Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany

Abstract

Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to Albetovirus, Alphaflexiviridae, Aspiviridae, Bromoviridae, Endornaviridae, Partitiviridae, Potyviridae, Solemoviridae, Tombusviridae and Virgaviridae. The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the Astroviridae and Potyviridae families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses.

Diversity of Picorna-Like Viruses in the Teltow Canal, Berlin, Germany

“…However, clear proof is lacking, and the available phylogenetic trees give no indications. In contrast, phylogenetic analyses of plant-associated viruses indicate the rampant exchange of capsid protein-encoding genes; for recent examples, see [17].…”

“…The viruses in this study were enriched from a 50 L water sample (sample ID collected in Berlin, Bäkebrücke (site coordinates: 52°26′03″ N, 13°18′57″ E), on 18 July 2017. Details of the enrichment procedure were described previously [8,16,17]. Briefly, five 10 L aliquots were vigorously stirred for 20 min, and the pH was adjusted from 8.1 to 3.5.…”

“…Then, the sequence data were extracted in FastQ format using bcl2FastQ v2. 19.1.403 (Illumina), and adapter sequences were removed with Cutadapt v1.8.3 software [19] as described previously [17]. After adapter trimming and the removal of duplicons, 70,018,635 read pairs were used for de novo assembly with clc_assembler v5.2.1 (Qiagen) using the parameters -p fb ss 50 500 and metaSPAdes v3.…”

“…The majority of metagenomic studies, however, focused on marine ecosystems, while the viromes of freshwater bodies remained underexplored [12][13][14][15]. In order to understand the virus diversity detected in two German rivers, we analyzed the RNA viromes of the Havel River and the Teltow Canal in Berlin and published partial results [8,16,17]. Here, we present the sequences of more than 500 PLVs detected in the Teltow Canal (named TC-PLVs), many of which are novel, with little similarity to known members of the Picornavirales.…”

Novel PotentialCannabisPathogen: Discovery of Tobacco necrosis virus A in a Diseased ColombianCannabis sativaPlant

“…The family Tombusviridae has experienced adjustments and the addition of new genera in the recent past. The members of the genus Necrovirus have been reassigned as it is no longer in use (Monger & Jeffries, 2018a;Prasad et al, 2019) Currently, Tombusviridae family is composed of three subfamilies: Procedovirinae, Regressovirinae and Calvusvirinae and eighteen genera such as Alphacarmovirus, Alphanecrovirus, Aureusvirus, Avenavirus, Betacarmovirus, Betanecrovirus, Dianthovirus, Gallantivirus, Gammacarmovirus, Macanavirus, Machlomovirus, Panicovirus, Pelarspovirus, Umbravirus, Tombusvirus, Tralespervirus, Zeavirus and Luteovirus (White, 2021;Zell et al, 2023). TNVA is taxonomically located within the Procedovirinae subfamily, known for its characteristic translational readthrough of a stop codon in the RdRp CDS sequence (White, 2021;Y.…”