Identification of new potential reservoirs of SARS-COV-2 among common Ugandan animals using molecular docking and sequence analysis

Abstract

In 2020, a beta coronavirus family member SARS-CoV-2, which causes a deadly respiratory disease in humans, went global. One of the severely impacted nations by COVID-19 was Uganda, especially during the second wave, which was caused by the omicron strain of the virus. Since Uganda is the home to a significant amount of biodiversity and the disease is recognized as a zoonotic one, SARS-CoV-2 infection in animals may act as a reservoir for the virus, or facilitate its propagation from animals to humans. Forty-two different Ugandan species' ACE2 amino acid sequences were gathered for this investigation from the NCBI database. Using these, comparative evaluations of the secondary structures of the ACE2 proteins from the various species were conducted. In order to identify potential reservoirs in this region, we used molecular docking and Multiple sequence alignment (MSA) approaches with reference to Human ACE2 and SARS COV 2 Spike protein. In-silico molecular docking of animal Angiotensin Converting Enzyme 2 receptors to the virus's S protein Receptor Binding Domain and Root-Mean-Square Deviation calculation with reference to the known host receptor 6M0J (human) showed that Macaca mulatta (Rhesus Monkey), Gorilla gorilla gorilla (Western Gorilla) and Pan paniscus (Pygmy Chimpanzee) respectively, had the highest potential to be SARS-CoV-2 reservoirs. These were trailed by Pan troglodytes, Piliocolobus tephrosceles and Papio anubis respectively. Furthermore, Multiple sequence alignment indicated that the ACE2 residues critical for interaction with the spike protein i.e. K31, E35, D38, M82 and K353 were all conserved in the Western Lowland Gorilla, Chimpanzee, Pygmy Chimpanzee, Ugandan Red Colobus, Olive Baboon, Rhesus Monkey and Green Monkey.