Genome Characterization of Bird-Related Rhabdoviruses Circulating in Africa

Abstract

Rhabdoviridae is the most diverse family of the negative, single-stranded RNA viruses, which includes 40 ecologically different genera that infect plants, insects, reptiles, fishes, and mammals, including humans, and birds. To date, only a few bird-related rhabdoviruses among the genera Sunrhavirus, Hapavirus, and Tupavirus have been described and analyzed at the molecular level. In this study, we characterized seven additional and previously unclassified rhabdoviruses, which were isolated from various bird species collected in Africa during the 1960s and 1970s. Based on the analysis of their genome sequences obtained by next generation sequencing, we observed a classical genomic structure, with the presence of the five canonical rhabdovirus genes, i.e., nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and polymerase (L). In addition, different additional open reading frames which code putative proteins of unknown function were identified, with the common presence of the C and the SH proteins, within the P gene and between the M and G genes, respectively. Genetic comparisons and phylogenetic analysis demonstrated that these seven bird-related rhabdoviruses could be considered as putative new species within the genus Sunrhavirus, where they clustered into a single group (named Clade III), a companion to two other groups that encompass mainly insect-related viruses. The results of this study shed light on the high diversity of the rhabdoviruses circulating in birds, mainly in Africa. Their close relationship with other insect-related sunrhaviruses raise questions about their potential role and impact as arboviruses that affect bird communities.

Keywords: Africa; NGS; Sunrhavirus; arbovirus; bird; genetic diversity; genome; rhabdovirus.

Figure 1

Schematic genome organization of the seven bird-related sunrhaviruses. The gray and black arrows represent the five canonical open reading frames (ORFs) (N, P, M, G, and L), and the putative additional ORFs (≥180 nt), respectively. The length (nucleotide and amino acid) of each ORF is indicated.

Figure 2

Phylogenetic classification of the seven bird sunrhaviruses. A maximum likelihood phylogenetic tree was made using IQ-TREE1.6.10, on the full amino acid sequence of the L protein, including seven bird-related sunrhaviruses and 229 other rhabdoviruses previously reported on GenBank, using the LG + G + L + F model with 10,000 ultrafast bootstraps. The rhabdovirus genera that were not related to birds were collapsed in the phylogenetic tree. Bird-related rhabdoviruses are indicated by a dedicated symbol, and the bird-related genera are shown in bold. Unclassified rhabdoviruses are indicated by black dots. The bird-related rhabdoviruses described in this study are highlighted in gray. All bootstrap proportion values (BSP) > 80% are specified. The scale bar indicates nucleotide substitutions per site.

Figure 3

Phylogenetic classification of all members of the genus Sunrhavirus, including the seven newly described bird-related sunrhaviruses. A maximum likelihood phylogenetic tree was made with PhyML 3.0 on the nucleotide concatenated ORFs (N-P-M-G-L), using the GTR + G + I model and with 1000 bootstrap replicates. The main animal reservoirs for each virus are indicated by specific cartoons, and the seven bird sunrhaviruses described in this study are highlighted in gray. The isolation country for each virus is presented in the right of the illustration. All bootstrap proportion values (BSP) >80% are specified. The scale bar indicates nucleotide substitutions per site. The classical rabies virus (RABV) was included as outlier in the phylogenetic analysis.