Prevalence and molecular characterization of important potato viruses in the Tokat province of Turkey

BACKGROUND

It is believed that viruses affect potato yield more than any other pathogens worldwide.

METHOD AND RESULTS

We report here on a survey of the four most common potato viruses in the Tokat Province of northern Turkey. Leaf samples were collected from potato plants showing signs of viral diseases in five districts of the province. Over 400 leaf samples were tested using RT-PCR with virus-specific primers. Among the one or more viruses detected in 218 (52%) leaf samples, Potato virus Y (PVY) was the most common (47.1%), followed by potato virus S (PVS; 16.7%), potato virus X (PVX; 6.0%) and potato leaf roll virus (PLRV; 5.3%). The most common mixed infections were PVY + PVS (6.9%). A phylogenetic analysis of the gene sequences showed all Turkish PVS isolates to be clustered with the PVS^O group, two PVY isolates with the PVY^N-WI group and one isolate with the PVY^NTN group. Turkish PVX isolates are in the Type X group of the two major PVX isolate groups. The Turkish PLRV isolates were separated into two major groups depending on the results of the phylogenetic analysis, with six cases in Group 1 and one in Group 2.

CONCLUSIONS

PVY, PVX, PVS and PLRV were detected in potato production areas in Tokat. A phylogenetic comparison of the gene sequences revealed all Turkish isolates to be immigrant members of the world populations of these viruses. Our results emphasize the importance of the strict quarantine control of plant materials entering Turkey.

Evolutionary history and global spatiotemporal pattern of alfalfa mosaic virus

Alfalfa mosaic virus (AMV) is an important plant virus causing considerable economic loss to alfalfa production. Knowledge of the evolutionary and demographic history of the pathogen is limited but essential to the development of effective and sustainable pathogen management schemes. In this study, we performed worldwide phylodynamic analyses of AMV based on 154 nucleotide sequences of the coat protein gene, sampled from 1985 to 2020, to understand the epidemiology of this pathogen. Bayesian phylogenetic reconstruction estimates that the crown group of AMV dates back to 1840 (95% credibility interval, 1687-1955). We revealed that AMV continuously evolves at a rate of 4.14 × 10^-4 substitutions/site/year (95% credibility interval, 1.04 × 10^-4 - 6.68 × 10^-4). Our phylogeographic analyses identified multiple migration links between Europe and other regions, implying that Europe played a key role in spreading the virus worldwide. Further analyses showed that the clustering pattern of AMV isolates is significantly correlated to geographic regions, indicating that geography-driven adaptation may be a factor that affects the evolution of AMV. Our findings may be potentially used in the development of effective control strategies for AMV.

Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

Genetic diversity analysis of papaya leaf distortion mosaic virus isolates infecting transgenic papaya "Huanong No. 1" in South China

The commercialized genetically modified papaya "Huanong No. 1" has been utilized to successfully control the destructive virus-papaya ringspot virus (PRSV) in South China since 2006. However, another new emerging virus, papaya leaf distortion mosaic virus (PLDMV), was found in some PRSV-resistant transgenic plants in Guangdong and Hainan provinces of South China through a field investigation from 2012 to 2019. The survey results showed that "Huanong No. 1" papaya plants are susceptible to PLDMV, and the disease prevalence in Hainan Province is generally higher than that in Guangdong Province. Twenty representative isolates were selected to inoculate "Huanong No. 1," and all of the inoculated plants showed obvious disease symptoms similar to those in the field, indicating that PLDMV is a new threat to widely cultivated transgenic papaya in South China. Phylogenetic analysis of 111 PLDMV isolates in Guangdong and Hainan based on the coat protein nucleotide sequences showed that PLDMV isolates can be divided into two groups. The Japan and Taiwan China isolates belong to group I, whereas the Guangdong and Hainan isolates belong to group II and can be further divided into two subgroups. The Guangdong and Hainan isolates are far different from the Japan and Taiwan China isolates and belong to a new lineage. Further analysis showed that the Guangdong and Hainan isolates had a high degree of genetic differentiation, and no recombination was found. These isolates deviated from neutral evolution and experienced population expansion events in the past, which might still be unstable. The results of this study provide a theoretical basis for clarifying the evolutionary mechanism and population genetics of the virus and for preventing and controlling the viral disease.

Identification, genetic diversity and recombination analysis of Watermelon Mosaic Virus isolates

Watermelon mosaic virus (WMV) is an important virus causing adverse effects on cucurbits throughout the world. In this study, we recorded WMV infection in the watermelon (Citrullus lanatus)-growing area of Alwar and Sikar in districts of Rajasthan, India. The RT-PCR-based detection was performed to confirm the presence of WMV, by using potyvirus-degenerated coat protein primers. Further, the complete genome sequences of two WMV isolates were compared with previously reported genome sequences. The complete genome of each isolate was 10,030 nt long, excluding the poly-A tails. Phylogeny relationships of the WMV isolates in the present study revealed the presence of uneven evolutionary pressure among the different WMV viral genomic segments. The analysis revealed that all the WMV isolates were divided into three clusters and the Indian WMV isolates cluster together with the French isolate. Recombination analysis of WMV exhibited significant recombination hotspots in the P1, NIa-Pro and Nib-CP regions. Our finding highlights the importance of genetic variability and recombination analysis to provide a better understanding of WMV molecular diversity.

Molecular Evolutionary Analysis of Potato Virus Y Infecting Potato Based on the VPg Gene

Potato virus Y (PVY) is an important plant pathogen infecting solanaceous crops, causing significant losses to global potato and tobacco production. Some aspects of the plant pathology and molecular biology of PVY have been studied intensively, but the evolutionary dynamics of this virus are poorly understood. Here, we performed a comprehensive set of rigorous evolutionary analyses using 177 nucleotide sequences of the viral genome linked protein (VPg) gene, which interacts with the plant eukaryotic translation initiation factor 4E (eIF4E). Our Bayesian analysis reveals that the VPg gene of PVY has been evolving at a rate of 5.60 × 10^–4 subs/site/year (95% credibility interval 3.35 × 10^–4–8.17 × 10^–4), which is equivalent to those of other plant-infecting RNA viruses. We identified different evolutionary constraints on the two clades of PVY, clade N and clade O, whose diverge time were estimated at the year 1861 CE (95% credibility interval 1750–1948 CE). We also found that genetic variations were correlated with geographic regions, suggesting that the evolution of this pathogen is strongly affected by geographical associated factors. Taken together, the results of our study have potential implications for the control strategies of PVY.

Temporal analysis and adaptive evolution of the global population of potato virus M

Potato virus M (PVM), which is a member of the genus Carlavirus in the family Betaflexviridae, causes critical economic losses of nightshade crops. PVM is transmitted by aphids in a non-persistent manner, by sap inoculation and also transmitted in tubers. Previously, several reports described the genetic structure of PVM. However, the evolutionary rate, timescale, spread and adaptation evolution of the virus have not been examined. In this study, we investigated the phylodynamics of PVM using 145 nucleotide sequences of the coat protein gene and 117 sequences of the cysteine-rich nucleic acid-binding protein (NABP) gene, which were sampled between 1985 and 2013. We found that at least three lineages with isolates that were defined geographically but not by the original host were clustered. The evolutionary rate of the NABP (1.06 × 10^-2) was faster than that of the CP (4.12 × 10^-3). The time to the most recent common ancestors (TMRCAs) is similar between CP (CIs 31-110) and NABP (CIs 28-33) genes. Based on CP and NABP genes, PVM migrated from China to Canada, Iran, India and European countries, and it circulated within China. Our study is the first attempt to evaluate the evolutionary rates, timescales and migration dynamics of PVM.

Genetic diversity and molecular evolution of Ornithogalum mosaic virus based on the coat protein gene sequence

Ornithogalum mosaic virus (OrMV) has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP) gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have significant subpopulation differentiation with an F_ST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with dN/dS values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from analysis of molecular variance (AMOVA) indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. Furthermore, OrMV isolates from the genera Ornithogalum, Lachenalia and Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation.

Phylogeography and Coevolution of Bamboo Mosaic Virus and Its Associated Satellite RNA

Bamboo mosaic virus (BaMV), a plant potexvirus, has been found only in infected bamboo species. It is frequently associated with a large, linear single-stranded satellite RNA (satBaMV) that encodes a non-structural protein. Decades of collecting across a wide geographic area in Asia have accumulated a sizable number of BaMV and satBaMV isolates. In this study, we reconstructed the BaMV phylogeny and satBaMV phylogeny with partial coat protein gene sequences and partial genomic sequences, respectively. The evolutionary relationships allowed us to infer the phylogeography of BaMV and satBaMV on the Asian continent and its outlying islands. The BaMV phylogeny suggests that the BaMV isolates from Taiwan, unsurprisingly, are most likely derived from China. Interestingly, the newly available satBaMV isolates from China were found to be most closely related to the previously established Clade III, which is found in India. The general pattern of clustering along the China/India and Taiwan divide led us to hypothesize that the Taiwan Strait has been a physical barrier to gene flow in the past evolutionary history of both BaMV and satBaMV. Lastly, cophylogeny analyses revealed a complex association pattern between BaMV and satBaMV isolates from China. In general, closely related BaMV sequences tend to carry closely related satBaMV sequences as well; but instances of mismatching with distantly related satBaMV isolates were also found. We hypothesize plausible scenarios of infection and superinfection of bamboo hosts that may be responsible for the observed association pattern. However, a more systematic sampling throughout the geographic distribution of various bamboo species is needed to unambiguously establish the origin, movement, and evolution of BaMV and satBaMV.

Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan

Potato virus Y (PVY) is an important plant pathogen causing considerable economic loss to potato production. Knowledge of the population genetic structure and evolutionary biology of the pathogen, particularly at a transnational scale, is limited but vital in developing sustainable management schemes. In this study, the population genetic structure and molecular evolution of PVY were studied using 127 first protein (P1) and 137 coat protein (CP) sequences generated from isolates collected from potato in China and Japan. High genetic differentiation was found between the populations from the two countries, with higher nucleotide diversity in Japan than China in both genes and a KST value of .216 in the concatenated sequences of the two genes. Sequences from the two countries clustered together according to their geographic origin. Further analyses showed that spatial genetic structure in the PVY populations was likely caused by demographic dynamics of the pathogen and natural selection generated by habitat heterogeneity. Purifying selection was detected at the majority of polymorphic sites although some clade-specific codons were under positive selection. In past decades, PVY has undergone a population expansion in China, whereas in Japan, the population size of the pathogen has remained relatively constant.

Geographically driven adaptation of chilli veinal mottle virus revealed by genetic diversity analysis of the coat protein gene

Chilli veinal mottle virus (ChiVMV) is an important plant pathogen with a wide host range. The genetic structure of ChiVMV was investigated by analyzing the coat protein (CP) genes of 87 ChiVMV isolates from seven Asian regions. Pairwise F ST values between ChiVMV populations ranged from 0.108 to 0.681, indicating a significant spatial structure for this pathogen. In phylogeny-trait association analysis, the viral isolates from the same region tended to group together, showing a distinct geographic feature. These results suggest that geographic driven adaptation may be an important determinant of the genetic diversity of ChiVMV.

Genetic diversity and molecular evolution of arabis mosaic virus based on the CP gene sequence

Arabis mosaic virus (ArMV) is a virus with a wide host range. In this study, the genetic diversity of ArMV and the molecular mechanisms underlying its evolution were investigated using the coat protein (CP) sequence. Of the 33 ArMV isolates studied, three were found to be recombinants. The other 30 recombination-free ArMV isolates could be separated into two major lineages with a significant F ST value (0.384) and tended to cluster according to their geographical origin. Different evolutionary constraints were detected for the two linages, pointing to a role of natural selection in the differentiation of ArMV.

Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase

The goal of this study was to identify neuraminidase (NA) residue mutants from human influenza AH1N1 using sequences from 1918 to 2012. Multiple alignment studies of complete NA sequences (5732) were performed. Subsequently, the crystallographic structure of the 1918 influenza (PDB ID: 3BEQ-A) was used as a wild-type structure and three-dimensional (3-D) template for homology modeling of the mutated selected NA sequences. The 3-D mutated NAs were refined using molecular dynamics (MD) simulations (50 ns). The refined 3-D models were used to perform docking studies using oseltamivir. Multiple sequence alignment studies showed seven representative mutations (A232V, K262R, V263I, T264V, S367L, S369N, and S369K). MD simulations applied to 3-D NAs showed that each NA had different active-site shapes according to structural surface visualization and docking results. Moreover, Cartesian principal component analyses (cPCA) show structural differences among these NA structures caused by mutations. These theoretical results suggest that the selected mutations that are located outside of the active site of NA could affect oseltamivir recognition and could be associated with resistance to oseltamivir.

Complete genome sequence of nine isolates of canna yellow streak virus reveals its relationship to the sugarcane mosaic virus (SCMV) subgroup of potyviruses

Complete genome sequences were obtained from nine isolates of canna yellow streak virus (CaYSV). CaYSV belongs to the sugarcane mosaic virus (SCMV) subgroup of potyviruses with johnsongrass mosaic virus (JGMV) as its closest relative. Multiple sequence alignments showed a pattern of amino acid substitutions in the CP sequences, which enabled us to relate these isolates to South East Asian or European isolates. Biological characterization of CaYSV identified Nicotiana benthamiana, Chenopodium quinoa and Phaseolus vulgaris as experimental hosts. Given the popularity and global trade of cannas, a clear picture of the genetic diversity of CaYSV is critical to disease management.

Full-genome analyses of a Potato Virus Y (PVY) isolate infecting pepper (Capsicum annuum L.) in the Republic of South Africa

Potato Virus Y (PVY) is a pathogen of economic importance in pepper and other major crop species in the family Solanaceae. Three major PVY strain groups: O, C, and N, have been distinguished on the basis of genome sequencing. In this study, the first full-genome sequence of a PVY isolate (JVW-186) infecting pepper from the province of KwaZulu-Natal, Republic of South Africa is reported. The complete genome sequence of JVW-186 was assembled from overlapping RT-PCR clones using MEGA 5 software. Two ORFs were identified at position 186 and 2915 of the sequence encoding the viral polyprotein and the frameshift translated protein P3N-PIPO, respectively. RDP4 software confirmed three recombination breakpoints at position 343, 1365, and 9308 of the sequence. At each recombination event, a 1,021-bp fragment at the 5' end in the region of the P1/HC-Pro protein and a 392-bp fragment in the region of the coat protein shared a high sequence similarity of 91.8 and 98.89 % to the potato borne PVY(C) isolate PRI-509 and the PVY(O) isolate SASA-110, respectively. The non-recombinant fragment 1 (342-bp) clustered within the C clade of PVY isolates; however, the large 7,942-bp fragment 3 did not cluster within any of the clades. This suggests the possibility of a PVY isolate that has evolved due to the dynamics of selection pressure or the likelihood of an ancestral PVY strain.

Surface plasmon resonance for monitoring the interaction of Potato virus Y with monoclonal antibodies

Surface plasmon resonance (SPR)-based biosensors have been widely utilized for measuring interactions of a variety of molecules. Fewer examples include higher biological entities such as bacteria and viruses, and even fewer deal with plant viruses. Here, we describe the optimization of an SPR sensor chip for evaluation of the interaction of the economically relevant filamentous Potato virus Y (PVY) with monoclonal antibodies. Different virus isolates were efficiently and stably bound to a previously immobilized polyclonal antibody surface, which remained stable over subsequent injection regeneration steps. The ability of the biosensor to detect and quantify PVY particles was compared with ELISA and RT-qPCR. Stably captured virus surfaces were successfully used to explore kinetic parameters of the interaction of a panel of monoclonal antibodies with two PVY isolates representing the main viral serotypes N and O. In addition, the optimized biosensor proved to be suitable for evaluating whether two given monoclonal antibodies compete for the same epitope within the viral particle surface. The strategy proposed in this work can help to improve existing serologic diagnostic tools that target PVY and will allow investigation of the inherent serological variability of the virus and exploration for new interactions of PVY particles with other proteins.