SARS-CoV-2 Variants

SARS-CoV-2 Variants

A new virus variant has one or more mutations that differentiate it from the wild-type or predominant virus variants already circulating among the general population. As expected, multiple variants of SARS-CoV-2 have been documented in the United States and globally throughout this pandemic. To inform local outbreak investigations and understand the national picture, scientists compare genetic differences among viruses to identify variants and how closely they are related to each other.

Several new variants that emerged in the fall of 2020 are concerning, most notably:

  • B.1.1.7: In the United Kingdom (UK), a variant of SARS-CoV-2 known as B.1.1.7 emerged. This variant carries a large number of mutations and has since been detected around the world, including in the United States (US). This variant was first detected in the US at the end of December 2020. In January 2021, scientists from the UK reported early evidence[1,2] that suggests the B.1.1.7 variant may be associated with an increased risk of death compared with other variants. More studies are needed to confirm this finding.
  • B.1.351: In South Africa, another variant of SARS-CoV-2 known as B.1.351 emerged independently of B.1.1.7. According to a non-peer-reviewed preprint article, this variant shares some mutations with B.1.1.7[3]. Cases attributed to B.1.351 have been detected outside of South Africa, and this variant was first detected in the US at the end of January 2021. Preliminary evidence from non-peer-reviewed publications suggests that the Moderna mRNA-1273 vaccine currently used in the US may be less effective against this variant[4], but additional studies are needed.
  • P.1: In Brazil, a variant of SARS-CoV-2 known as P.1 emerged; it was first identified in January 2021[5] in travelers from Brazil who arrived in Japan. This variant was detected in the US at the end of January 2021 [6]. The P.1 variant has 17 unique mutations, including three in the receptor binding domain of the spike protein (K417T, E484K, and N501Y), according to non-peer-reviewed preprint articles[7,8]. There is evidence to suggest that some of the mutations in the P.1 variant may affect the ability of antibodies (from natural infection or vaccination) to recognize and neutralize the virus[9], but additional studies are needed.

One specific mutation, called D614G, is shared by these three variants. It gives the variants the ability to spread more quickly than the predominant viruses, as described in a non-peer-reviewed preprint article[10,11]. There also is epidemiologic evidence that variants with this specific mutation spread more quickly than viruses without the mutation[12]. This mutation was one of the first documented in the US in the initial stages of the pandemic, after having initially circulated in Europe[13].

A new virus variant has one or more mutations that differentiate it from the wild-type or predominant virus variants already circulating among the general population. As expected, multiple variants of SARS-CoV-2 have been documented in the United States and globally throughout this pandemic. To inform local outbreak investigations and understand the national picture, scientists compare genetic differences among viruses to identify variants and how closely they are related to each other.

Several new variants that emerged in the fall of 2020 are concerning, most notably:

  • B.1.1.7: In the United Kingdom (UK), a variant of SARS-CoV-2 known as B.1.1.7 emerged. This variant carries a large number of mutations and has since been detected around the world, including in the United States (US). This variant was first detected in the US at the end of December 2020. In January 2021, scientists from the UK reported early evidence[1,2] that suggests the B.1.1.7 variant may be associated with an increased risk of death compared with other variants. More studies are needed to confirm this finding.
  • B.1.351: In South Africa, another variant of SARS-CoV-2 known as B.1.351 emerged independently of B.1.1.7. According to a non-peer-reviewed preprint article, this variant shares some mutations with B.1.1.7[3]. Cases attributed to B.1.351 have been detected outside of South Africa, and this variant was first detected in the US at the end of January 2021. Preliminary evidence from non-peer-reviewed publications suggests that the Moderna mRNA-1273 vaccine currently used in the US may be less effective against this variant[4], but additional studies are needed.
  • P.1: In Brazil, a variant of SARS-CoV-2 known as P.1 emerged; it was first identified in January 2021[5] in travelers from Brazil who arrived in Japan. This variant was detected in the US at the end of January 2021 [6]. The P.1 variant has 17 unique mutations, including three in the receptor binding domain of the spike protein (K417T, E484K, and N501Y), according to non-peer-reviewed preprint articles[7,8]. There is evidence to suggest that some of the mutations in the P.1 variant may affect the ability of antibodies (from natural infection or vaccination) to recognize and neutralize the virus[9], but additional studies are needed.

One specific mutation, called D614G, is shared by these three variants. It gives the variants the ability to spread more quickly than the predominant viruses, as described in a non-peer-reviewed preprint article[10,11]. There also is epidemiologic evidence that variants with this specific mutation spread more quickly than viruses without the mutation[12]. This mutation was one of the first documented in the US in the initial stages of the pandemic, after having initially circulated in Europe[13].

Selected Characteristics of SARS-CoV-2 Variants of Concern
Name
(Pangolin) 
Name
(Nextstrain) 
First Detected  Cases in
the US
Countries
Reporting
Cases
Key Mutations Transmissibility
Rate
B.1.1.7  20I/501Y.V1 United Kingdom Y 70
  • 69/70 deletion
  • 144Y deletion
  • N501Y
  • A570D
  • D614G
  • P681H
~50% increase 14,15
P.1  20J/501Y.V3 Japan/
Brazil
Y  >4
  • E484K
  • K417N/T
  • N501Y
  • D614G
Not determined
B.1.351  20H/501.V2 South Africa Y >30
  • K417N
  • E484K
  • N501Y
  • D614G
Not determined

Last Updated: Jan 27, 2021

References

  1. Horby P, Huntley C, Davies N et al. NERVTAG note on B.1.1.7 severity. New & Emerging Threats Advisory Group, Jan. 21, 2021. Retrieved from NERVTAG note on variant severityexternal icon.
  2. Public Health England. Investigation of novel SARS-CoV-2 variant: Variant of Concern 202012/01.202012/01. Technical briefing 3. 28 Dec 2020. Retrieved from Investigation of novel SARS-CoV-2 Variant: Variant of Concern 202012/01pdf iconexternal icon.
  3. *Tegally H, Wilkinson E, Giovanetti M, et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. MedRxiv 2020. doi: https://doi.org/10.1101/2020.12.21.20248640external icon.
  4. *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. doi: https://doi.org/10.1101/2021.01.25.427948external icon.
  5. National Institute of Infectious Diseases, Japan. (2021, January 12.) Brief report: New Variant Strain of SARS-CoV-2 Identified in Travelers from Brazil [Press release]. Retrieved from https://www.niid.go.jp/niid/en/2019-ncov-e/10108-covid19-33-en.htmlexternal icon.
  6. MN Department of Health. (2021, January 25). MDH lab testing confirms nation’s first known COVID-19 case associate with Brazil P.1 variant [Press release]. Retrieved from News release: MDH lab testing confirms nation’s first known COVID-19 case associated with Brazil P.1 variant (state.mn.us)external icon.
  7. *Faria NR, Claro IM, Candido D, et al. Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings. 12 Jan 2021. Retrieved from Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings – SARS-CoV-2 coronavirus / nCoV-2019 Genomic Epidemiologyexternal icon – Virological.
  8. *Resende PC, Bezerra JF, de Vasconcelos RHT, et al. Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020. 10 Jan 2021. Retrieved from Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020 – SARS-CoV-2 coronavirus / nCoV-2019 Genomic Epidemiology – Virologicalexternal icon.
  9. *Naveca F, de Costa C, Nascimento V, et al. SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil. Retrieved from SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil – SARS-CoV-2 coronavirus / nCoV-2019 Genomic Epidemiology – Virologicalexternal icon.
  10. *Bin Zhou, Tran Thi Nhu Thao, Donata Hoffmann, et al. SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility bioRxiv 2020.10.27 doi: https://doi.org/10.1101/2020.10.27.357558external icon.
  11. Volz E, Hill V, McCrone J, et al. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell 2021; 184(64-75). doi: https://doi.org/10.1016/j.cell.2020.11.020external icon.
  12. Korber B, Fischer WM, Gnanakaran S, et al. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2021; 182(812-7). doi: https://doi.org/10.1016/j.cell.2020.06.043external icon.
  13. Yurkovetskiy L, Wang X, Pascal KE, et al. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell 2020; 183(3): 739-1. doi: https://doi.org/10.1016/j.cell.2020.09.032external icon.
  14. *McCarthy KR, Rennick LJ, Namnulli S, et al. Natural deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. bioRxiv [Preprint posted online November 19, 2020] https://www.biorxiv.org/content/10.1101/2020.11.19.389916v1external icon.
  15. *Kemp SA, Harvey WT, Datir RP, et al. Recurrent emergence and transmission of a SARS-CoV-2 spike deletion ΔH69/V70. bioRxiv [Preprint posted online January 14, 2021] https://www.biorxiv.org/content/10.1101/2020.12.14.422555v4external icon .

*Non-peer-reviewed