In Silico Study Plan: Evolution Studies of Dog-Related Viruses That Can Evolve to Human Viruses
Creators: name: Hussain, Zahid
Publisher: name: Zenodo
Year: 2024
Subjects: In Silico Study Plan:
Evolution Studies
Dog-Related Viruses
That Can Evolve
Human Viruses

description: In Silico Study Plan: Evolution Studies of Dog-Related Viruses That Can Evolve to Human Viruses

Abstract

This in silico study aims to explore the zoonotic potential of dog-related viruses, such as canine parvovirus, canine coronavirus, and canine distemper virus, to adapt to human hosts. By leveraging computational tools and bioinformatics approaches, the study seeks to identify critical mutations, receptor-binding interactions, and the evolutionary dynamics required for host adaptation. It integrates multiple phases, from literature review and comparative genomics to structural modeling, immune evasion analysis, and zoonotic risk assessment. The findings will contribute to proactive surveillance and prevention of zoonotic transmission.






Objective: Investigating the evolutionary potential of zoonotic viruses, including dog-related viruses, requires advanced computational tools to analyze genomic, structural, and evolutionary features (Parrish et al., 2008).

Phase 1: Literature Review and Database Mining



Literature review and genome collection leverage resources like NCBI GenBank, UniProt, and PDB, which provide comprehensive data on viral genomes and protein structures (Benson et al., 2018; The UniProt Consortium, 2021).

Comparative studies of human-adapted viruses like SARS-CoV-2 and parvovirus B19 provide insights into zoonotic transition mechanisms (Huang et al., 2020).


Phase 2: Comparative Genomics and Mutation Identification



Tools like Clustal Omega and MAFFT enable precise multiple sequence alignment for genomic comparisons (Sievers & Higgins, 2014).

Phylogenetic tools such as MEGA and BEAST are critical for visualizing evolutionary relationships (Tamura et al., 2021).



 

 



Phase 3: Structural Modeling and Receptor Binding Studies



AlphaFold and I-TASSER facilitate accurate prediction of protein 3D structures (Jumper et al., 2021; Yang et al., 2015).

AutoDock and HADDOCK are used for receptor binding simulations, enabling the identification of mutations affecting binding affinity (Morris et al., 2009; van Zundert et al., 2016).


Phase 4: Evolutionary Dynamics and Fitness Modeling



Tools like PROVEAN and MutPred2 assess the functional impact of mutations (Choi et al., 2012).

Fitness landscape modeling highlights the adaptive potential of specific mutations (Ashenberg et al., 2017).


Phase 5: Immune Evasion and Host-Specific Adaptation



Epitope prediction using IEDB tools aids in understanding immune evasion (Vita et al., 2019).

Codon usage analysis with CodonW and CAIcal evaluates translational efficiency in human hosts (Puigbò et al., 2008).


Phase 6: Risk Assessment and Data Integration



Computational models like Spillover Risk Mapper are pivotal for assessing zoonotic transmission risk (Becker et al., 2021).

Data integration and visualization tools like Cytoscape provide intuitive representations of complex datasets (Shannon et al., 2003).


Phase 7: Publication and Policy Recommendations



Insights from this study will guide public health policies and enhance zoonotic disease surveillance (Karesh et al., 2012).