IN SILICO ANALYSIS OF CROSS-SPECIES SEQUENCE VARIABILITY IN HOST INTERFERON ANTIVIRAL PATHWAY PROTEINS AND SARS-COV-2 SUSCEPTIBILITY

In Silico Analysis of Cross-Species Sequence Variability in Host Interferon Antiviral Pathway Proteins and SARS-CoV-2 Susceptibility

In Silico Analysis of Cross-Species Sequence Variability in Host Interferon Antiviral Pathway Proteins and SARS-CoV-2 Susceptibility

Blog Article

Abstract


The interferon (IFN) signaling pathway plays a crucial role in the innate immune response against viral infections, including SARS-CoV-2. However, host susceptibility to SARS-CoV-2 varies across species, potentially due to differences in key antiviral pathway proteins. This study employs in silico analysis to examine sequence variability in interferon-stimulated genes (ISGs) and other antiviral effectors across multiple species. We identify conserved and divergent residues in IFN-related proteins, analyze their impact on protein function, and evaluate their potential contribution to species-specific differences in SARS-CoV-2 susceptibility. These findings provide insight into host-pathogen interactions and may inform future strategies for zoonotic virus surveillance and intervention.



Introduction


SARS-CoV-2, the causative agent of COVID-19, exhibits a broad host range, with varying levels of susceptibility among different species. The ability of a virus to establish infection depends on multiple factors, including host cell receptors, viral replication machinery, and the antiviral immune response. The interferon (IFN) pathway is a key component of innate immunity, activating interferon-stimulated genes (ISGs) that inhibit viral replication. However, sequence variability in IFN-related proteins may influence the effectiveness of the antiviral response, impacting species susceptibility to SARS-CoV-2.


This study employs bioinformatics approaches to analyze sequence conservation and divergence in key IFN antiviral proteins across different species. Understanding these variations may help identify genetic factors influencing host susceptibility and inform the development of antiviral strategies.



Methods


1. Selection of Host Species and Protein Targets



  • Representative species were selected based on known differences in SARS-CoV-2 susceptibility, including humans, primates, rodents, bats, and domestic animals.

  • Key IFN pathway proteins analyzed include:

    • Interferon regulatory factors (IRFs) – IRF3, IRF7

    • Pattern recognition receptors (PRRs) – MDA5 (IFIH1), RIG-I (DDX58)

    • Effector proteins – OAS1, MX1, IFITM3, ISG15




2. Sequence Retrieval and Multiple Sequence Alignment (MSA)



  • Protein sequences were obtained from NCBI GenBank and UniProt databases.

  • MSA was performed using Clustal Omega to identify conserved and variable residues.

  • Evolutionary relationships were inferred using phylogenetic tree analysis.


3. Structural and Functional Analysis



  • Homology modeling (using AlphaFold or Swiss-Model) was used to predict structural differences.

  • Functional annotations of sequence variations were analyzed using:

    • ConSurf – To assess evolutionary conservation of key residues.

    • PROVEAN/SIFT – To predict the impact of amino acid substitutions on protein function.




4. Host Susceptibility Correlation with SARS-CoV-2



  • Comparative analysis of IFN pathway protein variations was correlated with reported SARS-CoV-2 infection susceptibility across species.

  • Literature and experimental datasets on SARS-CoV-2 replication efficiency in different hosts were integrated.


Results


1. Sequence Variability in IFN Antiviral Proteins Across Species



  • High conservation: IRF3 and RIG-I showed strong conservation across species, indicating their essential role in antiviral defense.

  • Moderate variability: MX1 and IFITM3 exhibited species-specific differences, potentially affecting viral restriction mechanisms.

  • Significant divergence: OAS1 displayed marked sequence variation, particularly in rodents and bats, suggesting functional divergence in RNA degradation activity.


2. Structural Impact of Sequence Variations



  • Substitutions in IFITM3 transmembrane domain affected predicted membrane interactions, potentially altering viral entry inhibition.

  • Differences in MX1 GTPase domain may influence its ability to restrict SARS-CoV-2 replication.

  • OAS1 catalytic site variations correlated with differences in 2'-5' oligoadenylate synthetase activity, potentially affecting RNA degradation efficiency.


3. Correlation with SARS-CoV-2 Susceptibility



  • Species with specific OAS1 and MX1 variants (e.g., some bat species) showed reduced SARS-CoV-2 replication in experimental models.

  • High conservation of IRF3 and IRF7 suggested that core IFN signaling remains functional across species, but downstream effectors may differ in efficacy.


Discussion



  • Host genetic variation in antiviral proteins may shape SARS-CoV-2 susceptibility.

  • Species with divergent OAS1 and IFITM3 sequences may exhibit altered resistance to SARS-CoV-2, contributing to differences in viral replication efficiency.

  • These findings have implications for zoonotic spillover prediction, as identifying sequence variations in reservoir species may help assess the risk of future coronavirus emergence.


Conclusion


In silico analysis reveals that while core IFN signaling proteins are conserved, significant sequence variability exists in effector proteins across species. These variations may influence SARS-CoV-2 susceptibility and could guide future research on host-pathogen interactions. Further experimental validation is needed to confirm the functional impact of these sequence differences.



Future Directions



  • Functional validation of identified mutations using in vitro and in vivo models.

  • Expansion of sequence analysis to additional species to refine zoonotic risk assessment.

  • Investigation of alternative antiviral pathways that may compensate for sequence divergence.


Keywords


SARS-CoV-2, interferon pathway, host susceptibility, in silico analysis, sequence variability, zoonotic viruses, antiviral response


https://cvia-journal.org/rna-splicing-cardiac-diseases/

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