Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses

Abstract

Recent years have witnessed the discovery of several new viruses belonging to the family Arteriviridae, expanding the known diversity and host range of this group of complex RNA viruses. Although the pathological relevance of these new viruses is not always clear, several well-studied members of the family Arteriviridae are known to be important animal pathogens. Here, we report the complete genome sequences of four new arterivirus variants, belonging to two putative novel species. These new arteriviruses were discovered in African rodents and were given the names Lopma virus and Praja virus. Their genomes follow the characteristic genome organization of all known arteriviruses, even though they are only distantly related to currently known rodent-borne arteriviruses. Phylogenetic analysis shows that Lopma virus clusters in the subfamily Variarterivirinae, while Praja virus clusters near members of the subfamily Heroarterivirinae: the yet undescribed forest pouched giant rat arterivirus and hedgehog arterivirus 1. A co-divergence analysis of rodent-borne arteriviruses confirms that they share similar phylogenetic patterns with their hosts, with only very few cases of host shifting events throughout their evolutionary history. Overall, the genomes described here and their unique clustering with other arteriviruses further illustrate the existence of multiple rodent-borne arterivirus lineages, expanding our knowledge of the evolutionary origin of these viruses.

Novel Rodent Arterivirus Detected in the Brazilian Amazon

“…Besides PRRSV-1, EAV and LDV, most members of the family were detected or isolated in Old World countries, including all simian and other rodent-borne arteriviruses described [ 9 , 32 ]. Continuous sampling of distinct species of the genus, which is considerably speciose [ 46 ], along with other mammalian species native to the region in further surveillance studies, is essential to unravel the diversity and coevolutionary patterns of the Arteriviridae family in the Amazon and, in a broader context, within the American continent.…”

“…Arterivirids, including those not yet assigned to any species, are non-human mammalian viruses with a wide range of hosts, including horses, porcines, rodents, simians, shrews, possums, bank voles and hedgehogs, and the family is believed to be even more diverse [ 5 , 6 , 7 , 8 , 9 ]. Most of the first arteriviruses described are pathogens of significant veterinary importance, as equine arteritis virus (EAV), porcine reproductive and respiratory syndrome virus 1 and 2 (PRRSV-1/PRRSV-2) and simian hemorrhagic fever virus (SHFV), which produce overt disease in horses, domestic pigs and non-human primates, respectively.…”

“…Among the most recently described arteriviruses, wobbly possum disease virus (WPDV) and hedgehog arterivirus (HhAV-1) were imputed as causative agents of disease in captive possums and wild hedgehogs, respectively [ 6 , 8 ]. All the recently described rodent arteriviruses have Asian, African or European origin, sampled from individuals collected in China, Cameroon, Tanzania, Mozambique and Ukraine, mainly in metagenomic studies [ 7 , 9 , 10 ]. This report describes an almost complete genome of a novel rodent arterivirus, which might represent a new genus of the Arteriviridae family, the first, to our knowledge, detected in Brazil, and the most complete genomic record in Latin America [ 11 ].…”

Discovery and Genetic Characterization of Novel Paramyxoviruses Related to the Genus Henipavirus in Crocidura Species in the Republic of Korea

“…Cophylogenetic relationships of zoonotic viruses and natural reservoir hosts play a critical role in understanding the evolutionary process for coadaptation, spillover, and host sharing [60][61][62]. Multiple natural reservoirs harbor Orthohantavirus species, and in most cases, it is a specific relationship of "one virus-one host" [63].…”

Women in the European Virus Bioinformatics Center

“…She is particularly interested in characterizing the evolutionary processes and dynamics underlying pathogen genomic diversity across multiple scales. This goes from studying within- to between-hosts evolution, reconstructing deep and recent evolutionary events up to surveying both the virus and their hosts’ genomes [ 66 , 67 , 68 ]. To this aim, she uses a combination of wet-lab approaches (molecular biology methods, high-throughput sequencing) and computational tools (bioinformatics, phylogenetics, phylodynamics) [ 69 ].…”