High-throughput sequencing technologies have advanced RNA virus genomics, but recovering viral genomes from mammalian tissues remains challenging due to the predominance of host RNA. We evaluated two metatranscriptomic workflows to address these challenges. Our results demonstrate that the methods differed significantly in performance, with Method B achieving a 5-fold increase in RNA yield and improved RNA integrity over Method A. These differences resulted in the recovery of 4 complete hepacivirus genomes with Method B compared to fragmented or incomplete genomes with Method A. Additionally, Method B's library preparation workflow, incorporating rRNA depletion, enhanced viral genome recovery by reducing host RNA background. Our novel approach integrates an optimized RNA purification protocol with a customized bioinformatics strategy for improved viral genome recovery. Overall, our findings highlight the critical role of optimized homogenization, RNA purification, and library preparation in metatranscriptomic workflows, facilitating the more effective RNA virus genome recovery from complex mammalian tissues.

• MeSH
• genom virový * genetika   MeSH
• genová knihovna MeSH
• lidé MeSH
• RNA virová * genetika   izolace a purifikace   MeSH
• RNA-viry * genetika   MeSH
• savci virologie   MeSH
• transkriptom * MeSH
• vysoce účinné nukleotidové sekvenování * metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• RNA virová * MeSH

BACKGROUND: In the past decade, many new paramyxoviruses that do not belong to any of the seven established genera in the family Paramyxoviridae have been discovered. Amongst them are J-virus (JPV), Beilong virus (BeiPV) and Tailam virus (TlmPV), three paramyxovirus species found in rodents. Based on their similarities, it has been suggested that these viruses should compose a new genus, tentatively called 'Jeilongvirus'. RESULTS: Here we present the complete genomes of three newly discovered paramyxoviruses, one found in a bank vole (Myodes glareolus) from Slovenia and two in a single, co-infected Rungwe brush-furred rat (Lophuromys machangui) from Mozambique, that represent three new, separate species within the putative genus 'Jeilongvirus'. The genome organization of these viruses is similar to other paramyxoviruses, but like JPV, BeiPV and TlmPV, they possess an additional open reading frame, encoding a transmembrane protein, that is located between the F and G genes. As is the case for all Jeilongviruses, the G genes of the viruses described here are unusually large, and their encoded proteins are characterized by a remarkable amino acid composition pattern that is not seen in other paramyxoviruses, but resembles certain motifs found in Orthopneumovirus G proteins. CONCLUSIONS: The phylogenetic clustering of JPV, BeiPV and TlmPV with the viruses described here, as well as their shared features that set them apart from other paramyxoviruses, provide additional support for the recognition of the genus 'Jeilongvirus'.

• Klíčová slova
• Cell attachment protein, G protein, MMLPV-1, MMLPV-2, PMPV-1, Rodent paramyxovirus,
• MeSH
• fylogeneze MeSH
• genom virový * MeSH
• klonování DNA MeSH
• membránové proteiny genetika   MeSH
• Paramyxoviridae klasifikace   genetika   MeSH
• Paramyxovirinae klasifikace   genetika   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza DNA MeSH
• virové proteiny genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• membránové proteiny MeSH
• virové proteiny MeSH