Indian SARS-CoV-2 variant has unique infection and immune escape strategy say researchers

By Sally Robertson, B.Sc.Jun 23 2021Reviewed by Emily Henderson, B.Sc.

Researchers in Japan have conducted a study suggesting that the B.1.617 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in India has evolved a unique strategy to facilitate infection and evade the immunity induced by vaccination or natural infection.

Indian COVID-19 Variant. Image Credit: oasisamuel/Shutterstock.com

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

The SARS-CoV-2 virus is the agent responsible for the coronavirus disease 2019 (COVID-19 ) pandemic that continues to threaten global public health and the worldwide economy.

Bioinformatic analyses revealed that the mutation P681R is highly conserved in the viral spike protein of the B.1.617 lineage. The spike protein mediates the initial stage of the infection process when its receptor-binding domain (RBD) attaches to the host cell receptor angiotensin-converting enzyme 2 (ACE2).

The team showed that the presence of P681R significantly enhanced the efficacy of viral fusion, promoted cell-to-cell infection, and was associated with the formation of prominent syncytia. Syncytia are multinucleated cells that arise through the fusion of uninuclear cells.

The researchers say the P681R-mediated kinetics of viral fusion may not only contribute to immune escape but also more severe disease among individuals exposed to SARS-CoV-2.

Our data suggest that the P681R mutation is a hallmark characterizing the virological phenotype of this newest variant of concern, which may be associated with viral pathogenicity,”

Kei Sato, University of Tokyo

A pre-print version of the research paper is available on the bioRxiv* server, while the article undergoes peer review.

More about the variants of concern that have emerged

Following identification of the original SARS-CoV-2 virus in Wuhan, China in late December 2019, a new strain harboring the spike mutation D614G quickly became predominant due to its increased infectivity, fitness, and transmissibility.

Since then, variants containing multiple mutations have emerged, at least five of which have been classified as variants of concern. These include the B.1.1.7 lineage that emerged in the UK, the B.1.351 lineage that arose in South Africa, and the P.1 (Brazil), B.1.427/429 (United States), and B.1.617.2 (India) lineages.

Studies have shown that B.1.1.7, B.1.351, P.1, and B.1.427/429 are differentially resistant to neutralizing antibodies (nAbs) derived from COVID-19 convalescents and vaccinees. Since the spike RBD is immunodominant, approximately 90% of the nAbs present in anti-SARS-CoV-2 sera target this domain.

The lineage that emerged in India contains a unique mutation

At the end of 2020, the emergence of B.1.617 in India was associated with a huge surge in COVID-19 prevalence, with the incidence of new SARS-CoV-2 infections peaking at 400,000 per day.

This lineage comprises three sublineages (B.1.617.1, B.1.617.2, and B.1.617.3) and sublineage B.1.617.2 has been categorized as the most recent variant of concern.

Importantly, Public Health England has suggested that B.1.617.2 may be associated with an increased risk of hospitalization, compared with the B.1.1.7 lineage.

A recent study also showed that the B.1.617.2 variant exhibits resistance to the nAbs elicited by vaccination.

Interestingly, a unique mutation – P681R – has been identified in the spike protein of the B.1.617 lineage that has not yet been identified in any other variants of concern.

“Because the P681R mutation is located in the proximity of the furin cleavage site (FCS) of the SARS-CoV-2 S protein, it is possible that this substitution affects viral replication dynamics and potentially determines the virological characteristics of the B.1.617 variants,” says the team.

What did the researchers do?

The researchers downloaded and analyzed 1,761,037 SARS-CoV-2 genomes from the Global Initiative on Sharing All Influenza Data (GISAID) database.

They found that the P681R mutation was highly conserved in B.1.617 and was the most representative mutation (99.3%) in this lineage.

Next, the team conducted experiments using Vero cells infected with either B.1.617.1, B.1.617.2, or a D614G-bearing B.1.1 isolate.

Sato and colleagues found that levels of viral RNA were 150 times lower following infection with B.1.617.1 and B.1.617.2, compared with B.1.1 infection.

However, infection with the B.1.617.1 and B.1.617.2 viruses formed syncytia that were 2.3 and 2.7 times larger, respectively, than those formed following B.1.1 infection.

The researchers say the findings show that the B.1.617 lineages form syncytia and favor cell-to-cell infection, compared with the D614G-containing B.1.1 virus.

The presence of P681R significantly increased spike cleavage

Western blotting of HIV-1-based pseudoviruses carrying the P681R mutation revealed that the presence of P681R significantly increased cleavage of subunit 2 of the SARS-CoV-2 spike protein, suggesting that the mutation facilitates furin-mediated spike cleavage.

Furthermore, neutralizing assays of sera obtained from vaccinees who received two doses of the Pfizer BioNTech COVID-19 vaccine revealed that a D614G/P681R pseudovirus was significantly more resistant to vaccine-induced nAbs than a D614G pseudovirus.

“Although the P681R mutation is not located in the RBD of the SARS-CoV-2 spike protein, it rendered resistance to nAbs targeting the RBD,” writes the team.

The B.1.617 lineage has acquired a unique strategy to facilitate infection

The researchers say the study suggests that the B.1.617 lineage has acquired a unique strategy to facilitate infection and evade antiviral immunity.

The findings show that the P681R mutation enhances the cleavage of SARS-CoV-2 spike, enhances viral fusion, and promotes cell-to-cell infection, says the team.

Switching of the viral infection mode by the P681R mutation may be associated with the severity of viral infection. SARS-CoV-2 variants harboring the P681R mutation should therefore be surveyed in-depth,”

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources