The characterization of multiple novel paramyxovirus species highlights the diverse nature of the subfamily Orthoparamyxovirinae

Abstract

The subfamily Orthoparamyxovirinae is a group of single-stranded, negative-sense RNA viruses that contains many human, animal and zoonotic pathogens. While there are currently only 34 recognized member species in this subfamily, recent research has revealed that much of its diversity remains to be characterized. Using a newly developed nested PCR-based screening assay, we report here the discovery of fifteen orthoparamyxoviruses in rodents and shrews from Belgium and Guinea, thirteen of which are believed to represent new species. Using nanopore sequencing, complete genomes could be determined for almost all of these viruses, enabling a detailed evaluation of their genome characteristics. While most viruses are thought to belong to the rapidly expanding genus Jeilongvirus, we also identify novel members of the genera Narmovirus, Henipavirus and Morbillivirus. Together with other recently discovered orthoparamyxoviruses, both the henipaviruses and the morbillivirus discovered here appear to form distinct rodent-/shrew-borne clades within their respective genera, clustering separately from all currently classified member species. In the case of the henipaviruses, a comparison of the different members of this clade revealed the presence of a secondary conserved open reading frame, encoding for a transmembrane protein, within the F gene, the biological relevance of which remains to be established. While the characteristics of the viruses described here shed further light on the complex evolutionary origin of paramyxoviruses, they also illustrate that the diversity of this group of viruses in terms of genome organization appears to be much larger than previously assumed.

A South American mouse morbillivirus sheds light into a clade of rodent-borne morbilliviruses

“…In all cases, unequivocally, RoMV clustered with morbillivirus forming a sub-clade with the rodent WNfMV and LBbMV ( Supplementary Figure 10 ). It is essential to highlight that during the preparation of this work a putative morbillivirus was described linked to wood mouse ( Apodemus sylvaticus ) a murid rodent native to Europe (Vanmechelen et al, 2022). While the genome sequence of this “Apodemus morbillivirus” detected in a wood mouse cadaver that had been killed by cats or vehicles collected in Belgium is yet publicly unavailable, its reported phylogenetic clustering with both WNfMV and LBbMV is consistent with a the novel sister subclade of rodent-borne morbilliviruses described here.…”

Novel and classical morbilliviruses: Current knowledge of three divergent morbillivirus groups

“…MZ328284.1) from Berylmys bowersi . In Belgium, a virus identified in Apodemus sylvaticus was named apodemus morbillivirus 134 . A morbillivirus detected in the kidneys of South American long‐haired mice collected in Chile and Argentina was named ratón oliváceo morbillivirus (RoMV) 9 .…”

“…A morbillivirus detected in the kidneys of South American long‐haired mice collected in Chile and Argentina was named ratón oliváceo morbillivirus (RoMV) 9 . These rodent‐derived viruses are located in the same group on the phylogenetic tree as WNfMV and LBbMV 9,134 . Meanwhile, MBaMV and PoMV are located in the morbillivirus group that uses SLAM as a receptor and are close to CDV and PDV (Figure 1).…”

“…In Belgium, a virus identified in Apodemus sylvaticus was named apodemus morbillivirus. 134 A morbillivirus detected in the kidneys of South American longhaired mice collected in Chile and Argentina was named ratón oliváceo morbillivirus (RoMV). 9 These rodentderived viruses are located in the same group on the phylogenetic tree as WNfMV and LBbMV.…”

“…9 These rodentderived viruses are located in the same group on the phylogenetic tree as WNfMV and LBbMV. 9,134 Meanwhile, MBaMV and PoMV are located in the morbillivirus group that uses SLAM as a receptor and are close to CDV and PDV (Figure 1).…”