Tomato (Solanum lycopersicum L.) is one of the most important vegetable crops cultivated worldwide. The crop occupies 4.1 million hectares with an average productivity of 34 t/ha globally, whereas in India it is cultivated in 880,000 ha with a productivity of 21.2 t/ha (FAOSTAT 2014; DACFW 2015). Several biotic and abiotic stresses contribute to loss of productivity. Among the different biotic stresses, bud necrosis disease caused by peanut bud necrosis virus (PBNV) and persistently transmitted by thrips has become a severe threat in the major tomato growing areas of the country. Depending on the crop growth stage, variety and season, PBNV causes yield loss of tomato up to 80–100% (Venkata Ramana et al. 2011). Since tomato is cultivated throughout the year in southern India, inoculum is readily available making the disease a constant threat during all seasons. In recent years, due to climatic changes and increase in vector population (Thrips), bud necrosis disease occurs frequently on tomato posing a serious threat to its cultivation in North India by affecting different varieties/hybrids, thus leading to severe yield loss. In addition, other viral diseases such as leaf curl and mosaic are responsible for considerable yield loss in Northern India. Deliberating these facts, real-time pest surveillance was conducted in different farmers’ fields to monitor the incidence of viral disease on tomato as well as to determine the orthotospovirus species in the Indo-Gangetic Eastern Plain region of India. Under natural conditions, the infected tomato plants show symptoms such as complete burning of flowers and apical flower buds, necrosis on leaf veins, stems, petiole and fruits, mosaic, mottling and curling of leaves. The present study was carried out to investigate the virus or viruses associated with these diseases of tomato; moreover, real-time symptom surveillance was conducted with reference to weather parameters.

Roving surveys were undertaken in different tomato fields during 2015 and 2016 in Varanasi and Mirzapur districts of Uttar Pradesh (India), to evaluate and document the different viruses infecting tomato. Visual estimation of disease incidence was calculated by counting the number of infected plants diagonally across the entire field. A total of 11 villages belonging to Mirzapur and Varanasi districts were surveyed, at both the vegetative and fruiting stages of the crop (Table 1). During the survey, disease incidence of tomato plants showing virus and virus-like symptoms (mosaic, yellowing, leaf curls, witches’ broom and bud necrosis) was recorded from each location. Meanwhile, both diseased and healthy samples were collected for further analysis. Among the different symptoms, the highest incidence (>50%) was that of leaf curl noticed across the fields in both the districts at the vegetative and fruiting stage of crops followed by mosaic and bud necrosis burning of plants. The necrotic disease incidence ranged from 20 to 50%. Infected plants showed symptoms of concentric necrotic rings with green centre on leaves, necrotic lesions on the stem and floral parts and burning of apical buds, manifesting a general burnt up appearance of the infected fields (Fig. 1a-d).

Table 1 Details of field survey for collection of virus infected samples of tomato in Northern India
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Fig. 1
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Symptomatology and virus diagnosis in tomato plants surveyed in Indo-Gangetic plains. Tomato symptoms (a-d); Percentage of samples infected by the viruses tested (e); PCR detection of orthotospovirus using universal degenerate primer pair gl3617/gl4435c (f)

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A total of 34 tomato plant samples showing typical virus and virus-like symptoms were collected and brought to the Plant Pathology Laboratory, ICAR-Indian Institute of Vegetable Research, Varanasi. Initially, the samples were tested for tomato mosaic virus (ToMV), pepino mosaic virus (PepMV), capsicum chlorosis virus (CaCV) and tomato chlorosis virus (ToCV) by Double Antibody Sandwich - Enzyme Linked Immuno Sorbent Assay (DAS-ELISA) using different known polyclonal antibodies (DSMZ, Germany), and for peanut bud necrosis virus (PBNV) by Direct Antigen Coating- Enzyme Linked Immuno Sorbent Assay (DAC-ELISA) to confirm possible mixed infection of different viruses under field conditions. Thirteen of the 34 samples which displayed the symptoms of necrotic lesions on the stem and floral parts, and burning of apical buds were positive for PBNV infection; whereas six out of 34 samples showing mosaic symptoms were positive for ToMV (Table 2). Since the antiserum used for the detection of ToMV might also detect other tobamoviruses such as tomato mottle mosaic virus (ToMMV), tomato brown rugose fruit virus (TBRFV), and tobacco mosaic virus (TMV), etc., future analysis may be carried out to confirm the identity of the tobamovirus(es) associated with tomato crop.

Table 2 Detection of viruses from collected samples
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Moreover, total nucleic acid extracted from the infected tomato samples using CTAB method (Doyle and Doyle 1990) was tested by PCR using degenerate begomovirus primers (Rojas et al. 1993; Venkataravanappa et al. 2012) to know the status of begomoviruses associated with tomato in Indo-Gangetic eastern plains of India. Twenty-five out of 34 samples were confirmed with begomovirus infection. The samples were additionally tested using species-specific primers for tomato leaf curl New Delhi virus (ToLCNDV), tomato leaf curl Gujarat virus (ToLCGV), tomato leaf curl Palampur virus (ToLCPalV), tomato leaf curl Bangalore virus (ToLCBV) and tomato leaf curl Karnataka virus (ToLCKV). Among them, 12 samples were found to be infected with ToLCNDV, three samples with ToLCKV and one sample with ToLCPalV, while none of the samples were infected with ToLCBV (Table 2). Interestingly, combinations of more than one begomovirus (ToLCNDV+ToLCGV, ToLCNDV+ToLCKV, ToLCNDV+ToLCGV+ToLCKV and ToLCNDV+ToLCPalV+ToLCKV) were also detected in tomato plants exhibiting distinct symptoms of leaf curl. The begomovirus species-specific primers and the begomoviruses identified from the tomato crop are displayed in Tables 2 and 3. Similarly, total nucleic acid extractions were also tested by PCR using alpha (α) and betasatellites (β) specific primers (Briddon et al. 2002; Bull et al. 2003). Among 34 samples, 20 β-satellites, 27 α-satellites, 17 both β-satellites and α-satellites with helper virus and six β-satellites and α-satellites without helper virus were detected (Table 2). The α-satellites are self-replicating whereas β-satellites are always dependent on the specific helper components for their multiplication (Nawaz-ul-Rehman and Fauquet 2009; Briddon 2004). Furthermore among 13 samples positive for begomoviruses with species specific primers, eight samples were associated with α- (2 samples) and β-satellites (6 samples) and five samples are not associated with any of the α- and β-satellites. Since these samples are negative for ToLCNDV, ToLCGV, ToLCPalV, ToLCBV and ToLCKV, they very likely carry one or more uncharacterized begomovirus. Similarly, six samples negative for begomoviruses were positive for satellites. This might be due to evolution in the primer binding site preventing the detection of the same begomovirus species, or presence in the sample of a new begomovirus. Overall, the infection of multiple viruses in combinations such as PBNV + begomovirus (5), PBNV + ToMV (2) and PBNV + ToMV + begomvirus (4) were also detected (Fig. 1e). Earlier, several studies recorded multiple infections in tomato and cucurbits from different parts of the world (Gómez et al. 2010; Nagendran et al. 2017).

Table 3 Details of primers used in this study
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PBNV was mechanically transmitted from tomato to Vigna unguiculata (cv. ‘C152’). The inoculated plants manifested chlorotic circular spots with concentric rings 8–10 days post-inoculation. Later, PBNV infection of inoculated cowpea plants were confirmed using DAS-ELISA with polyclonal antisera of PBNV. In addition, to confirm serological assays, total RNA was isolated from the 13 symptomatic tomato samples using TRIzol® Reagent (Ambion Life Technologies, USA) according to manufacturer’s instructions. First strand cDNA synthesis was achieved using cDNA synthesis kit (Thermo Scientific, USA) as per manufacturer’s instructions. RT-PCR was carried out with orthotospovirus universal primer pair (gl3617/gl4435c-) corresponding to L RNA (Chu et al. 2001). The PCR delivered an amplicon size of ca. 800 bp in all symptomatic tomato samples but not in the non-symptomatic leaves (Fig. 1f) which confirms a orthotospovirus infection. The amplified products were cloned and sequenced. In BLAST search, the sequence shared 98% nucleotide identity with PBNV L RNA. Phylogenetic analysis carried out using MEGA 6.0 with known orthotospovirus sequences retrieved from GenBank database showed that the PBNV infecting tomato crops in the Indo-Gangetic plain were closely grouped with PBNV infecting peanut plant in Southern India (Fig. 2).

Fig. 2
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Phylogenetic tree based on nucleotide sequences of RdRp gene on L RNA of PBNV isolate infecting tomato () in Indo-Gangetic plain in comparison with other orthotospoviruses. The tree was constructed using the maximum likelihood method with 1000 bootstrap replicates

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Field surveys were conducted to record real time incidence of viral-like diseases on tomato (cv. ‘Kashi Vishesh’) at ICAR-Indian Institute of Vegetable Research (IIVR) farm during the two seasons of 2015–2016: (i) monsoon season [August to January - 37th to 3rd standard meteorological week (SMW)] and (ii) winter season (November to March – 45th to 7th SMW). The viral disease incidence was recorded based on visual symptoms evaluation in protected field (sprayed with insecticide for insect vector management) and unprotected field (without any insecticide spray) on a weekly basis, along with recorded weather parameters. The weather conditions (data obtained from the meteorological observatory located at ICAR-IIVR, Varanasi; Fig. 3a) affected bud necrosis disease incidence development under natural conditions. Disease incidence was found to increase in accordance with crop growth from 0 to 50% during monsoon season and 0 to 40% during winter season (Fig. 3b-c). Maximum disease incidence of 50% (monsoon season) and 40% (winter) was recorded during the 3rd SMW and 7th SMW, respectively (Fig. 3c). Initially, the incidence was low, then, it started to increase from the 43rd SMW forth during monsoon season and 46th SMW onwards during the winter season. An unusual severe incidence of necrotic symptoms coincided with long dry spells and high temperatures (more than 35 °C) from the 37th SMW onwards. The present findings are in agreement with the observations of Llamas-Llamas et al. (1998), who studied the effect of two temperature regimes (daytime, 29 ± 2 °C, night-time, 24 ± 3 °C; and daytime, 23 ± 1 °C, night-time, 18 ± 2 °C) on the symptoms induced by tomato spotted wilt virus (TSWV) in Physalis ixocarpa and Datura stramonium, where higher temperatures caused an increase in both incidence and rate of development of symptoms. Mean disease incidence was calculated using the standard error (analysis of significance) with the two seasons data. The average disease incidence of bud necrosis was 12.66 and 19.06% in the protected and unprotected fields respectively. Leaf curl was recorded at 10.02 and 15.02% in protected and unprotected fields respectively. Minimum incidence of mosaic was recorded in both protected (6.56%) and unprotected (7.77%) fields (Fig. 3d).

Fig. 3
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Meteorological parameters and major viral disease incidence on tomato during cropping seasons. Meteorological parameters during tomato cropping season (a); Weekly incidence of major viral diseases in tomato during monsoon season (b); Weekly incidence of major viral diseases in tomato during winter season (c); and Average viral disease incidence of different types over the monsoon and winter seasons in protected and unprotected tomato crops (d)

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From the results of present study, it is inferred that the causal agent for bud necrosis disease of tomato in Indo-Gangetic eastern plains of India is PBNV. Additionally, begomoviruses such as ToLCNDV, ToLCKV and ToLCPalV cause leaf curl diseases in association with their respective α- and β-satellites. At least one or several unidentified begomoviruses are likely infecting the tomato plants sampled in this study, probably affecting symptom development. Long dry spells associated with high temperatures may prove to be important epidemiological factors for the increase and spread of viral diseases in the tomato crop within this region. An integrated disease management strategy should be devised with all the feasible and suitable components for the Indo-Gangetic eastern plains of India as a part of our future work plan.