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

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. Our resualts suggest that similar hosts carry similar viruses, similar distribution area may facilitate inter-species transmission of bat viruses, and several endemic

NiV was first detected in Malaysia in 1999 during the outbreak of encephalitis and respiratory illness among pig farmers. Approximately 300 human cases of NiV infection with over 100 deaths have been reported, and sporadic outbreaks have occurred in Malaysia, Singapore, Bangladesh, the Philippines, and India (https://www.who.int/news-room/fact-sheets/detail/nipah-virus; https://www.cdc.gov/vhf/nipah/index.html).
Host-parasite specificity has been shown in malaria parasites (Ricklefs et al. 2004), bat flies (Nikon et al. 2011), bacteria (Lei and Olival 2014), and coronaviruses (Cui et al. 2007). As an ancient mammalian species (Teeling et al.2005), bats may have coevolved with their parasites. In this study, we use the bat cyt b gene and viral replicase polymerase sequence as the analysis object, for they are one of the most conservative fragment in the mammalian and viral genome, and more suitable for elucidating evolutionary relationships. Secondly, due to the stability of replicase polymerase makes them more readily available. Such as HKU6 and HKU7, we can got RNA dependent RNA polymerase (RdRp) of them but Spike is unavailable. We had also analyzed 440 bp and 816 bp coronavirus replicase fragments of hundreds of coronavirus sequence, but confidence interval of the evolutionary tree is too low. For getting more sequences of diverse viruses that long enough and from various states, we analyzed the complete nucleotide sequences of the RdRp gene of 60 coronaviruses from 37 bat species and 559 bp partial sequences of the RNA polymerase large (L) gene of 36 paramyxoviruses from 29 bat species to examine their phylogenetic patterns.

Methods
Bat Collection and Gene Amplification

Global-fit Analysis
The degree of congruence of phylogenetic topologies between bats and viruses were identified using the global-fit method of ParaFit (Legendre et al. 2002). The matrices of patristic distances were calculated from the maximum likelihood tree of host and virus phylogenies using the "cophenetic" randomizations was used to assess significance. The associated squared residuals were used to assess the importance of each host-virus link (Singh et al. 2016). To visualize bat-virus associations, their cophylogenetic trees were generated using the "cophylo" function of the R package phytools MERS related coronaviruses (MERSr-CoVs) were detected in bats from Europe, Africa, and Asia. All of these bats belonged to the family Vespertilionidae (Fig. 1     Asia to northwest Oceania (Fig. 2). HeV, NiV, and several unclassified paramyxoviruses were clustered in one clade (Fig. 2). These results indicated that closely related bats carried closely related paramyxoviruses. Some bat hosts of HeV and NiV were found to be also infected by TiV and MENV (Fig. 2).

Disccusion
We tried to ensure that the sequences' length was long enough to elucidate the evolutionary other SARSr-CoVs (Fig. 1), and showed lower nucleotide identity with human SARS-CoVs ( Table 2).
The observations suggest that the evolutionary relationship of viruses may be related to the geographical distribution distance and evolutionary distance of their hosts.
The BatCoV RaTG13/MN996532 is related to SARSr-CoV in the evolutionary tree (Fig. 1) Vespertilionidae bats distributed in Europe, Asia, and Africa (Fig. 2). These observations suggest that closely related viruses share similar host species and that these viruses were carried by an ancestor bat that migrated from one region to another and then diverged into different bat species.
NiV and HeV belong to the genus Henipavirus and cause highly fatal encephalitis in humans , Chua et al. 1999 In summary, results of this study showed that similar species of bats distribute in the same geographical areas, and that closely related bats harbor closely related viruses. Furthermore, our resulst imply that the overlap of home range is an important condition for virus inter-species transmission. Therefore, the similarity of bat viruses is related to both the evolution and geographical distribution of their hosts. In addition, the results suggest that the outbreak may be related to the