SARS-CoV-2 variant B.1.617 may be more transmissible and pathogenic due to spike cleavage

By Dr. Tomislav Meštrović, MD, Ph.D. May 31 2021

In a new research paper currently available on the bioRxiv* preprint server, a research group from the United Kingdom (UK) provides experimental evidence that B.1.617 lineage of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) – also known as the Indian variant of concern – shows enhanced cleavage of spike glycoprotein by furin, which can enhance its transmissibility and pathogenic traits.

Study: The SARS-CoV-2 variants associated with infections in India, B.1.617, show enhanced spike cleavage by furin. Image Credit: NIAID

The spike glycoprotein of SARS-CoV-2, a causative agent of the unremitting coronavirus disease 2019 (COVID-19) pandemic, initially contained a suboptimal cleavage site at the S1/S2 junction necessary for efficient transmission, pathogenicity and viral replication.

Naturally, this opened the door for the potential evolution of SARS-CoV-2 variants with increased transmission due to a more optimized cleavage site. One of initial examples was a UK variant (B.1.1.7) which harbors a P681H mutation that boosts post-translational S1/S2 cleavage during viral budding.

Recently, the B.1.617 variant emerged in India, concurrent with a significant disease burden across the whole country. Early evidence implied that it is highly transmissible, with its sublineages containing a panoply of spike glycoprotein mutations – including the P681R substitution projected to further optimize this furin cleavage site.

This is why a research group from the UK, led by Dr. Thomas P. Peacock from the Department of Infectious Disease at Imperial College London, decided to consider carefully the impact of mutation P681R on cleavage site S1/S2.

Assessing cleavage properties

Initially, these researchers isolated several B.1.617 SARS-CoV-2 variants and compared their S1/S2 cleavage patterns to that of a previously circulating viral strain that belonged to the lineage B.1.238, known to contain only D614G mutation.

Furthermore, in order to characterize which amino change in the spike glycoprotein of B.1.617 can be linked to its enhanced cleavage, the group has generated pseudovirus carrying the SARS-CoV-2 full B.1.617.1 spike glycoprotein and compared it to pseudovirus with D614G spike (here considered as wild-type virus).

Finally, they have performed specific assays to appraise whether the optimized cleavage site characteristic for B.1.617 spike glycoprotein enables improved cleavage directly by furin. More specifically, they have measured the propensity of recombinant furin to cleave fluorescently labeled peptides corresponding to the S1/S2 cleavage site of SARS-CoV-2.

Variant vs. wild type virus

The study has shown that spike glycoproteins of B.1.617 variant were all more highly cleaved (i.e., more than 50% cleaved) in comparison to the control virus (approximately 33% cleaved), with a higher proportion of cleaved S2 and a lower proportion of detectable full-length spike glycoprotein.

And while spike glycoprotein of a wild-type virus exhibited both full length and cleaved protein, B.1.617.1 showed significantly enhanced cleavage (i.e., up to 95%), coupled with almost a total lack of a full-length protein. This implies P681R alone is responsible for the enhanced cleavage of spike glycoprotein observed in the B.1.617 lineage.

More specifically, P681R substantially enhanced the ability of furin to cleave the peptide, reinforcing the notion that the arginine substitution can be considered responsible for the enhanced cleavage of the B.1.617 spike glycoprotein.

The need for close monitoring

In conclusion, this study has shown that enhanced S1/S2 cleavage observed in B.1.617 and B.1.1.7 SARS-CoV-2 variants (which both contain P681H mutation) may be contributing considerably to their increased transmissibility and even pathogenicity.

“As well as B.1.1.7 and B.1.617, several other emerging lineages contain mutations in the furin cleavage site”, say the authors in this bioRxiv paper. “We would advise that these lineages be kept under close monitoring for any early evidence of more rapid transmission or higher pathogenesis,” they add.

In any case, further research in this area may enable us to recognize more transmissible and potentially more fatal SARS-CoV-2 variants of concern rather swiftly, which may also help us to devise better mitigation strategies.