Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses

Simple Summary Coronaviruses are serious pathogens for both humans and animals. The name corona was designated because of the crown-like spikes on their surface. Currently, seven coronaviruses have been identified, such as 229E, NL63, OC43, HKU1, MERS-CoV, SARS-CoV, and SARS-CoV-2. Sometimes, animal coronaviruses infect humans and evolve due to genetic mutations, interspecies transmission, host adaptations, and favorable conditions. The main objective of this study was to analyze the genetic diversity and predict the emergence of new variants with novel properties. It has been reported that the spike protein gene plays an important role in host cell attachment and entry into host cells. The S gene has the highest mutation/deletion and is the most utilized target for vaccine/antiviral development. In this work, we discussed the genetic diversity, phylogenetic relationship, and recombination patterns of selected HCoVs with an emphasis on the newly emerged SARS-CoV-2 and MERS-CoV. The findings of this study showed that MERS-CoV and SARS-CoV-2 have significant sequence identities with the selected HCoVs. The phylogenetic and recombination results concluded that new variants may emerge in the future with novel properties that infect both humans and animals. This information will be helpful for global society to design and develop an effective vaccine and disease management strategy.Abstract Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002-2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent.