First Report of Potato Viruses Infecting Lamium purpureum in Ukraine

Weeds as reservoirs for destructive plant pathogens have a significant impact on the viral epidemiology, ecology and, as a result, on local economy, and are therefore being investigated in many parts of the world. Thus, the aim of this study was to investigate virus occurrence in red dead-nettle plants (Lamium purpureum L.) widespread in urban and field conditions throughout the in the Kyiv region of Ukraine. Methods. Field crop observations, visual diagnosis, biological testing of the virus, immunoassay (ELISA), polymerase chain reaction with reverse transcription (RT-PCR), sanger sequencing of partial genome sequences of PVX, PVY, PVS, PVM. Results. The results obtained in the study indicate that Lamium plants could be alternative weed hosts of number important viral diseases including potatoes and other vegetables. Serological and molecular test results evidence plants were infected by Potato virus X, Potato virus Y, Potato virus M, Potato virus S and therefore Lamium L. species can serve as a potential source of inoculum for wide range of vegetables and ornamentals. This study is the first report of Lamium plants being naturally infected with Potato virus M and Potato virus S in central Europe. Conclusions. These plants are alternative host of mixed infection with viruses belonging to different families: Alphaflexiviridae, Betaflexiviridae and Potyviridae.

SPREAD OF POTATO VIRAL DISEASE PATHOGENS IN CULTURE CULTIVATION ZONES

Objective. Monitoring observations over the phytovirological condition of potato planting in different regions of Ukraine, taking into account potato degeneration zones. Methods. Laboratory (virological, immunological, electronic microscopy), field, statistical. Results. The map and diagrams show the results of monitoring studies conducted in 2016–2020, during which 435 varieties of potatoes of Ukrainian and foreign selection were tested. In the zone of the lowest degeneration or the zone with a relatively low degree of infectious load, 100 % spread of pathogenic complexes involving potato virus Y in the Region of Zakarpattia, potato viruses M and Y in the Region of Chernivtsi, ranging from 89 % to 100 %. In the zone of strong degeneration of the culture or the zone with a high degree of infectious load, spread of pathogens of potato viral diseases is from 94 % to 100 %, and the vast majority of viruses belongs to pathogens of severe viral diseases. In the zones of mild and moderate degeneration, which belong to the zones with relatively low degree and with moderate degree of infectious load according to another diagram, potato virus M in monoinfection from 17 % to 50 %, in the pathogenic complex with potato virus S from 8 % to 36 %, with potato virus Y from 6 % to 32 % was detected. In the Region of Kyiv, the spread of potato virus Y+S complex reaches 65 %. In all areas, there is an extremely high level of infection of the culture with potato virus M, which is the cause of severe viral diseases of potatoes. Conclusion. The results of phytovirological monitoring show that the boundaries between potato degeneration zones are smoothed down. Climatic changes, active resettlement of virus vectors, intensification of trade relations with the constant import of foreign potato seed material result in the significant spread of pathogens of potato viral diseases.

Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.

High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus

High-throughput sequencing (HTS) analysis of tomato (Solanum lycopersicum) samples revealed the presence of Potato virus M (PVM) in this crop in Slovakia. Full-length genomes of three PVM isolates were obtained using both HTS and Sanger sequencing validation. While two isolates (T40 and T50) were shown to belong to major Group I, a divergent T20 isolate was phylogenetically unrelated to any known PVM variant, potentially representing a new phylogenetic group. Despite a relatively high intraspecies diversity (17.3 ± 0.3%), no evidence of recombination was detected in the dataset of available complete PVM sequences. Conventional screening of tomato plants in Slovakia using ELISA and RT-PCR further confirmed a frequent occurrence of PVM in this host. Developed RT-PCR showed its polyvalence to detect the PVM Group I isolates, however, in silico analysis of primer binding sites indicated its compromised use for Group II isolates. Our results further pinpoint the significance of HTS for unbiased unveiling of virus diversity and a need for continual optimisation of molecular detection tools.