OmniVira

Literature detail

Altered hACE2 binding affinity and S1/S2 cleavage efficiency of SARS-CoV-2 spike protein mutants affect viral cell entry.

Ke Wang1,2,3 Yu Pan4 Dianbing Wang4 Ye Yuan4 Min Li4 Yuanyuan Chen4 Lijun Bi4 Xian-En Zhang1,2,5
Affiliations 5 institutions
  1. National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
  2. Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China
  3. University of Chinese Academy of Sciences, Beijing, 100101, China.
  4. National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
  5. University of Chinese Academy of Sciences, Beijing, 100101, China. Electronic address: [email protected].
PMID 37343929 2023 Virol Sin eng ppublish
PubMed DOI Browse context

Article

Publication summary

SARS-CoV-2 variants are constantly emerging, hampering public health measures in controlling the number of infections. While it is well established that mutations in spike proteins observed for the different variants directly affect virus entry into host cells, there remains a need for further expansion of systematic and multifaceted comparisons. Here, we comprehensively studied the effect of spike protein mutations on spike expression and proteolytic activation, binding affinity, viral entry efficiency and host cell tropism of eight variants of concern (VOC) and variants of interest (VOI). We found that both the full-length spike and its receptor-binding domain (RBD) of Omicron bind to hACE2 with an affinity similar to that of the wild-type. In addition, Alpha, Beta, Delta and Lambda pseudoviruses gained significantly enhanced cell entry ability compared to the wild-type, while the Omicron pseudoviruses showed a slightly increased cell entry, suggesting the vastly increased rate of transmission observed for Omicron variant is not associated with its affinity to hACE2. We also found that the spikes of Omicron and Mu showed lower S1/S2 cleavage efficiency and inefficiently utilized TMPRSS2 to enter host cells than others, suggesting that they prefer the endocytosis pathway to enter host cells. Furthermore, all variants' pseudoviruses we tested gained the ability to enter the animal ACE2-expressing cells. Especially the infection potential of rats and mice showed significantly increased, strongly suggesting that rodents possibly become a reservoir for viral evolution. The insights gained from this study provide valuable guidance for a targeted approach to epidemic control, and contribute to a better understanding of SARS-CoV-2 evolution.

Binding affinity Host-tropism Omicron SARS-CoV-2 Variants of Concern (VOC) Viral entry COVID-19 Animals Humans Mice Mutation Rats SARS-CoV-2 Spike Glycoprotein, Coronavirus Virus Internalization SARS-CoV-2 variants spike protein, SARS-CoV-2

Structured evidence records

Evidence records

6 total
Receptor Usage 3 records
Receptor Usage Extraction confidence 0.95
Key finding

The Omicron variant spike and its RBD bind human ACE2 with similar affinity to the wild-type SARS-CoV-2.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

We found that both the full-length spike and its receptor-binding domain (RBD) of Omicron bind to hACE2 with an affinity similar to that of the wild-type.

Method
binding affinity assay
Receptors
hACE2
Receptor Usage Extraction confidence 0.95
Key finding

Omicron and Mu variant spikes showed reduced use of the TMPRSS2-mediated entry pathway and preferentially used endocytosis for cell entry.

Virus
SARS-CoV-2
Host
host cells
Location
Not specified
Supporting text

The spikes of Omicron and Mu showed lower S1/S2 cleavage efficiency and inefficiently utilized TMPRSS2 to enter host cells than others, suggesting that they prefer the endocytosis pathway to enter host cells.

Method
cell-entry assay
Host factors
TMPRSS2
Receptor Usage Extraction confidence 0.95
Key finding

SARS-CoV-2 variants gained the ability to use animal ACE2 receptors, with rat and mouse ACE2 supporting significantly increased cell entry.

Virus
SARS-CoV-2
Host
Rattus Mus
Location
Not specified
Supporting text

All variants' pseudoviruses we tested gained the ability to enter the animal ACE2-expressing cells. Especially the infection potential of rats and mice showed significantly increased.

Method
pseudovirus assay
Receptors
animal ACE2
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.70
Key finding

Comparative analysis of spike and receptor-binding domain mutations among eight SARS-CoV-2 variants showed altered hACE2 binding and S1/S2 cleavage efficiencies, elucidating evolutionary changes affecting viral entry and host range.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

Here, we comprehensively studied the effect of spike protein mutations on spike expression and proteolytic activation, binding affinity, viral entry efficiency and host cell tropism of eight variants of concern (VOC) and variants of interest (VOI). We found that both the full-length spike and its receptor-binding domain (RBD) of Omicron bind to hACE2 with an affinity similar to that of the wild-type.

Genes or proteins
spike; receptor-binding domain; S1/S2 cleavage site
Analysis methods
comparative genomic analysis
Host Range Experiment 1 records
Host Range Experiment Extraction confidence 0.90
Key finding

SARS-CoV-2 variants' pseudoviruses could enter cells expressing animal ACE2, with particularly increased entry efficiency for rat and mouse ACE2, indicating expanded host range potential toward rodents.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

Furthermore, all variants' pseudoviruses we tested gained the ability to enter the animal ACE2-expressing cells. Especially the infection potential of rats and mice showed significantly increased, strongly suggesting that rodents possibly become a reservoir for viral evolution.

Method
pseudovirus assay; cell-entry assay
Experimental system
pseudovirus assay
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.95
Key finding

Spike protein mutations in SARS-CoV-2 variants altered hACE2 binding affinity and S1/S2 cleavage efficiency, changing cell entry pathways and enabling infection of rodent ACE2-expressing cells.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

We found that both the full-length spike and its receptor-binding domain (RBD) of Omicron bind to hACE2 with an affinity similar to that of the wild-type. In addition, Alpha, Beta, Delta and Lambda pseudoviruses gained significantly enhanced cell entry ability compared to the wild-type, while the Omicron pseudoviruses showed a slightly increased cell entry. We also found that the spikes of Omicron and Mu showed lower S1/S2 cleavage efficiency and inefficiently utilized TMPRSS2 to enter host cells than others. Furthermore, all variants' pseudoviruses we tested gained the ability to enter the animal ACE2-expressing cells.

Genes or proteins
spike; RBD
Receptors
hACE2; ACE2
Host factors
TMPRSS2
Mechanism types
receptor_binding; cell_entry; tissue_tropism; polymerase_activity