The SARS-CoV-2 Y453F mink variant displays a striking increase in ACE-2 affinity but does not challenge antibody neutralization

Abstract

SARS-CoV-2 transmission from humans to animals has been reported for many domesticated species, including cats, dogs and minks. Identification of novel spike gene mutations appearing in minks has raised major concerns about potential immune evasion and challenges for the global vaccine strategy. The genetic variant, known as “cluster-five”, arose among farmed minks in Denmark and resulted in a complete shutdown of the world’s largest mink production. However, the functional properties of this new variant are not established. Here we present functional data on the Y453F cluster-five receptor-binding domain (RBD) and show that it does not decrease established humoral immunity or affect the neutralizing response in a vaccine model based on wild-type RBD or spike. However, it binds the human ACE-2 receptor with a four-fold higher affinity suggesting an enhanced transmission capacity and a possible challenge for viral control.

Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants

“…7). Thus, the complex structure reported here provides the molecular explanation why Mink-Y453F RBD demonstrated an increased binding affinity for hACE2 when compared to WT RBD, which is observed in this and previous studies 20,21 .…”

“…Although we and other groups found a higher binding affinity of Mink-Y453F RBD to hACE2 compared with WT RBD 20,21 , it has been reported that the OH group of RBD Y453 is involved in direct interaction with hACE2 H34 in the cryo-electron microscopy (cryo-EM) complex structure of full-length hACE2 bound to RBD and B 0 AT1 (with the resolution of 2.9 Å) 24 . Interestingly, this interaction was not observed in the crystal complex structures of the hACE2 ectodomain bound to RBD (PDB: 6LZG and 6M0J) (with the resolution of 2.5 Å) or bound to Mink-Y453F RBD in this study (with the resolution of 2.4 Å).…”

“…Concentrated supernatant containing hACE2-mFc or miACE2-mFc protein was captured on the chip using this immobilized antibody. Serially diluted WT RBD (12.5, 25, 50, 100, 200 nM), Alpha RBD and Mink-Y453F RBD (3.125, 6.25, 12.5, 25, 50 nM), Beta RBD, Gamma RBD, and Mink-N501T RBD (6.25, 12.5, 25, 50, 100 nM), Mink-F486L RBD (25,50,100,200, 400 nM), RBD K417N and RBD K417T (20,40,80,160, 320 nM), RBD N501Y/E484K (0.5, 1, 2, 4, 8 nM), RBD N501Y/K417N (4, 8, 16, 32, 64 nM), RBD N501Y/K417T (2, 4, 8, 16, 32 nM), and RBD E484K (5, 10, 20, 40, 80 nM) were flowed over the chip to evaluate hACE2 binding. Various concentrations of WT RBD (2.5, 5, 10, 20, 40 μM), Mink-Y453F RBD (40, 80, 160, 320, 640 nM), Mink-F486L RBD (160, 320, 640, 1280, 2560 nM), and Mink-N501T RBD (320, 640, 1280, 2560, 5120 nM) were also used to evaluate miACE2 binding.…”

The Emergence and Spread of Novel SARS-CoV-2 Variants

“…Cluster 5 (also known as “ΔFVI-spike”): Some researchers found that mutation Y453F in the RBD of S protein of this variant did not reduce existing humoral immunity or affect the neutralization response, but it increased transmissibility due to its enhanced affinity with ACE2 ( 42 ).…”

Neutralising antibody escape of SARS‐CoV‐2 spike protein: Risk assessment for antibody‐based Covid‐19 therapeutics and vaccines

“…It does not decrease established humoural immunity or affect the neutralising response in a vaccine model based on wild‐type RBD or Spike. However, it binds the human ACE‐2 receptor with a fourfold higher affinity suggesting an enhanced transmission capacity 130 . Following the lockdown and mass‐testing, Danish State Serum Institute (SSI) announced on 19 November 2020 that Cluster 5 in all probability had become extinct.…”