Identification of the molecular make-up of the Potato virus Y strain PVY(Z): genetic typing of PVY(Z)-NTN

Potato virus Y (PVY) strains were originally defined by interactions with different resistance genes in standard potato cultivars. Five distinct strain groups are defined that cause local or systemic hypersensitive responses (HRs) in genetic background with a corresponding N gene: PVY(O), PVY(N), PVY(C), PVY(Z), and PVY(E). The nucleotide sequences of multiple isolates of PVY(O) and PVY(N) differ from each other by ≈8% along their genomes. Additionally, complete genome sequences of multiple recombinant isolates are composed of segments of parental PVY(O) and PVY(N) sequences. Here, we report that recombinant isolate PVY-L26 induces an HR in potato 'Maris Bard' carrying the putative Nz gene, and is not recognized by two other resistance genes, Nc and Ny(tbr). These genetic responses in potato, combined with the inability of PVY-L26 to induce vein necrosis in tobacco, clearly define it as an isolate from the PVY(Z) strain group and provide the first information on genome structure and sequence of PVY(Z). The genome of PVY-L26 displays typical features of European NTN-type isolates with three recombinant junctions (PVY(EU-NTN)), and the PVY-L26 is named PVY(Z)-NTN. Three typical PVY(NTN) isolates and two PVY(N) isolates, all inducing vein necrosis in tobacco, were compared with PVY-L26. One PVY(NTN) isolate elicited HR reactions in Maris Bard, similar to PVY-L26, while two induced a severe systemic HR-like reaction quite different from the quasi-symptomless reaction induced by two PVY(N) isolates. 'Yukon Gold' potato from North America produced HR against several PVY(NTN) isolates, including PVY-L26, but only late and limited systemic necrosis against one PVY(N) isolate. Consequently, according to symptoms in potato indicators, both PVY(Z) and PVY(NTN) isolates appeared biologically very close and clearly distinct from PVY(O) and PVY(N) strain groups.     

Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains

The ordinary strain of Potato virus Y (PVY), PVY(O), causes mild mosaic in tobacco and induces necrosis and severe stunting in potato cultivars carrying the Ny gene. A novel substrain of PVY(O) was recently reported, PVY(O)-O5, which is spreading in the United States and is distinguished from other PVY(O) isolates serologically (i.e., reacting to the otherwise PVY(N)-specific monoclonal antibody 1F5). To characterize this new PVY(O)-O5 subgroup and address possible reasons for its continued spread, we conducted a molecular study of PVY(O) and PVY(O)-O5 isolates from a North American collection of PVY through whole-genome sequencing and phylogenetic analysis. In all, 44 PVY(O) isolates were sequenced, including 31 from the previously defined PVY(O)-O5 group, and subjected to whole-genome analysis. PVY(O)-O5 isolates formed a separate lineage within the PVY(O) genome cluster in the whole-genome phylogenetic tree and represented a novel evolutionary lineage of PVY from potato. On the other hand, the PVY(O) sequences separated into at least two distinct lineages on the whole-genome phylogenetic tree. To shed light on the origin of the three most common PVY recombinants, a more detailed phylogenetic analysis of a sequence fragment, nucleotides 2,406 to 5,821, that is present in all recombinant and nonrecombinant PVY(O) genomes was conducted. The analysis revealed that PVY(N:O) and PVY(N-Wi) recombinants acquired their PVY(O) segments from two separate PVY(O) lineages, whereas the PVY(NTN) recombinant acquired its PVY(O) segment from the same lineage as PVY(N:O). These data suggest that PVY(N:O) and PVY(N-Wi) recombinants originated from two separate recombination events involving two different PVY(O) parental genomes, whereas the PVY(NTN) recombinants likely originated from the PVY(N:O) genome via additional recombination events.     

Biological and sequence comparisons of Potato virus Y isolates associated with potato tuber necrotic ringspot disease

The biological and molecular relationships between a large number of Potato virus Y (PVY) isolates were examined, concentrating mainly on isolates associated with potato tuber necrotic ringspot disease (PTNRD). Following detailed analysis of the coat-protein gene, four main groups were identified which broadly corresponded to the phenotype of the different isolates. The groups comprised the ordinary strain (PVY^O), the necrotic strain (PVY^N), the C strain (PVY^C) and a group of recombinant (between ordinary and necrotic) isolates. In the latter group, all members were associated with PTNRD. However, four nonrecombinant isolates were also identified which were associated with PTNRD or tuber necrosis. Three were from tubers showing PTNRD symptoms in the field, while the fourth originated from symptomless tubers, but could cause necrotic rings on tubers under glasshouse conditions. The results show that although coat-protein recombination is always found associated with the PTNRD phenotype, some nonrecombinant isolates have very similar biological properties.     

Occurrence of Potato virus Y strain PVYNTN in foundation seed potatoes in Japan,and screening for symptoms in Japanese potato cultivars

In 2008 and 2009 seasons, a sudden increase in Potato virus Y (PVY) incidence was recorded in foundation seed potatoes in Hokkaido, northern Japan. This increase was obvious during the field inspection and the postharvest indexing. Molecular typing revealed that besides the previously reported strains of PVY^O and PVY^NA‐N, the most common strain identified was the recombinant PVY^NTN, with three characteristic recombinant junctions at the HC‐Pro, VPg and CP regions. No potato tuber necrotic ringspot disease (PTNRD) was observed in foundation seed potatoes in correlation with the presence of PVY^NTN. Moreover, an isolate with a typical PVY^NTN recombinant genome, namely Eu‐12Jp, did not induce PTNRD in 62 Japanese potato cultivars tested in both primarily and secondarily infected plants. Two cultivars carrying the extreme resistance gene Ry_chc were resistant to the infection with Eu‐12Jp, which presents potential sources of resistance to PVY^NTN. Eu‐12Jp induced systemic mottle in potato cultivars Desiree and King Edward carrying resistance genes Ny and Nc, respectively, but induced a hypersensitive reaction in potato cultivar Maris Bard, with the Nz hypothetical resistance gene typical of the PVY^Z strain group. Therefore, based on the genome structure and the reaction of the potato N resistance genes, Eu‐12Jp should be classified as PVY^Z‐NTN, as described for isolates from Idaho, USA recently. This is the first report of PVY^Z‐NTN in Japan and the sudden and increased occurrence of PVY^NTN/PVY^Z‐NTN represents a potential risk of PTNRD developing and increases the significance of PVY in Japan.     

Genetic diversity of Potato virus Y infecting tobacco crops in China

Genetic variability of Potato virus Y (PVY) isolates infecting potato has been characterized but little is known about genetic diversity of PVY isolates infecting tobacco crops. In this study, PVY isolates were collected from major tobacco-growing areas in China and single-lesion isolates were produced by serial inoculation on Chenopodium amaranticolor. Most isolates (88%) caused systemic veinal necrosis symptoms in tobacco. Of these, 16 isolates contained a PVY(O)-like coat protein (CP) and PVY(N)-like helper component proteinase (HC-pro) and, in this respect, were similar to the PVY(N-Wi), PVY(N:O), and PVY-HN2 isolates characterized from potato in Europe, the United States, and China, respectively; two isolates contained a PVY(O)-like HC-pro and a PVY(N)-like CP; another two isolates had recombination junctions in the CP-encoding region. Both the HC-pro and CP of PVY were under negative selection as a whole; however, seven amino acids in HC-pro and six amino acids in CP were under positive selection. Selection pressures differed between the subpopulations of PVY distinguished by phylogenetic analysis of HC-pro and CP sequences. When PVY isolates from potato were included, no host-specific clustering of the PVY isolates was observed in phylogenetic and nucleotide diversity analyses, suggesting frequent spread of PVY isolates between potato and tobacco crops in the field.     

PVYNTN-NW, a novel recombinant strain of Potato virus Y predominating in potato fields in Syria

Detailed characterization of a number of isolates of PVY^SYR, a novel recombinant strain of Potato virus Y (PVY) from Syria, was conducted to elucidate their origin, assess their significance and achieve a final classification of PVY^SYR. Recombination analysis grouped isolates of PVY^SYR into three recombination patterns, SYR-I, SYR-II and SYR-III, which varied in the first 700 nucleotides of their genomes, with the second recombination pattern, SYR-II, the most frequent. PVY^SYR isolates shared highest genomic identity and close phylogenetic relationships with PVY^NTN and PVY^NW isolates from Syria, suggesting a common origin and local emergence of these isolates in Syria. All PVY^SYR isolates (total of 20) induced tobacco veinal necrosis, but reacted to a PVY^O monoclonal antibody, typical characteristics of the previously reported PVY^NW (or PVY^N:O). In potato, however, four isolates tested (one of SYR-I and three of SYR-II) induced potato tuber necrotic ringspot disease (PTNRD), which is the characteristic phenotype of PVY^NTN. Given the shared properties of SYR-I and SYR-II isolates with PVY^NTN and PVY^NW, it was decided that they represent a new recombinant strain of the PVY^N strain group, with the proposed name PVY^NTN-NW. The classification of SYR-III will be possible only after testing the phenotype in potato. The high prevalence of PVY^NTN-NW in potatoes and weeds, as well as its ability to induce PTNRD, demonstrates its importance and the necessity for its control.     

马铃薯Y病毒中国分离物的分子株系组成

 马铃薯Y病毒(potato virus Y,PVY)主要侵染马铃薯和烟草等茄科作物,给世界农业造成巨大经济损失。本文对测定的23个及GenBank中注册的52个中国PVY分离物ORF序列进行了系统发育、重组和选择压等分析。系统发育分析表明,根据ORF序列可把我国75个PVY分离物和国外30个参比分离物分成O、C、E、NTN-NW(SYR-I型)、NTN-NW(SYR-II型)、NTN(NTN-a型)、NTN(NTN-b型)、NA-N/NTN、Eu-N、N-Wi(N:O型)和N-Wi(N-Wi型)等11个分子株系,其中中国PVY分离物属于除E和C株系外的9个分子株系。除ME162、guiyang、PVYzu、SD-G、WA-13和CN:JL-1:17等 6个分离物基因组中未检测到重组,其余69个分离物均存在明显重组。根据重组位点的不同,中国PVY可分为11种重组类型,其中5种为新的重组类型。选择压分析表明,中国PVY分离物的11个基因均处于负选择,其中核内含体b基因受到的选择压最大,PIPO受到的选择压最小。基因流分析表明,黑龙江、河南和山东PVY分离物间基因交流频繁,马铃薯与烟草PVY分离物之间基因交流频繁。本研究的结果明确了中国PVY分离物的分子株系组成,对指导PVY的检测和防控具有积极作用。     

Potato Virus Y from Petunia can cause Symptoms of Potato Tuber Necrotic Ringspot Disease (PTNRD)

A potyvirus known to be an important agent involved in causing a disease of trailing petunias, was identified as being a member of the necrotic strain of potato virus Y (PVY) using a number of monoclonal antibodies. The sequence of the coat protein gene for the PVY isolate was determined and when compared with sequences for other PVY strains it was shown to cluster closely with isolates of PVY^NTN and to have a recombination point present within the coat protein common with other isolates of PVY^NTN. When inoculated onto potato tuber necrotic ringspot disease (PTNRD) susceptible potato cultivars the petunia isolate was found to be capable of causing necrotic tuber symptoms, consistent with those caused by other isolates of PVY^NTN. Due to the number of similarities it is thought the petunia isolate belongs to the PVY^NTN group of isolates. Out of 24 species of bedding and pot plant crops tested, 19 were shown by mechanical inoculation to be susceptible to PVY, highlighting not only a clear risk to a number of commercially important plant species from PVY^NTN infected trailing petunias, but also other susceptible crops grown in these areas.     

马铃薯Y病毒在种薯中检出率及其株系鉴定

 马铃薯是我国重要粮食和经济作物。马铃薯Y病毒(potato virus Y,PVY)是危害马铃薯生产的重要病害。种植脱毒种薯是防治PVY最有效的途径。马铃薯种薯携带PVY问题严重,但种薯中PVY株系还不清楚。本研究利用PVY特异性抗体检测了7个马铃薯品种362个种薯,发现不同品种种薯带毒率差异较大,最高达12%。通过RT-PCR方法扩增获得了7个PVY分离物编码区全序列。重组分析发现7个分离物基因组均为重组型,根据重组位点的差异可以分为PVY^NTN-NW(SYR-II型)、Rec-1、Rec-2和Rec-3等4种重组类型,后3种为新重组类型。系统进化分析发现,分离物HQH18G3-10与PVY^NTN-NW(SYR-II型)处于同一个大的分支,但与中国PVY大田分离物聚集在一起形成一个相对独立的组,命名为PVY^NTN-NW(CN型);其余6个分离物与数据库中的中国分离物聚集在PVY^N-Wi组。这暗示PVY中国分离物具有相对独立的进化过程,PVY马铃薯大田分离物和种薯分离物进化上相近。所有分离物均能在珊西烟上引起典型叶脉坏死症状,HQH18G3-10引起的坏死症状最为严重。本研究首次报道了我国种薯内PVY发生情况,对分析病毒发生发展规律和防控具有借鉴作用。     

马铃薯Y病毒在种薯中检出率及其株系鉴定

马铃薯是我国重要粮食和经济作物。马铃薯Y病毒(potato virus Y,PVY)是危害马铃薯生产的重要病害。种植脱毒种薯是防治PVY最有效的途径。马铃薯种薯携带PVY问题严重,但种薯中PVY株系还不清楚。本研究利用PVY特异性抗体检测了7个马铃薯品种362个种薯,发现不同品种种薯带毒率差异较大,最高达12%。通过RT-PCR方法扩增获得了7个PVY分离物编码区全序列。重组分析发现7个分离物基因组均为重组型,根据重组位点的差异可以分为PVY^NTN-NW(SYR-II型)、Rec-1、Rec-2和Rec-3等4种重组类型,后3种为新重组类型。系统进化分析发现,分离物HQH18G3-10与PVY^NTN-NW(SYR-II型)处于同一个大的分支,但与中国PVY大田分离物聚集在一起形成一个相对独立的组,命名为PVY^NTN-NW(CN型);其余6个分离物与数据库中的中国分离物聚集在PVY^N-Wi组。这暗示PVY中国分离物具有相对独立的进化过程,PVY马铃薯大田分离物和种薯分离物进化上相近。所有分离物均能在珊...     

Incidence of potato viruses and characterisation of <Emphasis Type="Italic">Potato virus Y</Emphasis> variability in late season planted potato crops in Northern Tunisia

Surveys were conducted of symptomatic potato plants in late season crops, from the major potato production regions in Northern Tunisia, for infection with six common potato viruses. The presence of Potato leafroll virus (PLRV), Potato virus Y (PVY), Potato virus X (PVX), Potato virus A (PVA), Potato virus S (PVS) and Potato virus M (PVM) was confirmed serologically with virus infection levels up to 5.4, 90.2, 4.3, 3.8, 7.1 and 4.8%, respectively. As PVY was prevalent in all seven surveyed regions, further biological, serological and molecular typing of 32 PVY isolates was undertaken. Only one isolate was shown to induce PVY^O-type symptoms following transmission to tobacco and to react only against anti-PVY^O-C antibodies. Typical vein necrosis symptoms were obtained from 31 samples, six of which reacted against both anti-PVY^N and anti-PVY^O-C antibodies showing they contained mixed isolates, while 25 of them reacted only with anti-PVY^N antibodies. An immunocapture RT-PCR molecular test using a PVY^NTN specific primer pair set in the 5’NTR/P1 genomic region and examination of recombinant points in three genomic regions (HC-Pro/P3, CI/NIa and CP/3’NTR) showed that all 25 serotype-N PVY isolates were PVY^NTN variants with similar recombinations to the standard PVYNTN-H isolate. This is the first report of the occurrence of the PVY^NTN variant and its high incidence in late season potatoes in Tunisia.     

The effects of co‐infection by different Potato virus Y (PVY) isolates on virus concentration in solanaceous hosts and efficiency of transmission

The influence of co‐infection on concentration and accumulation of genetically different isolates of Potato virus Y (PVY) in potato and tobacco plants and the efficiency of transmission by Myzus persicae of PVY isolates from doubly versus singly infected plants were evaluated. The vector ability to simultaneously transmit two virus isolates was examined. Eight PVY isolates represented three strain groups: PVY^O (pathotype and serotype O), PVY^NW (pathotype N and serotype O), and PVY^NTN (pathotype and serotype N). Different diagnostic methods, including DAS‐ELISA, multiplex RT‐PCR, aphid transmission tests and bioassays, were applied to detect the presence of PVY isolates in source and assay plants. Significant reductions in concentrations of certain PVY isolates during co‐infection with other isolates were found both in potato and tobacco plants. The observed effects were both isolate‐ and host‐dependent in form. The highest rates of virus transmission by single aphids were recorded with PVY^NTN isolates, and the lowest ones with PVY^O isolates. Individual aphids of M. persicae were able to simultaneously transmit two PVY isolates. The frequency of transmission was generally low, but it reached as high as 20% for one of the isolate combinations. The findings presented in the work provide proof for antagonistic within‐plant interactions between isolates of PVY, with some implications of these interactions for virus transmission by aphid vectors. Consequently, this research contributes to a better understanding of the epidemiology of the disease caused by PVY.     

来自安徽不同寄主PVY分离物的血清学鉴定及其cp基因分子进化分析

 Tobacco and potato samples showing symptoms of PVY were collected from different regions in Anhui Province, and the ELISA results of partial samples were positive. The total RNA was extracted from the positive samples by TRIZOL methods. Specific primer pair was designed to amplify cp gene of PVY by RT-PCR. Sequencing results indicated that the full length of cp gene of PVY from tobacco (PVY-CP-4) and pota-to (PVY-CP-7) is 801 nts, and each of them encodes 266 amino acids. A phylogenetic tree based on alignment of cp nucleotide sequences was constructed and the sequence comparing of cp gene was conducted. The results showed that PVY-CP-4 could be grouped into one branch with PVY^O and PVY^N:O and shared the highest sequence similarity (99.4%) with PVY^O (EF026074). It was suggested that PVY-CP-4 derived from tobacco in Hefei might belong to PVY^O. PVY-CP-7 clustered together with PVYN and PVYNTN and formed another branch. Furthermore, PVY-CP-7 shared the highest sequence similarity (98.3%) with PVY^NTN(AJ890347), PVY^NTN (EF026075) and PVY^NTN(AJ585342). It was supposed that PVY-CP-7 derived from potato in Wuhe probably belonged to PVY^NTN.     

马铃薯Y 病毒贵州黔西烟草分离物P1 基因序列分析

 Potato virus Y (PVY) is the type member of the genus Potyvirus and infects several important solanaceous crops, including tobacco. PVY is one of the most widespread and economically destructive viruses.The P1 region of PVY had been used to determine the diversity, evolution and the homology based on the
geographic location of the virus. The P1 region of PVY tobacco isolate from Qianxi in Guizhou Province was cloned and sequenced. Database searches and multiple sequence alignment showed subtle variation within the same strain, while apparent variation between O strain and the other three strains, N, NTN and N∶O. Moreover, variation in P1 region of Qianxi isolate derived from the gene mutation rather than the recombination among genomes. Phylogenic analysis revealed that the clustering only discriminated O strain from others. Consequently, sequence analysis in P1 region is unable to afford strain determination.     

Brazilian Potato virus Y isolates identified as members of a new clade facilitate the reconstruction of evolutionary traits within this species

Potato virus Y (PVY) is a plant virus distributed worldwide that causes damage to several species of the Solanaceae family. It was established long ago that groups of PVY isolates defined by phylogenetic analyses correlate strongly with those demarcated by differential biological properties. Consequently, life‐history traits of this viral species can be inferred by phylogenetic analysis. In this study, characteristics of PVY isolates sampled in different tobacco fields in Brazil were analysed and most of the tested Brazilian PVY isolates were assigned to the recently described unconventional serogroup Y^U. The analysis of molecular diversity of the coat protein (CP) cistron from some Y^U isolates made it possible (i) to identify specific amino acid residues in the N‐terminal of the CP protein and (ii) to assign some Y^U isolates to a new PVY clade. The symptoms caused by isolates belonging to this new PVY ‘Brazilian’ clade and their ability to infect selected susceptible hosts led to the conclusion that neither veinal necrosis symptoms expressed on infected tobacco plants nor adaptation to potato or pepper hosts are ancestral characteristics of PVY. These observations suggest that PVY has gained a remarkable new biological property and broadened its host range over time.     

Characterization of potato Y potyvirus isolates from tomato crops in Islas Canarias (Spain)*

A disease caused by potato Y potyvirus (PVY) affects tomato plantations with variable severity in Tenerife Island. Affected plants show diverse symptoms such as necrotic lesions or mild to severe mosaic in leaves and whitish spots in green fruits that remain after ripening. Tomato PVY isolates and few potato and capsicum PVY isolates have been characterized on the basis of biological, serological and molecular criteria. All PVY isolates reacted positively to monoclonal antibodies specific for PVY^O/C or PVY^N strains, and nearly 50% of tomato PVY isolates were recognized by both. Differentiation of PVY strains according to the response of inoculated experimental plants was confusing due to the variability of viral aggressiveness and symptomatology induced. RFLP analysis of the CP gene and 3’untranslated region (UTR) revealed high variability. In addition to mixed infection by different PVY strains, the biological and molecular properties of those tomato PVY isolates that react to both monoclonal antibodies could be explained as the result of RNA recombination between distinct PVY strains which infect the same host plant.     

A novel type of Potato virus Y recombinant genome,determined for the genetic strain PVYE

Two Potato virus Y (PVY) isolates collected in Brazil, PVY‐AGA and PVY‐MON, were identified as recombinants between two parent genomes, PVY^NTN and PVY‐NE‐11, with a novel type of genomic pattern. The new recombinants had an ordinary PVY^NTN genome structure for approximately 6·7‐kb from the 5′‐end of the genome whereas the 3′‐terminal 3·0‐kb segment had two fragments of NE‐11‐like sequence separated by another small PVY^NTN‐like fragment. PVY strains are defined based on the hypersensitive resistance (HR) response in potato indicators. Both PVY‐AGA and PVY‐MON isolates did not induce the HR in potato cultivars carrying Ny, Nc, or (putative) Nz genes and thus were able to overcome all known resistance genes to PVY. Only one of the two isolates, PVY‐AGA, induced a vein necrosis reaction in tobacco. The biological responses of the potato indicators and tobacco defined PVY‐MON as an isolate of the PVY^E strain. To distinguish PVY‐AGA and PVY‐MON from other PVY^NTN isolates, an RT‐PCR test was developed utilizing new specific primers from the capsid protein gene area and producing a characteristic 955‐bp band. Serological profiling of these PVY isolates with three monoclonal antibodies revealed an unusual reactivity, where one of the two commercial PVY^N‐specific monoclonal antibodies did not recognize PVY‐AGA. The ability of these new PVY recombinants to overcome resistance genes in potato producing mild or no symptoms, combined with the lack of serological reactivity towards at least one PVY^N‐specific antibody may present a significant threat posed by these isolates to seed potato production areas.     

Necrotic diseases caused by viruses in Swedish potato tubers

Potato tuber necrosis in the form of spraing symptoms is caused by infection with Potato mop‐top virus (PMTV) or Tobacco rattle virus (TRV); spraing has become more important in the Swedish potato crop production. In this study, the presence in Sweden of three potato‐infecting viruses associated with necrotic symptoms in tubers was demonstrated: PMTV, TRV and Tobacco necrosis virus (TNV). This study shows that both PMTV and TRV are frequent in Swedish potato fields. PMTV was found in all Swedish counties, except the two most northern ones. TRV was present at several locations in southern and up to the central parts of Sweden. Both viruses were found further north than observed in earlier surveys. PMTV and TRV were analysed in tubers with spraing symptoms and it was not possible to decide visually if the symptoms were caused by either PMTV or TRV. Furthermore, a high occurrence of symptomless tuber infections was observed for several potato cultivars. A unique observation from this study was a mixed infection of both PMTV and TRV in tubers of cv. Berber, where no visual differences on symptom development were detectable for these tubers compared to single infections. During the survey, tubers of cv. Melody were found to display necrotic symptoms in the skin that are characteristic for the ABC disease. This suggested infection by TNV, which also could be confirmed.