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.

Special Issue: “Viral Genetic Diversity”

“…In particular, the richness of viruses is higher in undisturbed environments than in peri-urban areas. This richness of viruses is also observed in birds from Africa, and Luo et al describe bird-related rhabdoviruses, considered as new species of the genus Sunrhavirus [ 11 ]. Interestingly, the authors raise the question of whether bird-related rhabdoviruses could be an arbovirus that infects birds, considering the close genetic relationship of these rhabdoviruses with other insect-related sunrhaviruses.…”

Large circulation of a novel vesiculovirus in bats in the Mediterranean region

“…Nearly complete genome sequences of bat-related rhabdoviruses were obtained using next generation sequencing (NGS) Illumina technology as previously described (Pallandre et al, 2020;Luo et al, 2021a). Contigs were obtained by combining de novo assembly and mapping (both with CLC Assembly Cell, Qiagen) using a dedicated workflow implemented on the Galaxy platform of Institut Pasteur (Mareuil, 2017;Pallandre et al, 2020;Luo et al, 2021aLuo et al, , 2021b. Contigs were then assembled and manually edited to produce the final consensus genome sequences using Sequencher.…”

“…The virion is generally characterized by a linear single stranded negative-sense RNA genome of approximately 10–16 kb with five canonical genes encoding the nucleoprotein (N), the phosphoprotein (P), the matrix protein (M), the glycoprotein (G), and the RNA-dependent RNA polymerase (L) (Walker et al, 2022b). These viruses exhibit a large ecological diversity (Walker et al, 2015), with members able to infect plants (Dietzgen et al, 2020) but also animals such as birds (Luo et al, 2021b), reptiles (Vasilakis et al, 2019) or fishes (Walker et al, 2022a). Remarkably, rhabdoviruses were often isolated from insects or are categorized as arboviruses (Vasilakis et al, 2014; Contreras et al, 2017; Walker et al, 2022b).…”