- This variant was first detected in Nigeria and UK in December 2020.
- It has been seen in other countries, including U.S., Canada, Denmark, Britain, France, Belgium, Spain, Finland, Nigeria, Ghana, Jordan, Australia and Singapore.
- As of Feb. 17, 46 and 12 cases of the variant had been confirmed by gene sequencing in the UK and US, respectively.
- Biological characteristics of this new variant, such as infectivity, are still unknown. So, for now, it is a “variant under investigation.”
- The variant is defined by 3 mutations: E484K, Q677H, and F888L.
- Other alterations make it similar to the UK variant (B.1.7.7).
- A New Covid-19 Variant From Nigeria Raises Increased Concerns For Containment And Vaccination
- Forbes, USA, February 24, 2021
- Another new coronavirus variant seen in the UK
BBC, UK, February 16, 2021
- New Covid variant with potentially worrying mutations found in UK
The Guardian, February 15, 2021
- It was first detected in the US on October 23.
- Between 01 Dec 2020 and 19 Jan 2021, it rose to represent 27.8% and 11.3% of all SARS-CoV-2 genomes sequenced from Louisiana and New Mexico, respectively.
- The variant is defined by Q677P mutation.
- The proximity of this position to the polybasic cleavage site at the S1/S2 boundary are consistent with its potential functional relevance during cell entry
- Biological function of this variant is unknown.
- Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677
MedRxiv, February 14, 2021
Structure of SARS-CoV-2 Spike protein denoting location of Q677P within a disordered loop adjacent to the polybasic (furin) cleavage site (Cited from https://www.medrxiv.org/content/10.1101/2021.02.12.21251658v2.full.pdf).
- This variant was first detected in samples collected in New York City in November.
- On study found a steady increase (12.3%) in the detection rate from late December to mid-February in New York.
- Detection of B.1.526 variant is scattered in the Northeast of US.
- The variant has L5F, T95I, D253G, E484K, D614G, and A701V mutations in the spike protein.
- D253G resides in the antigenic supersite within the N-terminal domain, which is a target for neutralizing antibodies.
- The impact of the E484K mutation on antibody neutralization: neutralizing activities of convalescent plasma or vaccinee sera are lower by 7.7-fold or 3.4-fold, respectively, against the E484K variant (refer to the publication below).
- Evaluation of susceptibility of variants identified through global surveillance and in subjects treated with bamlanivimab is ongoing. Pseudovirus harboring the E484K substitution had reduced susceptibility to bamlanivimab. E484K reduced bamlanivimab neutralization >2000-fold.
- Fauci says Biden administration is taking new Covid variant in New York ‘very seriously’
CNBC, USA, March 1, 2021
- A New Coronavirus Variant Is Spreading in New York, Researchers Report
NYT, February 24, 2021
- A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York
MedRxiv, February 25, 2021
- The variant was first detected in Peru in December 2020 and currently is causing eighty percent of new cases of COVID-19 in Peru.
- The variant has become a dominant variant in South America and found in more than 30 countries.
- The variant has been categorized as a “variant of interest” by the World Health Organization.
- The researchers found that while pseudotyped virus expressing the C.37 viral spike protein was less susceptible to vaccine-elicited neutralizing antibodies. However, the reduction in neutralization was minor.
- Viral transmissibility and severity have not been well characterized yet.
- The variant contains a novel deletion (S:Δ247-253, located at the N-terminal domain) and G75V, T76I, D614G, L452Q, F490S, and T859N mutations in the Spike gene.
- Mutations L452Q and F490S locate in the Spike protein’s receptor-binding domain.
- L452R is known to be associated with increased affinity for the ACE2 receptor.
- F490S has been associated with reduced in vitro susceptibility to antibody neutralization.
- The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America
Medrxiv, July 3, 2021
- The variant was first identified in Colombia in January 2021, and there have been sporadic reports of cases and outbreaks in South America and Europe.
- While the global prevalence of Mu among sequenced Covid-19 cases has fallen below 0.1%, its prevalence has consistently increased in Colombia and Ecuador, around 39% and 13% of infections, respectively.
- The variant has a number of mutations: P681H, E484K and K417N. P681H is found in the Alpha variant and has been linked to enhancing viral transmission. E484K and K417N mutations may help the virus evade immunity defense. WHO is monitoring this variant’s ability to evade vaccine protections.
- A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality
MedRxiv, May 10, 2021
- The variant known as Epsilon was first detected in California, USA
- It has two distinct lineages, B.1.427 and B.1.429, in clade 20C
- The most recent common ancestor emerged on May 20, 2020 (95% highest posterior. The branches giving rise to the B.1.427 and B.1.429 lineages were predicted to have diverged In July and June, respectively.
- Increased frequency of detection from 0% to >50% of sequenced cases from September 2020 to January.
- Each lineage rising in parallel in California as well as in multiple other states.
- An estimated increase in transmission rate of the B.1.427/B.1.429 variant relative to circulating non-B.1.427/B.1.429 lineages was 18.6-24.2%.
- A moderate resistance to neutralization by antibodies elicited by prior infection (4.0 to 6.7-fold) or vaccination (2-fold).
- One person who tested positive for CAL.20C in January of this year had previously been infected with a different SARS-CoV-2 virus, in July 2020.
- B.1.429 variant is defined by 5 mutations: I4205V in ORF1a; D1183Y in ORF1b: S13I, W152C and L452R in the S protein.
- B.1.427 variant is defined by L452R mutation in the S protein.
- L452R mutation in the S protein locates in the receptor binding domain. L452R was first detected in minks in Denmark (March 2020).
- L452R mutation may stabilize the interaction between the spike protein and its human ACE2 receptor and thereby increase infectivity.
- Emergence of B.1.429 containing additional mutation (Q677H) in the spike protein.
- L452R mutation resulted in reduced or abolished neutralizing activity.
- Detection of the recurrent substitution Q677H in the spike protein of SARS-CoV-2 in cases descended from the lineage B.1.429
Virological, March 19, 2021
- Transmission, Infectivity, and Antibody Neutralization of an Emerging SARS-CoV-2 Variant in California Carrying a L452R Spike Protein Mutation.
BioRxiv, March 9, 2021
- Emergence of a Novel SARS-CoV-2 Variant in Southern California.
JAMA, February 11, 2021
- The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity.
Cell, July 17, 202