Coevolution of Coronavirus and Paramyxovirus with Their Bat Hosts in the Same Geographical Areas

Abstract Bat-borne viruses are relatively host specific. In this study, coevolution analyses were conducted on coronaviruses and paramyxoviruses and their bat hosts to investigate the potential mechanisms of such host specificity. The published nucleotide sequences of the RNA dependent RNA polymerase (RdRp) gene of 60 coronaviruses from 37 bat species and those of the RNA polymerase large (L) gene of 36 paramyxoviruses from 29 bat species were analyzed. Each of the coevolution signal detected was tested and verified by the ParaFit and PACo functions of the R program. Significant coevolution signals were detected in coronaviruses and paramyxoviruses and their bat hosts, and closely related bat hosts were found to carry viruses that are closely related. Results also suggest that similar geographical distribution and close phylogenetic relationship may have resulted in infection of different bat species by the same strain of virus. As the natural hosts of certain viruses were mostly found in their endemic and surrounding areas, we speculate that the ancestors of bat hosts of Middle East respiratory syndrome coronaviruses (MERS-CoVs) may belong to the family of Vespertilionidae and are evolutionarily close to Neoromicia capensis and Pipistrellus hesperidus bats that are present in Africa and west Asia. In addition, we speculate that bat coronaviruses that are closely related to the novel coronavirus 2019 (COVID-19) may be found in bats related to Rhinolophus affinis. Although the coevolution between viruses and bat host is not surprised, this is the first systematical summary elucidating the relationship between coronaviruses, paramyxoviruses, host and geographical areas. It provides a theoretical basis for the viruses trace.Significance Bat-borne coronaviruses and paramyxoviruses have caused a number of outbreaks worldwide, posing a great threat to the safety of human life and property. It is important to understand the bats-viruses evolutionary history and rules for the viruse tracing. In our long-term surveillance of bat viruses, we found that they are family, genus or species-specific. In this study, we are committed to show this phenomena through co-phylogenetic analysis. Host distribution were taken into account as an important analytical factor in this study. Our resualts suggest that similar hosts carry similar viruses, similar distribution area may facilitate inter-species transmission of bat viruses, and several endemic area were overlap with the natural host distribution. This study is of great significance for further study of bats-viruses evolutionary history and enhanced our awareness of virus prevention and control.# J. Liang and C. Zhu contributed equally to this study.