SARS-CoV-2 Origins and Evolution: Insights from Coronaviruses Recombination and Phylogenetic Analysis

It is imperative in the midst of a global epidemic to investigate the origins of the infectious agent especially when it has reached parts of the world with either ailing economies or pre-existing political turmoil consistent with non-functional health systems. To explore the possibility of cross species infection, genomic recombination and the emergence of novel coronaviruses in the near future we carried out recombination and phylogenetic analysis to determine the spatio-temporal evolution and origins of the current SARS-CoV-2 virus. Using two robust recombination tools, RDPv4.100 and SimPlot3.5.1 analysis, our findings prove that SARS-CoV-2 is a recombinant of pangolin and bat RaTG13 sequences as been previously shown elsewhere. We also report one novel recombination event between two SARS-CoV-2 sequences (SARS-CoV-2 sequence, MT188341, SARS-CoV-2 sequence, MT293183). Bearing in mind that the prerequisite for recombination is the occurrence of two viral sequences in the same reservoir, biological niche or host at the same time we postulate either co-infection with the two viral sequences, or superinfection. The possibility of recombination between the SARS-CoV-2 sequences poses the likelihood of the emergence of new more or less virulent “strains” of the virus. The future of science lies in our ability to be able to use computational based methods to predict the genetic sequences of infectious agents of the next epidemics. Addition of more SARS-CoV-2 sequences has a bearing on our understanding of the origin, evolution and clinical outcome prediction of given viral genomes. More SARS-CoV-2 sequences are needed to elucidate our understanding of this family of viruses.