Leaf Curl Disease a Significant Constraint in the Production of Tomato: Impact, Challenges, and Management

Abstract

Insect-borne plant viruses cause huge yield loss in the world’s most important crops. Understanding viral transmission mechanisms involves defining plant virus receptors inside their insect vectors. Tomato leaf curl virus (ToLCV) is the most devastating virus for worldwide tomato production. Understanding the biology of ToLCV and devising management techniques are critical in combating this global threat. Researchers are looking into using advanced technologies to detect plant viruses quickly and handle them properly for long-term agriculture. This review’s main goal is to highlight management solutions for effectively combating ToLCV outbreaks and worldwide spread. Resistance genes for plant viruses in agriculture have been identified using morphological, biochemical, and molecular markers from the ancient to the present era. Such techniques are extremely basic. Traditional virus identification methodologies should be integrated with current and advanced tools for efficient virus improvement in crops. This review’s main goal is to highlight management solutions for effectively combating ToLCV outbreaks and worldwide spread. For this aim, we focus on the impact of ToLCV on the world’s agriculture and the significance of recent advances in our comprehension of its interactions with its host and vector. Another important topic is the role of mutations and recombination in shaping the ToLCV genome’s evolution and regional distribution.

1. Introduction

In both tropics and subtropics of the world, tomato cultivation [Solanum lycopersicon L.] is significant and widespread. Tomato production has received greater attention recently because it is not only regarded as a dietary supply of the vitamins C, potassium, folate, and K, but also as a source of revenue and a significant factor in ensuring food security. China, India, the United States, Italy, Turkey, and Egypt are the world’s top tomato-producing nations. The total area under tomato cultivation worldwide is 4.582 Mha, with a yield of 150.51 mt. India is expected to have produced 21 million metric tons of tomatoes for the fiscal year 2021. India, which is second on the list of countries producing tomatoes during the measured period, accounts for 10.51 percent of the world’s total tomato production cultivated 781,000 hectares or more. Production: 243,367 hg/ha. It is the second most significant vegetable. The major states in India are Andhra Pradesh, Karnataka, Orissa, Maharashtra, West Bengal, Bihar, Gujarat, Chhattisgarh, Tamil Nadu, and Jharkhand. The highest tomato producer in India is Andhra Pradesh, which produces 5962.21 thousand tons of tomatoes annually (from FY 2015 to FY 2020). In comparison to the prior fiscal year, the cultivated area increased. Tomato production has received greater attention recently, and tomatoes are often regarded as protective foods due to their high lycopene content, which aids in the prevention of various cancers. However, there are numerous obstacles to the production of tomatoes.

Plant viruses are considered to be predominantly damaging to their cultivated crop hosts’ lives. In the majority of instances analyzed, virus-cultivated agricultural plant interactions have a detrimental impact on host morphology and physiology, resulting in disease [1, 2]. Viral diseases impact a lot of vegetable crops. The world’s food supply is seriously threatened by crop diseases brought on by pathogenic microbes. Viruses, viroids, phytoplasma, bacteria, fungi, and nematodes are some of the pathogens that cause infectious plant diseases. Viral diseases pose a serious threat to sustainable and productive agriculture globally, causing annual economic losses. Plant pathogen infections are one of the main factors limiting crop productivity globally, and any destructive issues are caused by the wide range of viral isolates with highly variable degrees of virulence. They are immovable and often pass from one plant to another via a live thing called a vector or carrier. Since they have piercing-sucking mouthparts that enable them to reach and feed on the contents of plant cells, aphids, whiteflies, thrips, and leafhoppers are the most frequent carriers of plant viruses. Viruses can also be spread by other insects, mites, nematodes, fungi, contaminated seeds, pollen, vegetative propagation material, plant-to-plant contact, and other pests [3]. Emerging diseases, which are characterized by a rapid rise in disease incidence, geographic scope, and/or pathogenicity, have the most impact. Although the source of plant viruses is unknown, various suggestions have been put forth that suggest a possible insect vector as a possible explanation for the similarities between some plant and animal viruses. Plant viruses are challenging to control because they are widespread throughout the world and are effectively transmitted to their host plants by vectors. Although the length and specificity of the interactions between viruses and vectors vary, some recurring motifs in vector transmission have emerged: Plant viruses bind to specific sites in or on vectors and are retained there until they are transmitted to their plant hosts; viruses bind to specific sites in or on vectors and are retained there until transmission to their plant hosts; and viruses determine the virion’s structural proteins, which are essential for transmission, as well as additional nonstructural helper proteins in some cases [4]. Entry, encapsulation, translation, replication, cell-to-cell movement, encapsidation, vascular transport, and plant-to-plant transmission—which can be horizontal through vectors or mechanical wounds, or vertical through seeds and pollen—are the basic steps in the successful infection of a plant by a virus. Viruses must combat host defenses such as RNA silencing and protein-mediated general and targeted immunity [5]. The majority of plant pathogenic viruses have an essential component to their infection cycle: acquisition and dissemination by an insect vector. Sap-sucking insects spread the virus in two ways: persistent transmission and nonpersistent transmission, which refer to how long it takes an insect to acquire and transmit the virus, and circulative transmission; in some cases, it then involves virus replication in the cells of the insect host. Plant viruses can interact with their insect host in a variety of ways. Replicating viruses can also cause the insect host to mount general and targeted defenses. A recurring character is a need for specific molecular interactions between the virus and host, frequently via proteins, for the virus to interact with its insect host or carrier. By preventing virus absorption and transmission, plant protection strategies can be supported by knowledge of the interactions between plant viruses and the insects that serve as their hosts. Here, we offer a perspective centered on identifying existing and novel strategies with research directions to facilitate control of plant viruses by better understanding and focusing on virus-insect molecular interactions with these interactions in insect vectors of plant viruses, and we consider technical advancements for their control that may be more broadly applicable to plant virus vectors [6].

The increase of publications published on the topic during the past 15 years demonstrates the resurgence of interest in plant virus evolution. In the past 5 years, several new viruses have been described, some of which have novel genetic characteristics that have prompted the suggestion of the formation of new genera and the revision of the virus taxonomy status. There is a need for work aimed at understanding the processes involved in plant viral evolution, because contemporary plant virus evolution research has been regarded from a molecular, rather than populational, approach. Plant viruses create a significant amount of genetic variation that is present both within and between species using a variety of ways. Plant RNA viruses and pararetroviruses most likely have replication processes that are very error-prone, leading to a lot of mutations and a quasispecies nature. Although the origin of the diversity in the plant DNA viruses is not entirely apparent, it does exist. Recombination and reassortment are commonly used by plant viruses as evolutionary forces, as are occasionally other methods including gene duplication and hyperinflation [7].

Even though there is no proof of variation in the mutation rate, the amount of variety detected in different species of plant viruses is extremely varied. Plant viruses are thought to result in significant annual losses across the globe. Recent climate change events may have made this problem worse, and climate change will likely have an impact on how diseases spread in the future, which may affect how plant viruses spread. Increases in temperature, atmospheric carbon dioxide concentration, water availability, and the frequency of extreme weather events will all have a direct and indirect impact on plant viruses by affecting their hosts and vectors. Climate change may have an impact on plant viruses’ virulence and pathogenicity, which will increase the frequency and scope of disease outbreaks. The natural defensive process of plants, known as autophagy, has become crucial in the interactions between plants and pathogens. In plants, it serves as an antiviral defense mechanism [8]. The virus alteration demonstrates how plant viruses can control, subvert, or even employ the autophagy system for pathogenicity. However, accumulating evidence from virus modification shows that: (1) high mutation rates are not necessarily adaptive, as a significant portion of the mutations is deleterious or lethal; (2) despite having a high potential for genetic variation, populations of plant viruses are not highly variable, and genetic stability is the norm rather than the exception; and (3) the degree of genetic variation constriction in virus-encoded proteins is comparable to that in their eukaryotic hosts and vectors [9].

Although it is difficult to trace the evolutionary history of viruses and practically impossible to regulate virus disease over the long term, their propensity for fast adaptation makes them a great model system for research on the broad mechanisms underlying molecular evolution. More exemplary research was done in the second half of the twentieth century, demonstrating the infectiousness of RNA alone, (ii) the resolution of RNA-protein interactions in the structure determined by X-ray fiber diffraction, (iii) the existence of a distinct region on the virus for the start of encapsidation, (iv) the definition of the virus sequence and open reading frames (ORFs); (v) open reading frames and the definition of the viral sequence (ORFs); and (vi) cDNA clone that is biologically active [10]. This substantially contributed to our comprehension of reproduction and transmission, resulting in a new understanding of viruses among scientists in a subsequent generation. In addition to improving our knowledge of the local ecology and fitness of mechanically transmitted viruses, this upcoming research must expand our understanding of virus structure and transporters of small molecules. The process of developing effective host-virus interactions, including how different species move through a vector in different ways. The top nine virus list is shown in Table 1, in descending order [19].

1.1 Viruses, crops affected, and damage caused

Hence, there is an urgent need to improve its productivity with the help of modern technological implementation to shield the tomato plants against various biotic and abiotic factors.

One of the main biotic limitations is virus-associated. One of the most significant factors restricting its cultivation and productivity is tomato leaf curl disease (ToLCD). It frequently suffers from a range of infections, which causes significant yield losses. Infections caused by fungi, bacteria, and phytoplasma are only a few of the many viral diseases that affect it. The most significant and damaging viral pathogen in many regions of the world is the tomato leaf curl virus (ToLCV), a geminivirus, which is responsible for all documented viral diseases in tomatoes [20, 21, 22, 23, 24, 25, 26, 27]. Based on the genome organization, host range, phylogenetic relationships, and insect vectors, geminiviruses have been classified into nine genera: Becurtovirus (two species), Begomovirus (>320 species), Curtovirus (three species), Mastrevirus (>30 species), Eragrovirus (one species), Topocuvirus (one species), and Turncurtovirus (one species). Begomovirus is the largest genus in the Geminiviridae family, and it contains multiple notable species, including ToLCV, which infects tomato cultures in Asia and Australia. ToLCV is the name given to a group of vector-transmitted geminivirus genus [28]. Geminiviruses are made up of one or two circular ssDNA genomic components of 2500–3000 nucleotides encapsulated in paired icosahedra or geminate particles (called geminiviruses), as we know them now. Inside the host cell, their ssDNA genome is converted into a dsDNA intermediate and rapidly replicated (Figure 1). The introduction of high-yielding tomato varieties has been accompanied by ToLCV infection [29, 30, 31]. In India, in Andhra Pradesh, the disease is widespread in tomatoes during the summer season in southern parts and autumn in northern parts and causes yield losses ranging from 27 to 100% [32, 33, 34].

Figure 1.

Å structure of a plant geminivirus—Nanoviruses have T = 1 icosahedral capsids of ∼18 nm in diameter.

1.2 Genome organization

Plant viruses belonging to the Geminiviridae family have circular genomes made of single-stranded (ss) DNA, which encodes their genetic material. The genomes of all geminiviruses are identical, as is DNA-A, the section of bipartite begomoviruses that encodes the proteins necessary for replication, control of gene expression, getting past host defenses, encapsidation, and insect transmission. Two proteins that enable intracellular and intercellular movement in host plants are encoded by the second component, DNA-B. The unknown is the origin of the DNA-B component. This work aimed to investigate the relationship between the bipartite begomovirus DNA-A and DNA-B components to unravel their evolutionary histories and gain insight into the potential origins of the DNA-B component [35].

One of the genomes recognized are begomovirus species, and they have all Old World origins (OW). Monopartite viruses have only one molecule of nucleic acid [36]. The majority of dsDNA viruses exist in monopartite forms. It has been demonstrated that monopartite begomoviruses interact with betasatellites, which are ssDNA satellites. In contrast to monopartite begomoviruses, which are phloem confined and only cause stunting and leaf curl symptoms, several bipartite begomoviruses infect both phloem and other tissues, causing leaf curling, crumpling, and mosaic/mottling symptoms, and are sap transmissible [37, 38, 39, 40].

1.2.1 Gene functions

The six ORFs that make up DNA-genome A’s are used to encode the signals for the six most significant viral proteins, which range in size from 11 to 40 kDa. Both viruses detect ORF. Monopartite begomoviruses have complementary-sense ORFs (C1–C4) and virion-sense ORFs (V1 and V2), respectively. Together with the V2 protein, the virion-sense coat protein (CP) promotes viral mobility in plants and is responsible for insect transmission. The sole viral protein necessary for viral DNA replication is the geminiviral replication-associated protein (Rep). The ToLCV intergenic region has a 120-bp segment that Rep particularly binds to. Two significant movement proteins, BV1 and BC1, are encoded by DNA-B and are in charge of long-distance mobility between cells. Globally, both economically significant and weed crops suffer enormous economic losses due to begomoviruses and their satellites. Monopartite begomoviruses typically develop a virus/satellite complex with a betasatellite and cause severe leaf curl in tomatoes Betasatellites linked with geminivirus play a variety of roles in pathogenesis [41]. In India, the papaya leaf curl virus (PaLCuV) associated with aster betasatellite yellow vein disease was found. In Pakistan, PeLCV infection of Pedilanthus tithymaloides plants was connected to the betasatellite for tobacco leaf curl [42, 43]. Recently, the alphasatellite, a 1.4-kb additional satellite DNA, has been connected to the tomato leaf curl virus (TYLCV). Although they multiply autonomously inside their hosts, they depend on the helper virus for encapsulation, movement inside the plant, and vector transmission. They can multiply independently within their hosts, but they, like betasatellites, depend on the helper virus for encapsulation, mobility inside the plant, and vector transmission. The earliest satellites discovered in relationship with the ToLCV were deltasatellites, an Australian example (ToLCV). Previously known as ToLCV-Sat, is currently called tomato leaf curl deltasatellite (ToLCD). The ToLCD (682 nt long) and the helper virus have no significant sequence similarities other than the origin of replication [44].

1.2.2 Geminiviruses replication

Geminiviruses employ their insect vectors to transfer their encapsidated DNA to plants. Due to the lack of a model system for eukaryotic replication, details of geminivirus replication remain unknown. Other research indicates that the replication initiator protein (Rep) is the viral protein most crucial to viral DNA replication. Yellow mungbean mosaic mutations in CR, Rep, AC5, and other replication-related components and viral proteins, as well as a lack of host factors, inhibited the replication of the India virus. When injected into protoplasts, DNA-A can replicate itself and contain the genes required for viral replication [45]. In mature plant cells, geminiviruses promote the expansion of the DNA replication apparatus to create a favorable environment for replication. On the other hand, a lot is still unknown about the process of C4-induced cell division. The physiological advantage of promoting cell division might produce a situation where DNA viruses can multiply easily. There is proof that ToLCV can be replicated within the vector, that is, whiteflies. A fivefold increase in viral accumulation was observed in the early stages of the insect’s life cycle, followed by a decline in the later stages, according to the first study to demonstrate this phenomenon, which was published in 2015.

V1, V2, and C3 displayed increased expression after nonviruliferous flies fed on TYLCV-infected tomato plants for 1 to 3 days. The midgut epithelial cells were also found to have complementary viral DNA, a sign of viruses that replicate [5, 46]. This suggests that these cells served as viral replication hubs. Another study found that insects that consumed diseased tomato plants accumulated 10 times more viral gene transcripts. In the later stages of the investigation, the reduction in virus titers was also attributed to autophagy [47]. Contrarily, experimental evidence supports the notion that TYLCV cannot replicate within its vector. The quantity of viral transcripts increases only during the acquisition phase and thereafter remains constant, according to other research, indicating that replication is not occurring [48, 49].

Many DNA viruses depend on their hosts’ transcription and replication systems. Geminiviruses only employ a small number of proteins, and they rely on host enzymes to carry out their functions. These genes are transcribed by begomoviruses using their bidirectional promoters. It produces several overlapping RNA species, some of which are polycistronic. The TATA box initiates transcription, and the RNA produced by the virus is polyadenylated, showing that the host transcription machinery aids in the geminivirus’ transcription. One complementary-sense transcript (BC1) is produced for DNA-B.

1.3 Tomato leaf curl virus

The Food and Agriculture Organization of the United Nations estimates that the tomato is the most widely grown tomato crop in the world, producing about 180 million tons annually [50]. Growing for the processing industry accounts for one-fourth of the 160 million tons. The annual processing capacity of factories operated by significant food corporations is about 39 million tons of tomatoes. In all tropical locations of the world, ToLCV is one of the most virulent viruses that can cause catastrophic illnesses in vegetable crops [51]. Since ToLCV was originally identified in solanaceous crops, numerous instances of harm to other crops have surfaced all across the world (Table 2). It has a devastating impact on the development and production of several plant groups with significant agricultural economic importance. In 1948, Vasudeva and Samraj reported the first ToLCV case in India. ToLCNDV has expanded to other vegetable and fiber crops, according to several studies from the last 10 years [52]. Tomato leaf curl New Delhi virus with mosaic and leaf curl disease has just been discovered in chrysanthemum. This virus is attributed to diseases in a wide variety of plant species, including fruit crops and ornamental plants [53]. These begomoviruses may act as reservoirs for crops that are crucial to the economy [2, 11, 50]. Because it causes one of the most prevalent and economically significant tomato diseases in the world, ToLCNDV significantly hinders tomato output in general [54]. As it has spread across the Indian subcontinent, ToLCNDV’s host range has significantly increased. India and Pakistan have reported cases of ToLCV linked to cotton leaf curl disease between 2013 and 2015 [55, 56]. The insects harm the plant directly by sucking phloem sap (Figure 2), which stunts growth, causes early wilting, prematures defoliation, and ultimately results in yield loss. They also damage the plant indirectly by excreting honeydew, which promotes the growth of fungi on the surfaces of leaves and fruit. When a peach plant was infected with the leaf curl virus, the leaves had very little chlorophyll and performed little or no photosynthesis. Previous research has suggested that ToLCV causes increased reactive oxygen species (ROS) production in tomato leaves infected with it [57].

S. No	Virus	Plant	Host range	Yield influence	Economic loss world wide	References
1.	Tobacco mosaic virus	Tobacco, pepper, cucumber, and ornamental crops	Tobacco, vegetables (especially in the Solanaceous family), and many ornamental species	Plant height, leaf length and width, and fresh and cured leaf yield are all factors to consider.	90%	[11]
2.	Tomato spotted wilt virus	Begonia, cowpea, impatiens, peanut, pepper, potato, squash, and tomato.	Monocots and dicots	Fruits’ fresh weight, width, length, and marketability were all documented.	100%	[12]
3.	Tomato leaf curl virus	Vegetable crops, ornamental, and fruit crops	Solanaceous plants	Plant leaf number and area, biomass, height, root length, and stem diameter and yield are all factors to consider.	100%	[13]
4.	Cucumber mosaic virus	Carrot, celery, cucurbits, legumes, lettuce, onion, pepper, spinach, tomato, and rarely potato	Vegetable, woody and non-woody, and ornamentals plants	The US Department of Agriculture’s Plant Yield and Nutritional Outlook Survey (PYTH) for 2014/15 shows an 89.89% drop in yield per plant compared to last year. The study also shows a decrease in plant height, root length and fresh plant weight.	60%	[14]
5.	Cauliflower mosaic virus	Brassicaceae (or mustard) family	Brassicaceae crops and solanaceous plants	Low seed yields. Lower temperature, plant development, especially in early infections, and the production of flowers can be blocked.	60%	[15]
6.	Cassava mosaic virus	Euphorbiaceae (for example, wild poinsettia and garden spurge)	Cassava (Manihotesculenta) and castor bean (Ricinuscommunis)	Height, stem diameter, leaf square, and yield of the plant	77.5% to 97.3%	[4]
7.	Plum pox virus	Peaches, apricots, plums, nectarine, almonds, and sweet and tart cherries.	Stone fruits	Fruit size and weight, pH, titratable acidity, total soluble solids, flesh hardness, and fruit skin color are all factors to consider.	80–100%	[16]
8.	Brome mosaic virus	Soybean and barley	Dicotyledonous and monocotyledonous plants	Plant height, stand establishment, grain production, and many yield components are all factors to consider.	7–10%s	[17]
9	Potato virus	Potato (Solanum tuberosum), tobacco (Nicotianatabacum), tomato (Solanum lycopersicum), and pepper (Capsicum spp.)	Solanaceae	Total yield, commercial and noncommercial yield, number of stems, number of tubers, and tuber weight	10–40%	[18]

Table 1.

The top 10 viruses list in rank order.

The top nine list includes, in rank order, (1) tobacco mosaic virus, (2) tomato spotted wilt virus, (3) tomato leaf curl virus, (4) cucumber mosaic virus, (5) cauliflower mosaic virus, (6) African cassava mosaic virus, (7) plum pox virus, (8) Brome mosaic virus, and (9) potato virus X.

S. No.	Name of country	Name of the crop
1	Algeria	Tomato leaf curl New Delhi virus infecting cucurbit
2	Antigua and Barbuda	Tomato yellow leaf curl virus (TYLCV)
3	Argentina	Tomato rugose yellow leaf curl virus (TRYLCV)
4	Australia	Tomato leaf curl virus (TLCV)
5	Australia	Tomato yellow leaf curl virus (TYLCV)
6	France	Tomato leaf curl New Delhi virus infected in Cucurbita pepo (field pumpkin)
7	Azerbaijan	Tomato yellow leaf curl virus
8	Bangladesh	Tomato leaf curl New Delhi virus
9	Barbados	Tomato yellow leaf curl virus
10	Belize	Tomato mosaic leaf curl virus in pepper, red kidney bean, squash, string bean, and tomato
11	Benin	Tomato yellow leaf curl virus
12	Bolivia	Whitefly (tomato leaf curl virus vector) was detected
13	Brazil	Tomato mottle leaf curl virus
14	Burkina Faso	Tomato leaf curl disease
15	Burma	Tomato yellow leaf curl virus
16	Burundi	Tomato yellow leaf curl virus (TYLCV) and tomato leaf curl virus (ToLCV)
17	Cambodia	Tomato yellow leaf curl Kanchanaburi virus
18	Cameroon	Tomato leaf curl Cameroon virus (ToLCCMV)
19	Guatemala	Tomato yellow leaf curl virus infecting tomato, tomatillo, and peppers
20	Chad	Cotton leaf curl Gezira virus (CLCuGV)
21	Chile	Tomato yellow leaf curl disease (TYLCD)
22	China	Tomato yellow leaf curl virus
23	Colombia	Begomovirus identified
24	Comoros Archipelago	Tobacco leaf curl Zimbabwe virus
25	Costa Rica	Tomato yellow leaf curl virus in Tomato
26	Cote d’Ivoire	Okra leaf curl disease (OLCD); Cotton leaf curl Gezira virus (CLCuGeV)
27	Cuba	Tomato yellow leaf curl virus infecting pepper plants
28	Cyprus	Tomato yellow leaf curl virus (TYLCV)
29	Dominican	Tomato yellow leaf curl virus
30	Ecuador	Cabbage leaf curl virus infecting common bean, cowpea, pigeon pea, and Mucuna pruriens
31	Egypt	Squash leaf curl virus to Squash (Cucurbita pepo)
32	El Salvador	Tomato dwarf leaf curl virus; Tomato saver leaf curl virus
33	Estonia	Tomato leaf curl New Delhi virus (Begomovirus, ToLCNDV—EPPO Alert List)
34	Ethiopia	Tomato yellow leaf curl virus
35	France	Tomato leaf curl New Delhi virus
36	Georgia	Cabbage leaf curl virus
37	Ghana	Tomato leaf curl Ghana virus
38	Greece	Tomato leaf curl New Delhi virus
39	Grenada	Tomato yellow leaf curl virus
40	Guatemala	Tomato yellow leaf curl virus infecting tomato, tomatillo, and peppers
41	Haiti	TYLCV-Is was unintentionally identified
42	Hawaii	Tomato yellow leaf curl virus
43	India	Tomato leaf curl virus
44	Indonesia	Pepper yellow leaf curl Indonesia virus
45	Iran	Alfalfa leaf curl virus from alfalfa
46	Iraq	Tomato yellow leaf curl virus (TYLCV)
47	Israel	Tomato yellow leaf curl virus
48	Italy	Tomato yellow leaf curl virus
49	Jamaica	Tomato dwarf leaf curl virus
50	Japan	Tobacco leaf curl Japan virus
51	Jordan	Alfalfa leaf curl virus affecting alfalfa (Medicago sativa) in Jordan, Lebanon, Syria, and Tunisia
52	Yugoslavia	Pelargonium leaf curl virus
53	Korea	Papaya leaf curl virus
54	Kuwait	Tomato yellow leaf curl virus
55	Laos	Tomato yellow leaf curl Kanchanaburi virus infecting eggplant
56	Lebanon	First report of squash leaf curl virus in cucurbits
57	Libya	Tomato yellow leaf curl virus
58	Malaysia	Pepper vein yellows virus and pepper yellow leaf curl virus infecting chilli pepper (Capsicum annuum)
59	Mali	Tomato leaf curl Mali virus and tomato yellow leaf crumple virus
60	Mauritius	Tomato yellow leaf curl virus in tomato
61	Mauritania	Tomato yellow leaf curl virus
62	México	Tomato yellow leaf curl virus
63	Mongolia	Tomato yellow leaf curl virus
64	Morocco	Tomato yellow leaf curl virus
65	Mozambique	Tomato curly stunt virus, a new begomovirus of tomato within the tomato yellow leaf curl virus
66	Namibia	Tomato leaf curl Kunene virus
67	Nepal	Tomato leaf curl betasatellite infecting Carica papaya
68	Netherlands	Tomato yellow leaf curl virus in tomato
69	Nicaragua	Tomato severe leaf curl virus from Nicaragua
70	Nigeria	Tomato leaf curl disease
71	Oman	Tomato leaf curl Albatinah virus
72	Pakistan	Tomato leaf curl Palampur virus on Bitter Gourd
73	Panama	Tomato leaf curl Sinaloa virus infecting tomato crops
74	Philippines	Whitefly-transmissible geminiviruses-bgomovirus DNA fragments were detected
75	Piedmont-Sardinia	Tomato yellow leaf curl Sardinia virus
76	Portugal	Tomato yellow leaf curl virus
77	Saudi-Arabia	Tomato yellow leaf curl virus (TYLCV)
78	Senegal	Tomato yellow leaf curl
79	Seychelles	Tomato leaf curl virus
80	Somalia	Tomato leaf curl
81	South Africa	Tomato yellow leaf curl virus
82	Sudan	Tomato leaf curl Sudan virus
83	Spain	Tomato yellow leaf curl virus
84	Sri Lanka	Tomato yellow leaf curl virus
85	Syria	Alfalfa leaf curl virus affecting alfalfa (Medicago sativa)
86	Tanzania	Tomato yellow leaf curl Tanzania virus
87	Uganda	Sweet potato leaf curl Uganda virus (SPLCUV)
88	Saudi Arabia	Tomato yellow leaf curl virus [TYLCV]
89	Venezuela	Tomato yellow leaf curl virus
90	Vietnam	Corchorus yellow vein Vietnam virus (CoYVV)
91	Yemen	Tomato leaf curl Sudan virus
92	Zambia	Tobacco with leaf curling symptoms
93	Zimbabwe	Tobacco leaf curl Zimbabwe virus

Table 2.

There were reports of huge crop devastation all across the world due to ToLCV.

Figure 2.

Schematic representation of Bemisia tabaci [insect vector]-mediated transmission of plant viruses in leaf—Spreads begomoviruses by sucking the sap from the phloem of leaf curl virus-infected plants (red geminate particles). As a result of the infection, the plants show characteristic begomovirus symptoms such as vein yellowing, foliar yellow mosaics, and leaf curling.

1.4 Occurrence and yield loss

According to geographic distribution, the ToLCD is expanding quickly. It affects tomatoes and significantly reduces agricultural yields in the Southeast United States and around the world [58]. If infected, susceptible tomato types could lose up to 100% of their production (142,251). The tobacco leaf curl virus on tomato first appeared naturally in India in 1942 according to Pruthi and Samuel, who were followed by Vasudeva and Samraj in 1948. Later, Andhra Pradesh, Hyderabad [59, 60], and Tamil Nadu [61] first reported the detailed characterization of ToLCV from Karnataka by Govindu and his coworkers in 1964. The prevalence of ToLCD in South India rapidly increases from 27 to 90 percent in susceptible cultivars, leading to yield losses of up to 90 percent [62]. The virus’s extreme invasiveness and a dearth of efficient control methods allowed it to spread globally and cause a serious pandemic. Nine different ToLCV isolates have been found in India [11]. In the United States, the TYLCV-like ToLCV has been identified [63, 64]. The tomato leaf curl viral illness, which has a significantly high disease incidence in both the Rabi and Summer seasons, 96.80 percent and 98.43 percent, respectively, according to Khandare et al. [65], produces severe leaf curl disease. However, the first reports of tomato yellow leaf curd disease and the connection between radish leaf curl virus (RaLCV) isolates and a tobacco disease were both made in 2012 by Singh and his colleagues [66]. The majority of Indian isolates of ToLCVs are caused by a monopartite tomato leaf curl Joydebpur virus (ToLCJoV) that causes severe leaf curl. Numerous plants, including natural fibers and chillies, have been discovered to be infected by monopartite ToLCJoVs [67]. Tomato leaf curl Palampur virus (ToLCPalV) strains/variants’ importance is an increasing hazard to cucurbit output in India. Because of the recombination breakpoint of the viral genome, these valuable crops are now being destroyed and impacted by ToLCV. ToLCV has emerged as a major limiting factor and problem for farmers and scientists alike, with a special focus on management initiatives for preventing the spread of ToLCD. Because of the economic importance of LCV, efforts have been made to understand LCV pathophysiology and generate tolerant plants using breeding and transgenic techniques [61].

1.5 Geographical distribution

Cucumber mosaic virus (CMV), tomato spotted wilt virus (TSWV), tomato aspermy virus (TAV), tobacco mosaic virus (TMV), tomato bushy stunt virus (TBSV), potato Y virus (PVY), and ToLCV are among the viruses that infect tomatoes [68, 69, 70]. Additionally, mixed infections frequently contain these viruses [71]. In the southern region of India, a monopartite ToLCV is the most prevalent of the various ToLCVs [72]. There are several species of begomoviruses, viz. bipartite tomato leaf curl Palampur virus (ToLCPalV) and tomato leaf curl New Delhi virus (ToLCNDV), monopartite tomato leaf curl Kerala virus (ToLCKeV), tomato leaf curl Patna virus (ToLCPaV), tomato leaf curl Ranchi virus (ToLCRnV), tomato leaf curl Rajasthan virus (ToLCRaV), tomato leaf curl Pune virus (ToLCPV), tomato leaf curl Bangalore virus (ToLCBaV), tomato leaf curl Lucknow virus (ToLCLuV), tomato leaf curl Karnataka virus (ToLCKaV), tomato leaf curl Gujarat virus (ToLCGuV), and tomato leaf curl Joydebpur virus (ToLCJoV). The begomovirus, ToLCGuV, that exists in both mono and bipartite forms has been reported from Varanasi [73]. Both of these categories are common in India [74, 75]. ToLCNDV is a rare Old World bipartite begomovirus. It is ubiquitous on the Indian subcontinent but found elsewhere in the Far East, Middle East, North Africa, and Europe [76, 77]. According to Sahu et al., the occurrence of Guar leaf curl alphasatellite (GLCuA) could be attributed to whitefly migration from Pakistan [78, 79]. ToLCV has been linked to infections in a variety of hosts between 2000 and 2010 [80]. Only the DNA-A component appears to be present in the monopartite genomes of the tomato leaf curl Bangalore virus from Bangalore [81, 82] and tomato leaf curl Karnataka virus from Karnataka [83]. The PaLCuV has been found in many different crops across the globe [84]. Numerous begomoviruses may pick papaya plants to survive in a variety of uncertain environments. The presence of chili leaf curl virus and its related tomato leaf curl betasatellite in the Cucurbita maxima host reveals the virus’s potential harm to this crop [85]. There is a chance that this virus complex could speed up the spread to other crops. There is a risk that the virus could spread to other countries via air, sea, and possibly through borders, particularly among countries that share borders. It is critical to avoid any chance of the virus spreading to new hosts in other nations by enacting effective quarantine legislation.

1.6 Virus-vector interaction

There are often two components to a vector-transmitted pathogen: host-pathogen interaction and vector-virus contact (Figure 3). In the past, research on plant-virus interactions has focused on viral mobility, replication, symptom development, and the plant’s reaction to infection. Vector-virus interaction, on the other hand, has been an insufficient investigation.

Figure 3.

The infection cycle starts when the vector comes into contact with the virus in the plant and acquires it. The virus must then survive long enough in or on the vector to be transmitted to a new host and released into the plant cell.

One of the most invasive creatures is the Bemisiatabaci [Hemiptera: Aleyrodidae], often known as the whitefly as a vector for ToLCV. It has been ranked among the top 100 worst invasive alien species in the world. It is a cryptic species that includes at least 39 Hemiptera species and is found naturally throughout the world’s tropical and subtropical regions [86]. In the last 20 years, B. tabaci has spread around the globe, likely as a result of the transportation of agricultural products [87]. It has become one of the most destructive agricultural pests. The bug damages the plant directly by sucking phloem sap, which results in stunted development, early wilting, premature defoliation, and ultimately a loss of production, as well as indirectly by excreting honeydew, which encourages fungal growth on the surfaces of leaves and fruits [88]. Over 600 plant species are targeted by Bemisiatabaci, and viruliferous whiteflies creating a feeding site directly contributes to leaf curl virus transmission to plant hosts [89]. Alfalfa leaf curl virus (ALCV), which is spread by Aphids craccivora [90], is one of two Capulavirus species that are spread by aphids. Aphid transmission was only found in 2015, even though the Aphididae family contains most species described as plant virus vectors [91, 92]. An unclassified geminivirus from the genus Capulavirus can spread ALCV [93]. Being polyphagous explains B. tobaci wide host range and ability to spread a lot of viruses to more than 300 plant species from 63 families [94]. Forty-nine begomovirus species have been related to ToLCD, while 17 have been linked to TYLCD [95, 96]. The two primary tomato geminiviruses that infect tomatoes and significantly reduce output are ToLCV and TYLCV [97].

The key features of ToLCV acquisition, retention, and egestion by the vector have been the focus of investigations into how viruses interact with their host’s machinery fluids. The maxillary stylet is made up of three stylets: a mandibular stylet and the salivary canal. Individual whiteflies may acquire varying amounts of viral particles in their exoskeletons even when fed on the same tissue for the same significant period. In insects, the precibarium and cibarium taste organs control whether virus particles move through circulatory or noncirculatory channels. Circulating persistent viruses circulate and stay in the body of the insect for the majority of its life, whereas noncirculative viruses never breach the gut barrier [77]. Any alteration to the protein that supports virus retention and transmission (CP) interferes with both processes [98]. ToLCV uses endosymbionts from whiteflies that release proteins to stop damage in the open circulatory system. ToLCV’s CP interacts with GroEL, a molecular chaperone, and is shielded from deterioration. It has been demonstrated that Hsp70 interacts with CP and blocks transmission. The continuous cycle between the host and vector due to their circulative pathway affects prospective agricultural output all over the world. ToLCV particles enter the salivary glands of viruliferous flies while they feed on phloem sap and are then discharged into plants [99].

1.7 Plant-virus interaction

Geminiviruses are intracellular parasites that must successfully influence plant cell activities to multiply, block antiviral defenses, and spread throughout the plant [44, 100]. They inject viral DNA into the host cell during infection, disrupting the host gene silencing system. During viral infection, the production of ROS in the host cells is raised to prevent systemic virus migration up to specific cells [63]. To counteract the self-damage produced by ROS, the host creates glutathione peroxidases (GPXs), which lower ROS levels in the cells. The competence of a virus to co-opt and alter processes in a particular host plant will influence how the virus-plant relationship turns out. To hijack the molecular machinery of the host cell, geminiviruses produce a small number (between 4 and 8) of tiny, rapid evolving, multifunctional proteins, encoded by bidirectional and partially overlapping ORFs [101]. ToLCV is a whitefly-transmitted vector-borne disease (Figure 4), and this is the first time ToLCNDV has been identified as a seed-transmissible virus in zucchini squash plants in Italy. The leaf curl virus was found in early seedlings sprouted organically from fallen fruits [18]. After being injected into the host, virus particles multiply and travel to other areas of the body, causing symptoms [102]. Geminiviruses manipulate E2F transcription factor activity to produce an S-phase environment [103]. Beet curly top virus (BCTV) infection causes cell expansion (hypertrophy) and division (hyperplasia) [104].

Figure 4.

Plant-pathogen interactions-global environmental change, study the environmental parameters (biotic and abiotic) influencing the biology of plant viruses and their transmission by vectors.

DNA virus replication in differentiated plant cells requires the induction of cell division. To achieve efficient replication, DNA viruses encode the C4 protein, which encourages cell proliferation. The viral protein may interact with yeast and alter its growth and development, since the expression of BCTV C4 caused a 100-fold decrease in transformation efficiency [105, 106]. The glycogen synthesis kinase-3 (GSK3) homolog in N. benthamiana, NbSK, is hijacked by the C4 protein of the tomato leaf curl Yunnan virus (TLCYnV). According to Mei and his coworkers in 2018 [107], SK is a target of geminivirus C4, and activation of cell division is necessary for DNA virus replication in differentiated plant cells. According to Chandan et al., infected tomato plants exhibited increased expression of LeCTR1, one of the ethylene signaling pathway’s negative regulators. LeCTr1 gene silencing caused by the tobacco rattle virus (TRV) increased ToLCJoV infection tolerance [101].

1.8 ToLCV recombination, mutation, and evolution

Begomovirus disease complexes are quickly developing to increase their host range and overcome resistance sources through recombination, component capture, and mutations.

1.8.1 Mutation

Genetic variation in the tomato yellow leaf curl Sardinia virus [TYLCSV] is a result of interspecific recombination as well as mutation, natural selection, and genetic drift [108]. RNA viruses have a high mutation rate as a result of error-prone replication mediated by viral RNA-dependent RNA polymerases (RDRP). Recombination that occurs during mixed infections and mutations is what drives viral evolution. DNA viruses like TYLCV, whose replication is facilitated by plant DNA polymerases, should have modest mutation rates as a result of proofreading activity [109]. However, studies disagree with these assumptions, and considerable variability has been reported. Serious outbreaks have been triggered by recombinant TYLCVs with resistance-breaking capabilities [110, 111].

1.8.2 Recombination and evolution

Mixed infections and high viral replication levels are two conditions that may promote recombination [103]. As recombination hotspots, the IR, V1, V2, and C1 regions of the genome have been identified [112, 113, 114, 115, 116, 117, 118]. Studies from the Punjab regions of Pakistan and India recently suggest that CLCuMuV has reemerged in the Indian subcontinent, which is consistent with observations from earlier studies. Its dominance and frequent emergence in North Indian regions have been demonstrated by recent studies [55]. Researchers examined and studied recombination events in the viruses to see if they had any consequence on viral transmission due to the high diversity of begomoviruses in North India. Geminiviruses have evolved and appeared as a result of recombination. The Cotton Leaf Curl Multan betasatellite [CLCuMBC1]'s satellite conserved region (SCR) and A-rich portions were particularly prone to recombination [67]. Additionally, recombination was found in the Rep and A-rich regions of the GLCuA, supporting earlier findings that suggested these sites were recombination hotspots [11]. As shown by DNA-A components of ToLCNDV isolates [119], recombinations involving genomic sequences from other begomoviruses or sequences of unknown origin are frequent in this genus.

Recombination happened in 458 occurrences among begomoviruses related to cotton leaf curl disease during 459 mixed infections [120]. If these viruses travel to other locations, 460, where they are common, new viruses may emerge [4]. The Recombination Detection Program version 4 [RDP4] was used to identify possible recombination events in sequences [121]. SeqMan and GenBankBLASTn were used to put together sequence reads (Table 3). MEGA7 was used to perform pairwise nucleotide sequence analysis and build phylogenetic trees [139]. This sequence analysis is useful to determine the threshold level at 91 percent sequence identified demarcation for begomovirus classification that has been set [140].

Genus	Species	Host	Genome	Genbank Accession Number	Reference
Alfamovirus	Alfalfa mosaic virus	Potato (Solanum Tuberosum), pea (Pisum Sativum), tobacco (Nicotiana Tabacum), tomato (Lycopersicon Esculentum), and bluebeard (Caryopteris Incana)	(+)Ssrna-9.1 Kb	LC485016 To LC485018	[12]
Alphaendornavirus	BPEV (bell pepper alphaendornavirus)	Capsicum annuum	Dsrna-17.6 Kb	MH094752.1	[74]
Betanecrovirus	Tobacco necrosis virus D (TNV-D)	Herbaceous Species	Linear, Ssrna(+)-4 kb	FN543421	[61]
Begomovirus	Cabbage leaf curl virus	Dicotyledonous plants—tomatoes, beans, squash, cassava, and cotton	(+)Ssrna-2.8 Kbp	MK087038-DNA-A; MK087039-DNA-B	[12]
	Cleome leaf crumple virus
	Euphorbia mosaic virus
	Sri Lankan cassava mosaic virus
	Tomato yellow leaf curl virus
	South African cassava mosaic virus
Bromovirus	Brome mosaic virus	Cowpea	Ssrna(+) 4.7 Kb	LG146066	[20]
	Cassia yellow blotch virus	Cassia
	Cowpea chlorotic mottle virus	Cowpea
	Spring beauty latent virus
Carmovirus	Cardamine chlorotic fleck virus	Cowpea	Ssrna - 4.8 Kbp.	NC_001600	[122]
	Turnip crinkle virus	Brassicaceae family
Carlavirus	Potato latent virus	Allium species; Onion, leek, garlic, shallot, and Allium scorodoprasum	Single-Stranded Positive-Sense RNA-8.7 Kb	AF271218	[123]
Caulimovirus	Cauliflower mosaic virus	Vegetables, ornamentals, and weeds	Ds DNA	M90541	[15]
Cheravirus	Apple latent spherical virus	Caryophyllaceae, Chenopodiaceae, Cryptomeria, Fabaceae, Cucurbitaceae, Gentianaceae, Pinus, Rosaceae, Rutaceae, Solanaceae, and Arabidopsis	Ssrna(+)	NC_003788	[124]
Cilevirus	Citrus leprosis virus C	Citrus, Chenopodium quinoa, C. Amaranticolor, and Gomphrena globosa	Linear Ssrna(+)	MT554553	[125]
	Solanum Violaefolium ringspot virus	Solanaceae family
Comovirus	Turnip ringspot virus	Legumes (bean, cowpea, pea, soybean, and clover)	Bipartite Linear Ssrna(+)	GQ222382	[126]
Cucumovirus	Cucumber mosaic virus	Legumes and solanaceous	Tripartite Linear Ssrna(+) Genome	HV194209	[127]
Curtovirus	Beet curly top virus	Dicotyledonous plants	Monopartite, Circular, Ssdna Genome	MW234427; NC_043649	[31]
	Beet severe curly top virus	Beetroot
	Spinach curly top virus	Spinach
Dichorhavirus	Clerodendrum chlorotic spot virus, coffee ringspot virus	Orchid, citrus, coffee, clerodendrum, and hibiscus	Negative-Stranded RNA Linear-6.4–6.7 Kb	KF812525 and KF812526	[128]
Elaviroid	Elvd (eggplant latent viroid)	Eggplant (Solanum melongena), tomato, cucumber, chrysanthemum, and citron	Viroid	NC_039241	[129]
Fabavirus	BBWV (broad bean wilt virus)	Fabaceae, Solanaceae, Cucurbitaceae, and Chenopodiaceae, including Vigna unguiculata, Vicia faba, Pisum sativum, Nicotiana occidentalis, Nicotiana benthamiana, Solanum lycopersicum, Cucurbita moschata, Cucumis sativus, Chenopodium amaranticolor, and C. quinoa	(+)Ssrna	KT923141	[130, 131]
Ilarvirus	TSV (tobacco streak virus)	Woody plants—cowpea	(+)Ssrna	MF784816	[125]
Ipomovirus	Tmmov (tomato mild mottle virus)	Non-gramineous or gramineous host plants	(+)Ssrna	NC_038920	[1]
Macluravirus	Arlv (artichoke latent virus)	Monocots and dicots	(+)Ssrna	NC_026759	[49]
Mastrevirus	Cpcdv (chickpea chlorotic dwarf virus)	Cereals and some vegetable crops; Solanaceae and Fabaceae; Monocot plant species	Ssdna	LN865163	[128]
Nanovirus	Faba bean necrotic yellow virus	Only the monocot species	The Double-Stranded DNA Viruses; The Single-Stranded DNA Viruses; The Double-Stranded RNA Viruses; Single-Stranded-Sense Strand (+ Form) RNA Viruses; Double-Stranded DNA With RNA Intermediate- 1 kb	MN716783	[132]
Nepovirus	Arabis mosaic virus	Woody And Herbaceous Plants	Bipartite Linear Ssrna(+) Genome—1.8 Kbp	GQ369530	[133]
	Cherry leaf roll virus	Plums, cherries, peaches
	Tobacco ringspot virus	Tobacco
	Tomato spotted wilt virus	Tomato
Orthotospovirus	TSWV (tomato spotted wilt orthotospovirus), IYSV (iris yellow spot orthotospovirus),	Weeds, woody plants such as kiwifruit, mulberry, and macadamia nut		OK469365	[134, 135]
Polerovirus	Beet mild yellowing virus	Solanaceous hosts and weed	Positive-Sense Single-Stranded RNA—6.2 Kb	NC_003491	[136]
	Beet western yellows vrus	Taproots plant
	Turnip yellows virus	White, fleshy taproot
Potexvirus	Plantago asiatica mosaic virus	Mono- and dicotyledonous plant species	Monopartite Ssrna Genome Of 5.9–7.0 Kb	LC592412	[14]
Potyvirus	Lettuce mosaic virus	N. Benthamiana is one of the most permissive hosts	Positive-Sense, Single-Stranded RNA—9000–12,000 Nucleotide	MZ318158	[21]
	Plum pox virus	Each, almond, and cherry, and ornamentals
	Tobacco etch virus	Tobacco
	Turnip mosaic virus	Turnip
	Watermelon mosaic virus	Watermelon
Sobemovirus	Turnip rosette virus	Dicotyledonous and monocotyledonous plants	Single-Stranded RNA—4149 Nt.	AY177608	[137]
Tobamovirus	Oilseed rape mosaic virus	Tobacco, potato, tomato, and squash	Single Linear Positive-Sense Single-Stranded RNA—6.3–66 Kb	EF432728	[138]
	Tobacco mosaic virus	Tobacco
	Turnip vein-clearing virus	Turnip
Tobravirus	Pepper ringspot virus	Herbaceous and few woody plant species	Bipartite, Positive-Sense, Single-Stranded RNA Around 26.84. 5 kb-8600–11,300 Nucleotides	NC_003669	[135]
	Tobacco rattle virus	Tobacco
Tospovirus	Iris yellow spot virus	Ornamental, vegetable, fruit, and other annual and perennial plants	Tripartite Negative And Ambisense RNA—8.9-Kb	MF359021	[123]
Tymovirus	Turnip yellow mosaic virus	Monocotyledonous plant	Single Molecule Of Positive-Sense Single-Stranded RNA Of 6.0–7.5 Kb In Length.	AH002387 J02418 K00602 V01419	[126]
Umbravirus	TBTV (tobacco bushy top virus)	Cowpea; Potato; Groundnut	(+)Ssrna-Linear, Positive-Sense, Single-Stranded RNA, 4200–6900 Nucleotides	TBTV-YBSh, MW579556; TBTV-YKMPL, MW579557	[10]
	Tmov (Tobacco mottle virus)

Table 3.

Some plant viruses are shown in the table, along with their Genbank accession numbers.

2. Plant viruses management and detection

Human activity is creating conditions that encourage the spread of begomoviruses. To avoid ToLCV outbreaks and agricultural losses, administrative, legal, and technological procedures should be implemented. Insect vector biological management may also be explored to minimize insect vector infestation and disease dissemination. We discuss recent developments in the identification, characterization, and detection of plant viruses and virus-like compounds using nano-coupled molecular method approaches in this review article [141]. The objective of this essay was to accurately identify the most significant plant viruses as reported by Molecular Techniques contributors. We are well aware that between disciplines and regions, importance and priority might differ locally (Table 4). In the past, biological assays were a crucial tool for determining a plant’s health condition as well as for the identification and characterization of a specific virus. The labor- and time-intensive biological indexing has few practical uses nowadays, though it is still important for plant virus research. Instead, molecular diagnostics is the primary method used for the precise and sensitive detection of the majority of viruses and virus-like diseases [151]. Some recent developments in point-of-care (POC) nucleic acid extraction technology are summarized in this study. Emerging bacterial, viral, fungal, and other pathogen-caused human and plant diseases present a persistent threat to global health and food security [152]. Although there are numerous pipelines for finding plant viruses, they all have a similar structure. In POC diagnostics, plant samples are examined right away at the sampling site for disease screening. Rapid point-of-care (POC) molecular diagnostics of plant diseases is becoming increasingly important for disease control and agricultural protection. The identification of the disease-causing pathogens and their pathogenesis is revealed at the genomic level by nucleic acid-based molecular diagnostics. One of the most important and efficient steps in creating control strategies for plant viral infections is still the development of reliable and early detection technologies [117].

2.1 Conventional measures before, during, and after vegetation

The virus itself is frequently not the main problem, but rather the vector that it travels on. To reduce the population of B. tabaci, insecticides including imidacloprid, acetamiprid, dinotefuran, and thiamethoxam are frequently applied. Whitefly infestation in nurseries may be avoided by using netting. Eretmocerus eremicus and other biocontrol agents could be very effective control agents. One of the main challenges in managing pathogens is keeping a pathogen alive in many hosts. Alternate hosts serve as a repository for inoculum both during the growing season and during periods when there is no crop. Recent research indicates that the effectiveness of using chitosan as a biocontrol agent against ToLCV has increased when combined with pseudomonas. Because begomoviruses are so common, breeders should take them into account when making selections for resistance.

2.2 Biotechnological approaches for viral disease diagnosis

The family Geminiviridae (genus Begomovirus) has more than 100 different viruses. Because of improvements in cloning and low-cost sequencing, the number of accessible genome sequences has significantly increased. Tomatoes have a small DNA genome that is simple to clone. Numerous tomato viruses can be identified, as well as new or emerging viruses and viroids, using general virus detection technologies like enzyme-linked immunosorbent assay (ELISA) or polymerase chain reaction (PCR). For the accurate identification of well-known and novel viruses and viroids, a bioinformatics pipeline based on the alignment and assembly of sRNA or DNA sequences is necessary. Key viral genes called ToLCNDV miRs affect the fundamental processes involved in virus emergence. RNAi-based viral gene silencing and sense/antisense technology have been used to create transgenic resistance. The use of next-generation sequencing [NGS] technology to quickly, precisely, and affordably detect miRs has become commonplace. The generation of markers for marker-assisted selection (MAS) of resistant genotypes may now be done swiftly because to the development of NGS technology and high-throughput genotyping platforms [153]. The use of transgenic methods to control viral infections is extremely successful. The public hostility to genetically modified organisms (GMOs) in developing countries like India has inhibited their implementation. Infection is reduced by 75% in transgenic tomato plants that produce dsRNA-containing sequences from the IR, V1, and V2 regions of TYLCV-Oman. The identification of VSR may lead to the development of disease resistance strategies and other biotechnological applications. RNA silencing sometimes referred to as RNA interference or RNAi shields plants from viroids and invading viruses [111]. The AC4/C4 protein is a pathogenicity protein that impacts plant development and can be used as a useful tool for research into cell cycle regulation, hormone signaling, cell differentiation, and plant development. It has been demonstrated that transgenic lines of AC4 viruses led to abnormal phenotypes and developmental patterns in several different host plants. Disease-resistant tomato varieties can assist with gene-pivoting and resistance-breeding [154].

Elite tomato breeding lines were chosen using a mix of phenotypic and molecular screening techniques for ToLCD, late blight, and RKN. To develop fresh market tomato lines that are begomovirus-resistant, AVRDC, The World Vegetable Center, initiated a campaign. A lipid transfer protein, nucleotide-binding site, and leucine-rich repeat (NBS-LRR) proteins, posttranscriptional gene silencing machinery and other defense genes are expressed specifically in the host in response to ToLCNDV infection. To build resistance against various ToLCV strains, six resistance loci have been employed in tomato plants. Of the six resistance/tolerance loci, Ty-1, Ty-2, and Ty-3 are the ones that are used most frequently. These results suggest that these Ty loci increase host defense via a different mechanism from the R gene-mediated hypersensitive response (HR). Increased expression of genes associated with the lignin and SA biosynthesis pathways has been related to improved plant virus defense, according to reports. A global miR profiling study has shown that a large number of miRs were differently changed in ToLCV-ND-infected Pusa Ruby tomato leaf tissue. The study also identified miRs that demonstrated differential expression between the sensitive and tolerant cultivars. ToLCD resistance is conferred by the expression of artificial microRNA targeting the ATP-binding region of AC1 in transgenic tomatoes without affecting tomato output. The antisera’s usefulness in begomovirus identification in field samples and reservoir hosts is demonstrated by polyclonal antibodies generated using purified intact virus and rCP of tomato leaf curl Bangalore virus [155]. From tomato and N. benthamiana leaves that had been treated with the virus, ToLCBV was successfully purified. Different Indian isolates of the begomovirus in plant and weed species might be recognized using monoclonal antibodies. ToLCBVC viral infections were caused by biologist Devaraja in tomato samples as well as other crop and weed plant types. Total viral resistance is provided by transgenic plants that produce Cas9 and dual gRNAs that target different regions of the cotton leaf curl Multan virus (CLCuMuV) single-stranded DNA genome, offering a special method for developing geminivirus resistance. Clustered, regularly interspaced short palindromic repeats/CRISPR-associated proteins are the foundation of the genome-editing technique CRISPR/Cas. It originated from the bacterial and archaeal adaptive immune systems that resist viruses [156, 157].

2.3 Nanotechnology-based nucleic acid/viral particle detection

High-throughput sequencing (HTS) has enabled virologists to identify an unprecedented number of viruses, advancing our understanding of the variety of viruses in nature and, in particular, revealing the virome of many crops. The gaps in our knowledge of virus biology have, however, frequently become wider as a result of these new virus discoveries. Enzyme-linked immunosorbent assays (ELISA) and direct tissue blot immunoassays are two immunological methods now utilized to detect infections in plants (DTBIA). For the identification and detection of pathogens, DNA-based techniques such as polymerase chain reaction (PCR), real-time PCR (RTPCR), and dot blot hybridization have also been proposed [158].

The sensitivity and specificity of virus nucleic acid sequence identity are predicted to be improved by using nanotechnology-based techniques, which are thought to be more effective, safer, and target-specific. Compounds made of nanoparticles (NPs) can simulate ligand and receptor binding to particular target-specific plant diseases, such as the interaction between an antigen and an antibody. The gold standard for plant disease diagnostics uses molecular assays based on nucleic acids and antibodies. Being one of the most fascinating and dynamic fields of research, nanotechnology has a significant impact on a wide range of fields, including science, engineering, medicine, and agriculture. Nanomaterials, whose diameters typically vary from 1 to 100 nm, can offer enhanced surface-to-volume ratios as well as special chemical, optical, and electrical properties, making them excellent candidates for the analysis of plant diseases. For the quick detection of a variety of human and plant illnesses, lateral flow assays (LFA) and electrochemical sensors have been used as some nano-based approaches (Table 5). Fast identification of plant diseases is now possible because of portable imaging equipment (such as cellphones) backed by nanostructures. Due to the extraordinary biosecurity of designed molecular recognitions at the nanoscale, which has seen exceptional development in the past decade, nanoscale materials are promising possibilities for plant disease detection. Overall, thanks to recent advancements in rapid plant DNA extraction technology made possible by microneedles, tiny DNA sequencing chips, and smartphone-based volatile organic (VOC) sensors, many traditional laboratory tests, like nucleic acid amplification, sequencing, and volatile organic compound (VOC) analysis, may now be performed directly in the crop field in a much faster and more affordable manner [163].

Viruses	Material DNA/RNA	Method of detection	Advantages	Limitations	References
Asparagus viruses	DNA	cDNA macroarray	Detect multiple viruses	High cost and the large number of probe	[27, 142]
Potato viruses	RNA	Generic methods	Potential to test for a large number of targets in a single assay	Cannot use casts or instance of with parameterized types	[18]
Viruses with non-polyadenylated genomes	RNA	rRNA-selective depression method	To detect a broad range of viruses	High-throughput and cost-effective method	[143]
Tomato yellow leaf curl virus (TYLCV)	DNA	LAMP-coupled CRISPR-Cas12	Rapid and sensitive detection	May be not yet	[144]
Any viruses	Both DNA and RNA	Oxford Nanopore Technologies (ONT) sequencing	Nucleotide sequences in real time without the need for prior amplification.	It tends to be error-prone	[145]
Citrus tristeza virus	RNA	High-throughput sequencing (HTS)	More comprehensive and standard operating procedures	Short-read technology is that short read must be mapped to genome that is not always available	[146]
Potyviruses	DNA/RNA	‘Direct RT-RPA	Target virus directly from plant leaf extracts.; The minimal sample preparation requirements and the possibility of storing RPA reagents without cold chain storage	Detection with CDV RNA extracted from strains	[147]
Latent viruses	RNA	RT-qPCR assays	Amplifying the target from positive controls without showing any detectable amplification in negative and nontarget controls and revealed high sensitivity by reliably detecting	It requires separate priming reactions for each target. It is also wasteful if only limited amounts of RNA are available	[148]
Grapevine viruses	RNA	A multiplex RT-PCR	Simultaneous detection of nine viruses at once	(1) The self-inhibition among different sets of primers; (2) low amplification efficiency; and (3) no identical efficiency on different templates	[149]
Both DNA/RNA virus	DNA/RNA	Dot-immunobinding assay	Economical to screen more than 1000 samples against 15 known plant viruses in a very short time	The biotinylation process may alter the structure and properties of the proteins of interest	[150]
Cucurbit-Infecting Viruses	DNA/RNA	Fluorescent microsphere-based assay	Simplicity, speediness, and sensitiveness	Not yet	[16]

Table 4.

For the identification of plant viruses and virus-like pathogens, nanotechnology integrated molecular method techniques.

Virus	Plant	Nano-based device	Advantages	Limitations	References
Orchid viruses	Cattleya, Cymbidium, Dendrobium, Odontoglossum hybrids, and Phalaenopsis	Gold nanorods (AuNRs); Fiber optic particle plasmon resonance (FOPPR)	Faster analysis, better reproducibility, and lower detection limit than ELISA	Conventional UV–vis spectroscopy is constrained by weak resolution and a low signal-to-noise ratio, which may not be enough to detect proteins at low quantities. The LSPR optical fiber biosensor, which is based on wavelengths, might experience the same restriction.	[159]
Citrus tristeza virus (CTV)	Citrus trees	Gold nanoparticles (AuNPs) to develop a specific and sensitive fluorescence resonance energy transfer (FRET)-based nanobiosensor for detecting	Rapid, sensitive, specific, and efficient in detecting viruses	Mass transfer limitation.; Process at low frequencies	[6]
Cauliflower mosaic virus 35 s (CaMV35S)	Brassicaceae and Solanaceae species	Forster resonance energy transfer	Applied to identify the real sample. Most utility and reliable for quantification of GMOs in food.	Low signal-to-noise ratio	[83, 160]
Citrus tristezavirus	Rutaceae	Amplification (RPA) detection on gold nanoparticle-modified electrodes	In-field diagnostic application and effective replacement to polymerase chain reaction (PCR)	Heat sources are needed for getting detectable signals, which represents an important practical limitation	[161]
Citrus tristeza virus	Citrus	Solid-phase isothermal recombinase polymerase	Sensitive, specific, rapid, and efficient in detecting viruses	Not yet	[162]

Table 5.

Only a few methods use nanotechnology-based electrochemical nucleic acid sensing in disease diagnosis.

2.3.1 Challenges in nanotechnology

The environmental impact and toxicity of engineered nanomaterials, the quickness of data sharing and disease forecasting, and long-term sensor stability in extreme conditions like extreme cold or heat, prolonged sun exposure, and heavy wear are the three main challenges that currently exist for plant diagnostic tools. The first issue is that safety issues must be resolved before any nanosensors can be commercialized and used in the field because some nanoparticles, like QDs, may be hazardous. More thorough toxicity testing and regulation are required for nanosensors that will be used on living plants or consumable agriculture and food items, because dangerous nanomaterial residues may infiltrate the food chain and be consumed by end users. Regarding the second issue, the new generation of nanosensors is anticipated to be more wirelessly connected and capable of providing measurement in close to real time as the primary requirement for disease diagnosis is consistently the timely report and forecast of infection events on-site. Finally, before any sensors can be deployed to the actual yield, more resilient and robust sensors that can endure a wide range of environmental factors (such as temperature, humidity, air pollution, etc.) in the agricultural yield are predicted [164].

2.4 Need to resolve

2.4.1 Several outstanding questions and future directions are highlighted

• Luan et al. show that TYLCV infection can trigger whitefly immune responses, potentially leading to viral particle destruction within the body of viruliferous whiteflies. These findings suggest that TYLCV infection causes physiological changes and immunological responses in whiteflies, which is harmful. However, the precise mechanisms driving the whitefly’s immunological responses to begomoviruses remain unknown [49].

• Ashish Prasad et al. [102].

  • What role in the pathophysiology of TYLCV do endogenous noncoding RNAs, such as sRNAs and lncRNAs, play?

  • Is there another way to safeguard against the virus? It is imperative to hunt for new sources of resistance given the virus’s quick global spread.

  • Investigations focusing on this area may help to fix the problem, because there is still debate on whether TYLCV can reproduce inside the whitefly.

  • The effect of suppressor TYLCV proteins in dampening the host RNA-silencing machinery has been investigated extensively. It is yet unclear if they can inhibit proteins involved in other processes, such as the ubiquitin-proteasome system or autophagy.

• Zaidi et al. [77].

  • By pyramiding various poisons, can we develop broadspectrum resistance against chewing and sap-sucking insects?

  • Tma12 kills B. tabaci in two ways.

  • Will phloem-specific promoters improve the performance of dsRNA and Tam12?

  • Will the poisons cause B. tabaci to become resistant?

  • Can the simultaneous expression of many toxins and/or dsRNAs prevent resistance breaking?

  • Will these strategies work against other begomoviruses including those that cause cassava mosaic viruses (CMVs) and tomato yellow leaf curl virus (TYLCV)?

  • Adapted from a drawing of B. tabaci sucking phloem sap.

• Rolling circle replication (RCR)-dependent geminivirus replication requires the viral replication initiator protein (Rep) and the conserved common region (CR), but the precise mechanisms of geminivirus replication are still unknown due to the lack of a eukaryotic model system [97].

• One of the viral symptom determinants that have the potential to lead to abnormal cell division is the C4 protein expressed by the geminivirus [107]. On the other hand, it is unclear what chemical process C4 uses to promote cell division.

• GAs are a defensive measure, geminiviruses encode viral proteins that lower viral DNA methylation and transcriptional gene repression (TGS). However, it is still uncertain how viral proteins contribute to TGS suppression at the molecular level.

• According to DNA-A components of ToLCNDV isolates, recombinations in this genus frequently involve genomic sequences from other begomoviruses or sequences of unknown origin. The taxonomic status of these recombinants is determined by their relatedness to the original virus(es) and putatively altered biological characteristics [77].

• The dsDNA intermediates used by geminiviruses to replicate their genome in the nucleus may be a target for methylation-mediated TGS [98]. Cytosine DNA methylation is an efficient defense strategy against geminiviruses in plants, because methylation of the viral genome results in transcriptional gene repression (TGS). Geminiviruses produce viral proteins that, as a defense mechanism, reduce viral DNA methylation and TGS. On the other hand, it is yet unclear how viral proteins contribute to TGS suppression at the molecular level.

• The insect vector Bemisiatabaci does not appear to be the site of tomato yellow leaf curl virus replication [81]. Due to the characteristic of an extended host range, controlling and reducing losses brought on by mixed begomoviral infection is challenging. To lessen agricultural losses brought on by begomoviruses, a long-term disease management strategy must be devised while the effects of begomovirus infection on commercially farmed crops like papaya must be continuously monitored [73].

3. Concluding remarks

One of the most widely investigated plants viral diseases is the ToLCV. On the Indian subcontinent, ToLCV is the most hazardous bipartite begomovirus, and it has quickly spread to other regions of the world. The implementation of innovative management techniques is dependent on the availability of information regarding ToLCV-associated viruses and their epidemics, which is lacking. ToLCNDV has an incredibly diverse population, with mutations that have different host ranges and some that are better adapted to infecting particular host plants. The invention of novel techniques to defend plants from infection will be facilitated by an understanding of the fundamental mechanisms behind such host adaptation. GM techniques based on gene silencing have presented exceptionally significant options for plant viral resistance tactics, and their long-term promise should not be overlooked. Conventional control procedures alone are insufficient for ToLCV control. However, combining many of these approaches following suggestions based on an understanding of the disease’s epidemiology may make managing ToLCNDV outbreaks easier. As a result, it is suggested that integrated management techniques integrating numerous control practices be used. However, more research about the epidemiology and ecology of this multifaceted disease is needed to develop efficient management strategies. Because this virus does seem to have a quicker response time than available controls, we should be able to predict the nature and diversity of ToLCV outbreaks in a more dynamic environment, which will have drastic effects on virus vectors. The discovery of more potent and long-lasting strategies to prevent epidemics also depends on a detailed awareness of ToLCV polymorphism and the factors that influence the growth of its inhabitants.

Conflicts of interest

The authors declare no conflicts of interest.