Molecular characterization of a new tobacco rattle virus (TRV) RNA2 and identification of different TRV RNA1/RNA2 pairings in various potato-growing areas in Germany

Co-Infection of Tobacco Rattle and Cycas Necrotic Stunt Viruses in Paeonia lactiflora: Detection Strategies, Potential Origins of Infection, and Implications for Paeonia Germplasm Conservation

Increasing reports of tobacco rattle virus (TRV) and cycas necrotic stunt virus (CNSV) in herbaceous Paeonia worldwide highlight the importance of conserving the genetic resources of this economically important ornamental and medicinal crop. The unknown origin(s) of infection, differential susceptibility of peony cultivars to these viruses, and elusive disease phenotypes for CNSV in peonies make early detection and management challenging. Here, we report the presence of TRV and CNSV in plants of the University of Michigan living peony collection in the United States and a molecular characterization of their strains. Using sequences of the TRV 194 K RNA polymerase gene, we confirmed TRV infections in seven symptomatic plants (1.07% of all plants in the collection). Using newly developed primers, we recovered sequences of the CNSV RdRp gene and the polyprotein 1 gene region from nine out of twelve samples analyzed, including three from symptomless plants. Four of the nine plants had TRV and CNSV co-infections and showed more severe disease symptoms than plants only infected with TRV. Phylogenetic analyses of isolates from the University of Michigan living peony collection and publicly available isolates point to multiple origins of TRV and CNSV infections in this collection. This is the first report of TRV/CNSV co-infection and of a symptomatic detection of CNSV on cultivated P. lactiflora.

Serological survey and metagenomic discovery of potato viruses in Rwanda and Burundi reveals absence of PVY in Burundi and first report of TRV in potatoes in sub-Saharan Africa

Worldwide, potato (Solanum tuberosum L.) is the third most important food crop after rice and wheat. Its production is however constrained by several virus diseases. The occurrence and distribution of the economically important viruses and associated insect vectors is however not known for Rwanda and Burundi, where potato is an important food security and income crop. We surveyed 194 potato fields for viruses and insect vectors. Aphids were commonly found infesting farmers' potato fields in contrast to whiteflies. Testing by Enzyme Linked Immunosorbent Assay (ELISA) for six potato viruses identified five viruses: potato leafroll virus (PLRV), potato virus X, S, M and Y (PVX, PVS, PVM, PVY) in Rwanda and two viruses (PLRV and PVS) in Burundi. A subset of samples were analyzed using small RNA sequencing and assembly (sRSA) and additionally revealed presence of PVX and for the first time, tobacco rattle virus (TRV) in Burundi. PLRV and PVS were most common while PVY was rare and not found in Burundi, which is highly unusual. To our knowledge, this is the first report of TRV infecting potatoes in sub-Saharan Africa. Phylogenetic analysis of 14 complete viral genomes determined by sRSA suggested multiple introductions of viruses into the region.

Identification of internal poly(A) tracts (IPATs) of variable lengths in a novel tobacco rattle virus RNA2 in potatoes

The nucleotide (nt) sequences of two closely related isolates (CeWF-2 and CeWGH-2) of a novel tobacco rattle virus (TRV) RNA2 were determined. The sequences of their RNA2-specific regions were almost identical and contained four open reading frames (ORFs) in an arrangement similar to that found in the previously described TRV TpO1 RNA2. Their predicted ORF 1 gene products shared 97 % amino acid sequence identity with the TpO1 coat protein, but the ORF 2 and ORF 3 gene products shared only 82 % sequence identity, and no appreciable sequence similarity was found between the CeWF-2/CeWGH-2 and TpO1 ORF 4 gene products. In the CeWGH-2 sequence, the RNA2-specific and RNA1-related regions were separated by seven adenine (A) residues. In CeWF-2, however, an internal poly(A) tract (IPAT) of variable size consisting of ca. 20 to 30 (A) residues was found. This is the first report of an IPAT occurring in a tobravirus RNA2.