Discovery and Evolutionary Analysis of a Novel Bat-Borne Paramyxovirus

Abstract

Paramyxoviruses are a group of RNA viruses, such as mumps virus, measles virus, Nipah virus, Hendra virus, Newcastle disease virus, and parainfluenza virus, usually transmitted by airborne droplets that are predominantly responsible for acute respiratory diseases. In this paper, we identified a novel paramyxovirus belonging to genus Jeilongvirus infecting 4/112 (3.6%) bats from two trapping sites of Hainan Province of China. In these animals, the viral RNA was detected exclusively in kidney tissues. This is the first full-length Jeilongvirus genome (18,095 nucleotides) from bats of genus Hipposideros, which exhibits a canonical genome organization and encodes SH and TM proteins. Results, based on phylogenic analysis and genetic distances, indicate that the novel paramyxovirus formed an independent lineage belonging to genus Jeilongvirus, representing, thus, a novel species. In addition, the virus-host macro-evolutionary analysis revealed that host-switching was not only a common co-phylogenetic event, but also a potential mechanism by which rats are infected by bat-origin Jeilongvirus through cross-species virus transmission, indicating a bat origin of the genus Jeilongvirus. Overall, our study broadens the viral diversity, geographical distribution, host range, and evolution of genus Jeilongvirus.

Keywords: Jeilongvirus; bat; co-evolutionary; paramyxovirus; virus discovery.

Figure 1

The distribution map of Jeilongvirus and the sampling sites of this study. The distribution regions of Jeilongvirus are labeled in red, while the sampling sites are marked with words.

Figure 2

Comparisons between the genome organization of HaParaV and those of representatives of genus Jeilongvirus. The genomes are drawn with a unified length scale. The function of each protein is shown with a short description. The “HN” represents haemagglutinin-neuraminidase (HN) protein. The virus identified in this study is labeled with a red font.

Figure 3

Phylogenetic analysis based on L proteins of subfamily Orthoparamyxovirinae. The evolutionary tree was inferred using amino acid sequences by the Maximum Likelihood algorithm with 1000 bootstraps. Only bootstrap values above 90% are shown. The accession numbers of each virus are labeled in brackets after corresponding viral names. The virus identified in this study is labeled with red font.

Figure 4

Phylogenetic analyses based on F (A) and N (B) protein amino acid sequences of genus Jeilongvirus, respectively. The evolutionary tree was inferred using amino acid sequences by the Maximum Likelihood algorithm with 1000 bootstraps. Only bootstrap values above 90% are shown.

Figure 5

The genetic distances between the virus identified in this study and members of genus Jeilongvirus. The p-distance values are estimated using amino acid sequences of complete L proteins. The numbers (1–24) below the picture represent the corresponding viral names on the right side of the picture. The p-distance values were showed as colored circles. The rows and columns were clustered based on paired values. The scale values range from 0.5 to 1. The virus identified in this study is labeled with red font.

Figure 6

Host-virus co-phylogenetic analysis of Jeilongvirus. The virus identified in this study is labeled with red font. The host tree was inferred using TreeTime. The phylogenetic tree of viruses was built based on L proteins. Co-speciation, host-switching, duplication, and loss events are labeled with filled circles, arrows, empty circles, and dotted lines at the nodes, respectively. The colors of circles represent different placements: red for all other placements worse, and yellow for equally good placement exists. The names of the viruses are labeled with red font, and virus from this study is labeled with bold type. The small picture represents the corresponding host type.