Molecular detection, phylogenetic and whole genome sequence analyses of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta variant isolated from domestic cats (Felis catus) in Egypt

Reverse zoonoses, which arise from interactions between humans and animals, are facilitated by the similarity of angiotensin-converting enzyme 2 (ACE2) cell receptors across different hosts and the high mutation rate of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), enabling transmission across species. This study aimed to explore the transmission of SARS-CoV-2 between humans and companion animals by conducting molecular investigations on nasopharyngeal and oropharyngeal swabs from 100 domestic Cats (Felis catus) in Egypt which had contact with SARS-CoV-2 positive owners from December 2021 to March 2022. Swabs were screened using real-time RT-PCR and the positive sample was further analyzed using whole-genome sequencing and phylogenetic analysis. The feline SARS-CoV-2 strain belonged to the Delta variant showing 99.6 %–99.7 % nucleotide sequence identity to human SARS-CoV-2 viruses collected during the same period. Amino acid mutations were observed in key regions of the spike protein (T19R, T478K, D614G, and P681R) and other genomic regions, including ORF1b, ORF1a, ORF3a, and ORF9b. Unique traits included the presence of T19R in the N-terminal domain NTD and I82T mutations in the Membrane protein. Structural analysis revealed fewer hydrogen bonds and salt bridges compared to the Delta variant viruses, showing altered spike-ACE2 interactions. Transmembrane protease serine subclass 2 (TMPRSS2) docking indicated strong binding affinity, suggesting a potential for interspecies adaptation. The present study highlights the potential occurrence of SARS-CoV-2 spillover between humans and their companion animals. Public health precautionary and preventive measures should be implemented to reduce transmission of SARS-CoV-2 between humans and companion animals.