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SARS-CoV-2 lineage B.1.617

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Lineage B.1.617 is a lineage of SARS-CoV-2, the virus that causes COVID-19.[1] Analysis of samples from Maharashtra had revealed that compared to December 2020, there was an increase in the fraction of samples with the E484Q and L452R mutations.[2] Lineage B.1.617 has three sublineages according to the PANGO nomenclature:

History

The first B.1.617 genome sequence was submitted to GISAID in fall 2020 according to one source.[3] The team at PANGO behind manually curating the phylogenetic tree of SARS-CoV-2 noted the earliest sequence was from December 7, 2020. They proposed a new designation for the variant containing the mutations at the spike protein including G142D, L452R, E484Q, D614G, P681R among others and this variant went to be assigned PANGO lineage B.1.617 on 1 April 2021.[4] They revised the phylogenetic tree to include three sublineages of B.1.617 on 21 April 2021 after noticing that not all genome sequences being assigned by the PANGOLIN tool contained the same set of mutations.[5]

Up until mid-April 2021, India submitted the most B.1.617 genomes, followed in frequency by UK and the US. Based on genome information, lineage B.1.617 was first detected in the UK on 22 Feb 2021, and in the US on 23 Feb 2021.[3]

After detecting 77 cases of lineage B.1.617 in the UK in mid-April 2021, Public Health England designated the lineage as a variant under investigation.[6] In less than two months, the Delta variant would go on to become the dominant variant in the UK with researchers stating early evidence suggested there may be an increased risk of hospitalization for Delta compared to the previously dominant Alpha variant.[7]

Mutations

Novel Coronavirus SARS-CoV-2 'Spike' Protein

Here are some of the common mutations present in the spike protein of lineage B.1.617. Not all sublineages of B.1.617 share the same mutations:

  • L452R. The substitution at position 452, a leucine-to-arginine substitution, confers stronger affinity of the spike protein for the ACE2 receptor and decreased recognition capability of the immune system.[8][9] These mutations, when taken individually, are not unique to the variant; rather, their simultaneous occurrence is.[8][10] This mutation is present in all three sublineages of B.1.617.
  • T478K. The substitution at position 478, a threonine-to-lysine substitution, is only found in lineage B.1.617.2.[citation needed]
  • E484Q. The substitution at position 484, a glutamic acid-to-glutamine substitution, confers lineage B.1.617 stronger binding potential to the human ACE2 receptor, as well as better ability to evade hosts' immune systems in comparison to other variants. This mutation is not present in the B.1.617.2 genome.[11]
  • D614G. The substitution at position 614, an aspartic acid-to-glycine substitution, is shared with other highly transmissible lineages like B.1.1.7, B.1.351 and P.1.[12]
  • P681R. The substitution at position 681, a proline-to-arginine substitution, which, according to William A. Haseltine, may boost cell-level infectivity of the variant "by facilitating cleavage of the S precursor protein to the active S1/S2 configuration".[11] This mutation is present in all three sublineages of B.1.617.

References

  1. ^ "Lineage B.1.617". PANGO lineages. Retrieved 2021-06-12.
  2. ^ "Genome Sequencing by INSACOG shows variants of concern and a Novel variant in India". Press Information Bureau Government of India. 24 March 2021.
  3. ^ a b "Expert reaction to cases of variant B.1.617 (the 'Indian variant') being investigated in the UK". Science Media Centre. Retrieved 20 April 2021.
  4. ^ "Proposed new B.1 sublineage circulating in India #38". GitHub. Retrieved 2021-04-02.
  5. ^ "Potential sequences that should be included in B.1.617 #49". GitHub. Retrieved 2021-02-28.
  6. ^ "Confirmed cases of COVID-19 variants identified in UK". www.gov.uk. 15 April 2021. Archived from the original on 16 April 2021. This article contains OGL licensed text This article incorporates text published under the British Open Government Licence v3.0:
  7. ^ "Confirmed cases of COVID-19 variants identified in UK". www.gov.uk. 3 June 2021. Archived from the original on 4 June 2021. This article contains OGL licensed text This article incorporates text published under the British Open Government Licence v3.0:
  8. ^ a b Starr, Tyler N.; Greaney, Allison J.; Dingens, Adam S.; Bloom, Jesse D. (April 2021). "Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016". Cell Reports Medicine. 2 (4): 100255. doi:10.1016/j.xcrm.2021.100255. PMC 8020059. PMID 33842902.
  9. ^ Zhang, Wenjuan; Davis, Brian D.; Chen, Stephanie S.; Sincuir Martinez, Jorge M.; Plummer, Jasmine T.; Vail, Eric (6 April 2021). "Emergence of a Novel SARS-CoV-2 Variant in Southern California". JAMA. 325 (13): 1324–1326. doi:10.1001/jama.2021.1612. PMC 7879386. PMID 33571356.{{cite journal}}: CS1 maint: PMC embargo expired (link)
  10. ^ Koshy, Jacob (8 April 2021). "Coronavirus | Indian 'double mutant' strain named B.1.617". The Hindu. Retrieved 2021-04-19. Though these mutations have individually been found in several other coronavirus variants, the presence of both these mutations together have been first found in some coronavirus genomes from India.
  11. ^ a b Haseltine, William. "An Indian SARS-CoV-2 Variant Lands In California. More Danger Ahead?". Forbes. Retrieved 20 April 2021.
  12. ^ "SARS-CoV-2 variants of concern as of 3 June 2021". European Centre for Disease Prevention and Control. Archived from the original on 2021-06-03. {{cite web}}: |archive-date= / |archive-url= timestamp mismatch; 2021-06-11 suggested (help)
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