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SARS-CoV-2: Origin, Intermediate Host and Allergenicity Features and Hypotheses.

Yuyi Huang1, Junmou Xie1, Yuhe Guo1

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Summary

This study identifies rodents as potential intermediate hosts for SARS-CoV-2 and SARS-CoV, based on spike protein analysis. It also reveals high binding affinities between viral spike proteins and human leukocyte antigen (HLA) molecules, indicating potential allergenicity.

Keywords:
MHC binding affinitySARS-CoV-2allergenicityearly immunizationintermediary reservoirself-limitationspike proteinspontaneous mutation

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Area of Science:

  • Virology
  • Immunology
  • Epidemiology

Background:

  • The emergence of SARS-CoV-2 (causing COVID-19) and its relation to SARS-CoV necessitates understanding viral origins and host interactions.
  • Phylogenetic analysis is crucial for tracing viral evolution and identifying natural and intermediate hosts.

Purpose of the Study:

  • To investigate potential intermediate hosts for SARS-CoV-2 and SARS-CoV.
  • To evaluate the allergenicity of SARS-CoV-2 and SARS-CoV spike proteins through HLA binding affinities.
  • To explore the influence of climate factors on coronavirus virulence and propose prophylactic strategies.

Main Methods:

  • Phylogenetic analysis of viral spike proteins to determine evolutionary relationships.
  • Bioinformatic analysis of spike protein fragments for host specificity.
  • Calculation of binding affinities between HLA molecules and viral spike proteins.
  • Correlation analysis of climate data with outbreak locations and timing.

Main Results:

  • Phylogenetic analysis suggests bats as the natural origin of SARS-CoV-2.
  • Rodents (Rattus norvegicus and Mus musculus) are indicated as potential intermediate hosts.
  • Both SARS-CoV-2 and SARS-CoV spike proteins exhibit super-high binding affinities to fourteen HLA class I and II molecules.
  • A potential infection rate of 7.36% (Chinese) and 4.78% (Americans) is estimated for individuals with high-affinity HLA alleles.
  • Common climatic factors (high temperature, low precipitation) at outbreak sites may promote viral virulence.

Conclusions:

  • Rodents likely serve as intermediate hosts for SARS-CoV-2 and SARS-CoV.
  • The high HLA binding affinities suggest significant allergenicity and potential for severe disease.
  • Climate factors may play a role in the evolution of more virulent coronaviruses.
  • Early immunization with allergenically-engineered viruses, alongside surveillance, is proposed as a prophylactic measure.