Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption

Abstract

COVID-19 patients transmitted SARS-CoV-2 to minks in the Netherlands in April 2020.Subsequently, the mink-associated virus (miSARS-CoV-2) spilled back over into humans.Genetic sequences of the miSARS-CoV-2 identified a new genetic variant known as "Cluster 5" that contained mutations in the spike protein. However, the functional properties of these "Cluster 5" mutations have not been well established. In this study, we found that the Y453F mutation located in the RBD domain of miSARS-CoV-2 is an adaptive mutation that enhances binding to mink ACE2 and other orthologs of Mustela species without compromising, and even enhancing, its ability to utilize human ACE2 as a receptor for entry.Structural analysis suggested that despite the similarity in the overall binding mode of SARS-CoV-2 RBD to human and mink ACE2, Y34 of mink ACE2 was better suited to interact with a Phe rather than a Tyr at position 453 of the viral RBD due to less steric clash and tighter hydrophobic-driven interaction. Additionally, the Y453F spike exhibited resistance to convalescent serum, posing a risk for vaccine development. Thus, our study suggests that since the initial transmission from humans, SARS-CoV-2 evolved to adapt to the mink host, leading to widespread circulation among minks while still retaining its ability to efficiently utilize human ACE2 for entry, thus allowing for transmission of the miSARS-CoV-2 back into humans. These findings underscore the importance of active surveillance of SARS-CoV-2 evolution in Mustela species and other susceptible hosts in order to prevent future outbreaks.

Characterization of entry pathways, species-specific ACE2 residues determining entry, and antibody neutralization evasion of Omicron BA.1, BA.1.1, BA.2, and BA.3 variants

“…While S373P and Q498R substitutions had no significant effect compared to D614G, the mink-adapted Y453F substitution led to enhanced usage of African green monkey, ferret, Chinese hamster, Syrian golden hamster, white-tailed deer, and swine ACE2 receptors. A previous report has indicated the Y453F substitution enhanced spike interaction with Mustela species ACE2 orthologs, including minks, ferrets and stouts, while not compromising human ACE2 usage (Figure 5I, Table 1) 40 . Our findings extend this report and provide further insights into the effect of Y453F substitution for other species' ACE2.…”

“…Substitutions in the RBD have been linked to SARS-CoV-2 adaptation to new hosts, such as ferrets 39 , mouse 33 , mink 40 and white-tailed deer 41 . The ongoing dominance and circulation of Omicron VOCs pose a significant risk for reverse zoonosis and spill back into the humans.…”

The spike glycoprotein of highly pathogenic human coronaviruses: structural insights for understanding infection, evolution and inhibition

“…A cryo‐EM study of this variant's S protein found closed, one RBD ‘up’ and two RBD ‘up’ states [43]. Structural analysis indicated that the Y453F substitution in the RBD is a species‐specific adaptive mutation, increasing binding to mink ACE2 [43,104]. This mutated virus strain circulated among the farmed minks, eventually leading to the first known animal‐to‐human transmission of SARS‐CoV‐2 [105].…”

Inhibition of SAR S-CoV-2 infection and replication by lactoferrin, MUC1 and α-lactalbumin identified in human breastmilk

“…MUC1 encoding from Ala23 to Gly167 is expressed with a Fc tag at the C-terminus and purchased from Novoprotein (China). replacing viral nucleocapsid gene (N) were made as previously described 7 . Caco-2-N cells were infected with the trVLP to amplify viruses 28 .…”

“…In addition, the ongoing pandemic has resulted in several viral variants [3][4][5] . These variants may potentially alter viral transmission, pathogenicity, efficacy of drug treatment as well as the binding capacity of vaccine elicited antibodies [6][7][8][9] . In this situation, it raises the need of several effective drugs with low toxicity to treat this disease.…”