SARS-CoV-2 Delta variant: a new potential threat

SARS-CoV-2 Delta variant: a new potential threat

The fast-spreading Delta variant (B.1.617.2) of SARS-CoV-2 is crumbling the precious progress against the COVID-19 pandemic, even in countries that seemed to have the corona infection under control. With 60% more transmissibility, Delta variant is considered as the most hypertransmissible contagious variant identified to date and reported to cause more severe illness than its original counterpart. Having spread to at least 90 countries, the Delta variant is fueling recurring outbreaks around the globe and prompting new lockdowns.

What is the Delta variant?

SARS-CoV-2 Delta variant is a variant of lineage B.1.617. It was first detected and reported in India in late 2020. The Delta variant contains at least 23 mutations in its genome compared to the original SARS-CoV-2 strain. Of the several other mutations in the Delta genome, three substitutions in the spike protein - T478K, P681R and L452R- are of special concern.

In T478K mutation the substitution occurs from the residue threonine (T) to lysine (L). In P681R mutation the substitution from proline (P) to arginine (R) results in boosting cell-level infectivity. In L452R mutation the substitution of leucine (L) to arginine (R) confers much stronger affinity of the spike protein for the ACE-2 receptor.

The three neutral amino acids are substituted with three positively charged amino acids contributing to the overall increase to the charge distribution of the spike protein. This makes the protein change its shape and dramatically affect the interactions with human ACE-2 receptors, which cause stronger binding and increasing cell entry efficiency.

Why is the Delta variant of special concern?

SARS-CoV-2 Delta variant consists of three important but most dangerous mutations. Individual mutations are not so unique to SARS-CoV-2 virus, but their simultaneous occurrence in a single variant made the Delta variant deadlier. The sequential series of mutations contribute to the overall change in conformation to the spike protein and make it more favorable to interact and bind with the ACE-2 receptor. Therefore, the variant increases its transmissibility and may potentially escape the antibody neutralization by our immune system, causing more severe infection. People with complete vaccination against COVID-19 are still shielded to some extent, but those who are not may face more dangerous consequences of the Delta variant.

How effective are vaccines against the Delta variant?

The Vaccine is the most effective tool to counter COVID-19 as it remains potent, preventing severe illness and deaths even against the mutants. A study published in The Lancet showed that the DNA-based Vaxzevria vaccine developed by the University of Oxford and AstraZeneca has 60% efficacy in preventing illness from the delta variant, while the other vaccine by Pfizer/BioNTech has 79% efficacy. Both vaccines were shown to be effective in preventing illness related hospitalizations from the delta variant.

A recent study published in a preprint server bioRxiv claimed that the single-shot Janssen COVID-19 vaccine generates strong, persistent protection against delta superspreader and other highly prevalent variants. The other mRNA vaccine developer Moderna announced the outcome of their new lab-based study showing the vaccine produced promising protection against the delta variant including others currently circulating.


  • The Lancet
  • Science journal
  • CoVariants
  • Johnson & Johnson updates
  • Pfizer press release