The variant known as Delta or B.1.617.2 was first detected in India in December 2020 and became the most commonly reported variant in the country from mid-April 2021.
As of 19 of May 2021, the variant had been detected in 43 countries across 6 continents in
GISAID It has now been detected in 21 other countries, including the UK, US, Singapore and Australia.
In the UK, there has been a rapid increase in cases with this variant associated with travel to India and community transmission.
A modeling study predicts that there is a “realistic possibility” that B.1.617.2 is 50% more transmissible than B.1.1.7.
Variant is defined by 19R, (G142D), 156del, 157del, R158G, L452R, T478K, D614G, P681R, D950N mutations in the spike protein.
Several of these mutations may impact on immune responses directed towards the key antigenic regions of receptor binding protein (452 and 478) and deletion of part of the N terminal domain
This variant, known as Kappa, was first detected in India on 5 October, 2020.
The variant accounts for almost 70% of genomes submitted by India to GISAID. Most isolates sequenced by India originated from Maharashtra and West Bengal, but B.1.617 has been identified in several other states.
It has now been detected in 21 other countries, including the UK, US, Singapore and Australia.
This variant is defined by G142D, E154K, L452R, E484Q, D614G, P681R, Q1071H mutations in the spike protein.
E484Q and L452R mutations that have been linked to increased transmissibility and an ability to evade immune protection. E484Q mutation was found in B.1.351 (South Africa), P.1. (Brazil), and B.1.525/ B.1.526 variants. L452R mutation was also found in the California variant.
P681R mutation is located near the cleavage site between S1 and S2. This change may increase the infectivity of the virus particles by facilitating cleavage of the S precursor protein to the active S1/S2 configuration.
This variant was the first sublineage of B.1.617 variant to be detected in October 2020 in India.
This sublineage has remained relatively uncommon compared to the two other sublineages, B.1.617.1 and B.1.617.2.
Variant is defined by T19R, G142D, L452R, E484Q, D614G, P681R, D950N mutations in the spike protein.
A recent study showed that the hamsters infected with B.1.617.1 demonstrated increased body weight loss, higher viral load in lungs and pronounced lung lesions as compared to B.1 variant. Further studies will be required to confirm its disease severity.
It is not clear whether this variant enhances the disease severity.
Use of a live virus assay showed that the B.1.617.1 variant is 6.8-fold more resistant to neutralization by sera from COVID-19 convalescent and Moderna and Pfizer vaccinated individuals.
Despite this, a majority of the sera from convalescent individuals and all sera from vaccinated individuals were still able to neutralize the B.1.617.1 variant.
Protective immunity by the mRNA vaccines tested here are likely retained against the B.1.617.1 variant. This needs to be further evaluated by evaluating clinical data from vaccinated individuals.
In the U.K. trial, efficacy of 2-dose Pfizer vaccine against this variant was 87.9% (93.4% against B.1.1.7); 2-dose AstraZeneca showed 59.8% efficacy against this variant and 66.1% against B.1.1.7.
B.1.617 S protein-mediated entry was efficiently inhibited by Etesevimab (LY-CoV016), Imdevimab (REGN10987) and by a cocktail of Casirivimab (REGN10933) and Imdevimab.
B.1.617 was resistant against Bamlanivimab (LY-CoV555).
The current molecular tests detect most of the variants and thus are able to diagnose COVID-19 infection by such variants. Yet, the fine identification of the type of variants is still based on sequence analysis although multiplex PCR test are being evaluated.
Indeed, the current variants of concern show distinctive mutations in the spike protein. Due to such mutations, most diagnostic tests for COVID-19 have been designed by targeting not only the spike protein but also other conserved proteins. For example, molecular tests designed to detect multiple SARS-CoV-2 genes (i.e., multiplex reverse transcription polymerase chain reaction targeting ORF1ab, N, and E genes) are less susceptible to the effects of genetic variation than tests designed to detect a single gene. The FDA is also monitoring the potential effects of genetic variation in molecular tests that have received Emergency Use Authorization and provides information about the tests.
Overall, the precise characterization of the variants still relies on genomic sequencing analysis. For instance, CDC is currently increasing sequence surveillance to more than 6000 samples per week to efficiently monitor the variants of concerns and other emerging variants. COVID-19 caused by variants in the U.S. can be found here.