Comparative Genome Analysis of Infectious Human and Domestic Animal Coronaviruses

Coronaviruses, which mainly cause gastrointestinal and respiratory infections, have been identified in various species. Among the extensive genomic data of disease-causing Coronaviruses in humans and animals, some similarities can be analyzed by in-silico methods.   

In the present study, comparative genome analysis of medical and veterinary medicine Coronaviruses was performed to obtain more accurate information about the genetic similarities and differences of different members of this family.

The genomic sequences were retrieved from NCBI and Virus Pathogen Resource databases. Using the NCBI database blast algorithm, all sequences were aligned with the SARS-CoV-2 genome sequence, and similarity was obtained. Amino acid sequences of structural and non-structural proteins associated with coding regions (CDS) were aligned separately with the SARS-CoV-2, and their similarities were calculated. The 3D structure from each protein was compared with the corresponding protein in SARS-CoV-2, and Template Modeling Scores (TM-Score) were obtained. A phylogenetic tree of different species of the Coronaviridae family was drawn based on nucleotide and amino acid sequence data.

Nonstructural coding gene sequences detected the highest interspecies similarities in nucleotide, amino acid sequence, and 3D structure (nsp12, nsp13, nsp14, and nsp16). The ORF1ab, encoding non-structural proteins, carries essential functions for viral replication.

This study showed that the transcription complex is highly conserved among human and animal Coronaviruses. A comparison and analysis of the Coronaviridae transcription complex can be considered a key target for diagnosing, developing antiviral therapies, and designing vaccines.