed to confirm this finding.
  • Early reports found no evidence to suggest that the variant has any impact on the severity of disease or vaccine efficacy.[2],[3],[4]

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. For instance, the Oxford/Astrazeneca vaccine has been shown in a preliminary report[5] to be only 22% effective against mild-moderate COVID-19 caused by this strain.

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.

SARS-CoV-2 Variants in the United States

Figure 2
Descriptive text is not available for this image

Emerging SARS-CoV-2 Variant Cases in the United States. Pictured here are cases of the UK strain (Variant B.1.1.7) as of February 22, 2021.

Click for live updates.

Source: US Centers for Disease Control

*The cases identified above are based on a sampling of SARS-CoV-2-positive specimens and do not represent the total number of B.1.1.7, B.1.351, and P.1 lineage cases that may be circulating in the United States and may not match numbers reported by states, territories, tribes, and local officials.

Table 1. US COVID-19 Cases Caused by Variants

Variant

Cases

States Reporting

B.1.1.7

1661

44

B.1.351

22

10

P.1

5

4

Cases above are based on a sampling of SARS-CoV-2-positive specimens and do not represent the total number of B.1.1.7, B.1.351, and P.1 lineage cases that may be circulating in the United States and may not match numbers reported by states, territories, tribes, and local officials.

Source: US Centers for Disease Control as of Feburary 21, 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. 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]
  3. 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]
  4. Weisblum Y, Schmidt F, Zhang F, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020;9.  [PMID:33112236]
  5. 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...]
  6. Baric RS. Emergence of a Highly Fit SARS-CoV-2 Variant. N Engl J Med. 2020;383(27):2684-2686.  [PMID:33326716]
  7. Plante JA, Liu Y, Liu J, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2020.  [PMID:33106671]
  8. 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]
Last updated: February 22, 2021