New Variants


Last updated: 2020 Dec 30
Topic of Interest
Key Features
Reference
Date
Comments
Initial name VUI 202012/01 A UK government [Public Health England] news release 12/14/2020 First (01) 'Variant (of conern) Under Investigation' (VUI) in the 12th month of 2020, following detection of faster spreading lineage of Sars-Cov-2
Current name 1 VOC 202012/01 An article from the UK government organization, Public Health England, titled, Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01 12/21/2020 Confirmed 'Variant Of Concern' (VOC) identified in the 12th month of 2020, following detection of faster spreading lineage of Sars-Cov-2
Current name 2 B.1.1.7 Article written on behalf of COVID-19 Genomics Consortium UK 12/20/2020 Naming based on the method described beforecin an article in Nature Microbiology journal (July 2020)
Epidemiological The new variant can spread (~71%) faster than other SARS-CoV-2 virus variants currently circulating in the UK NERVETAG meeting minutes 12/21/2020 R-value for B.1.1.7 seems to be 1.57 or 1.72 (R is the number of other individuals that one infected person can pass on a virus to, the number for other lineages seems to be '<'1)
DNA/protein sequence Unusually large number of mutations noticed: 13 non-synonymous mutations, 4 deletions and 6 synonymous mutations. This includes 4 mutations (of which 1 is a deletion) in Orf1ab, 8 (2 deletions)in the spike gene, 3 (a stop codon) in Orf8 and 1 in the N gene. The latter include the following ones in the spike protein: HV 69-70del, Y145 del, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H UK reports new variant, termed VUI 202012/01 - GISAID [https://www.gisaid.org/references/gisaid-in-the- [news/uk-reports-new-variant-termed-vui-20201201/ ] and an article from Public Health England: Investigation of novel SARS-COV-2 variant, Variant of Concern 202012/01 12/20/2020 There is evidence that one mutation, D614G, may confer increased ability to spread more quickly than the wild-type (a comment in CDC report dated 30 Dec 2020)
Structure N501Y is likely to likely to influence the structure and function if the spike protein. Y145del is where some antibodies like neutralizing 4A8 bind, and this and other deletions may also be important. The effect of other mutations is less clear. An early Q27stop codon in orf8 could be relevant (orf8 deletion known to result in reduced capacity of the virus). GISAID in the news 12/20/2020 While homology modelling studies have indicated key differences in some of the proteins, cumulative influence of the mutations in the spike protein or other proteins is yet to be studied.
Patholophysiology No significant differences noticed yet If there were drastic enhancements or reductions in the pathophysiological aspects, they would have been probably noticed by now.
Influence on vaccination Vaccines are likely to be effective Emerging SARS-Cov-2 variants (an article in CDC website) 12/30/2020 Whereas the mutations in viruses can indeed make vaccines ineffective, the number of mutations in SARS-Cov-2 do not seem to be high enough. Hence, current vaccines may work. But the capacity of vaccines to prevent infection by new variants has to be tested.
Impact of diagnostics Existing rapid antigen tests and RT-qPCR tests for SARS-Cov-2 are likely to detect the new variant UK Govt. press release   Emerging SARS-Cov-2 variants 12/23/2020 Some of the primers used in RT-qPCR-based kits would not work. In fact, initial identification of the new variant was made due to the failure to detect primers that spanned the deleted nucleotides. But then, most kits use multiple primer-pairs. Similarly antigen testing kits seem to use polyclonal antibodies, hence work.
Geographical B.1.1.7 is first detected in UK. A variant (501Y.V2 or B.1.351) in South Africa shares some of the mutations of B.1.1.7, while Nigeria has witnessed a different variant CDC website 12/30/2020 Multiple reports indicate the spread of B.1.1.7 to more than countries by 1st January 2021. The South African variant B.1.351 also seems to be spreading faster than other variants.


Articles
A UK government [Public Health England] news release
An article from the UK government organization, Public Health England, titled, Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01
Article written on behalf of COVID-19 Genomics Consortium UK
NERVETAG meeting minutes
UK reports new variant, termed VUI 202012/01 - GISAID
An article from Public Health England: Investigation of novel SARS-COV-2 variant, Variant of Concern 202012/01
An article from Public Health England: Investigation of novel SARS-COV-2 variant, Variant of Concern 202012/01An article in CDC website: Emerging SARS-Cov-2 variants
A UK Govt. press release