Viruses are the biotrophic parasites of plants, cause a wide variety of symptoms, and are responsible for considerable yield loss in a variety of crops. The genera, viz., Tospovirus, Ilarvirus, Cucumovirus, and Potyvirus, are the major RNA plant viruses that infect cultivated crops worldwide which leads to huge loss. The virus disease management relies upon the use of prophylactic measures, cultural practices, planting resistant cultivars, vector control options, and molecular approaches. The efforts made through the conventional breeding program by developing resistant cultivars against viruses that are not successful in all crops due to unavailability of resistant sources. Alternatively, the RNA silencing technology has been explored as an advanced biotechnological tool for the control of virus diseases in crop plants. The antiviral mechanism through RNA silencing in plants is also known as RNA interference (RNAi) or posttranscriptional gene-silencing (PTGS). RNA silencing is a surveillance response induced by double-stranded RNA (dsRNA), wherein the dsRNA is cleaved into short small interfering RNA (siRNA), which is the key attribute for sequence-specific degradation of mRNA. The plants expressing sense and antisense gene fragments of viruses have shown resistance to virus. The inverted repeat constructs producing self-complementary RNAs (hairpin RNAs) from viral origin have efficiently induced virus resistance in transgenic plants through RNA-silencing mechanism. RNA silencing has expedited the molecular basis of plant antiviral systems, since it allows more accurate downregulation of gene expression without influencing the expression of other genes.

Plant virus epidemics can lead to crop losses to the extent that it can shorten the supply of food in the world. Plant virus management has always been at a point where researchers feel that they lack management methods as they are available in other plant pathogens or in other words pathogens (bacteria and fungi) infecting plants can be managed but it is difficult to manage plant viruses once they have infected plants. It is also very important to diagnose the pathogens correctly in order to manage them. Management of plant viruses can be done by classical or traditional approaches and molecular methods. There has been a shift from traditional methods to molecular methods gradually from the last century. This has also led to improvement in the management strategies. Shifting to NGS in virus identification has brought revolution in understanding the genome of the viruses. Advent of RNAi techniques and NGS technology have further improved the management methods. Upcoming approaches such as CRISPER/Cas exploitation for plant virus management is the latest area where researchers are exploring the best possible plant virus management strategies.

Papaya ring spot virus (PRSV), a member of the genus Potyvirus (family Potyviridae), is a major constraint for papaya as well as cucurbits cultivation worldwide. PRSV virions are filamentous and flexuous measuring 760–800×12nm with monopartite single-stranded positive-sense RNA as its genome. PRSV is grouped into papaya-infecting pathotype-P (PRSV-P) and nonpapaya-infecting pathotype-W (PRSV-W) and is transmitted in a nonpersistent mode by numerous aphid species. Pathotype-P infects papaya as well as cucurbits while pathotype-W doesn’t infect papaya. The disease was reported in 1940s from Hawaii. Since then, various aspects of PRSV have been thoroughly characterized in last eight decades of research. The advancements in molecular biology and genomics have helped in designing and developing the effective virus control measures. The transgenic papaya cultivars Rainbow and SunUp were developed and commercially released in Hawaii in 1998, which saved Hawaii's papaya industry from the devastation by PRSV. This review highlights the research work carried out on various aspects on characterization and management of PRSV.

Banana bract mosaic virus belonging to the genus potyvirus is one of the serious banana-infecting viruses causing bract mosaic disease which is responsible for a significant negative impact on the production and productivity in India and the Philippines. The virus is a flexuous rod-shaped containing single-stranded positive-sense RNA genome with a length of 9708 to 9713 nucleotides long and codes for a polyprotein of 3125 amino acids, and the polyprotein gets cleaved by nine proteases to yield 10 functional matured proteins. This virus induces mosaic symptoms on the leaf, leaf sheath, midrib, fruits, petiole, and malformation fingers and bunches. So far BBrMV is reported to cause diseases on banana, cardamom, and flowering ginger, and its distribution is limited to a few countries including India. As on date, only four full-length complete genome sequences are reported and nucleotide sequences of the complete genome of the BBrMV-TRY (banana) isolate were 96.7% identical with BBrMV-WAY (cardamom) followed by BBrMV-PHI (banana) (94.6%) and BBrMV-HAW (flowering ginger) (94.4%). The genetic diversity of BBrMV isolates was analyzed based on the sequences available in the public database. Based on the coat-protein-encoding gene of BBrMV isolates, two distinct isolates, TN14 and TN16, were identified which had a divergence of 19.8% and 17% at nt and 15.4% and 7.7% at aa level, respectively, with other isolates. The evolutionary distance, polymorphism at the sequence level, the presence of SNPs and INDELs, and the codon-based analysis and genetic differentiation between the BBrMV populations based on the sequence of three genes, viz. the HC-Pro, VPg, and CP were performed. Based on SNPs analysis, a maximum of 74, 36, 177 SNPs, and a minimum of 24, 17, 15SNPs, for HC-Pro, VPg, and CP genes were detected. The codon-based selection analysis of HC-Pro, VPg, and CP revealed that most of the codons fell under negative selection, and some were under positive selection. The gene flow between BBrMV populations was infrequent. Phylogenetic analysis and the results revealed the closeness of BBrMV-TRY with BBrMV cardamom isolate. Recombination analysis showed only four potential recombinants in both the HC-Pro and CP genes, respectively, whereas VPg had a single recombinant. In the management of this disease, the detection plays an important role in eliminating the virus from mother plants used for mass tissue culture propagation, confirming the elimination of the virus attempted by meristem tip culture and other therapies. The higher dose of fertilizer leads to the compensation of yield loss due to this virus in banana. Molecular approaches like transgenics, RNAi, and genome editing can be applied to develop resistance against this virus in banana, and so far only a few attempts were made to develop genetically engineered plants using these approaches.

Citrus tristeza virus (CTV) is the most economically important virus disease of citrus in the world, having lost more than 100 million trees on sour orange rootstock. The virus primarily spreads by infected budwood and several aphid species in a semipersistent manner. CTV is a member of the Closterovirus genus in the family Closteroviridae and is the largest nonsegmented plant RNA virus. Genetic variation between isolates is unevenly distributed along the CTV gRNA, the most conserved region being the 3′-UTR, with over 95% identity and the most variable being the 5′-UTR, with identity values as low as 44%. Based on phylogenetic analysis of the complete genomic sequences, CTV strains fall into eight broad genotypes. CTV is a regulated Class-A plant pest, and a monoclonal antibody (MCA13) can be used in ELISA for preliminary screening for potentially severe as well as exotic strains of CTV to California.

Potatoes are the third most important food crop in the world after rice and wheat, and their production as food is constantly increasing with the increase in the size of the human population. One of the factors that strongly influence the yield and quality of production are viral diseases that cause great damage to potato growers. More than 50 different viruses have been reported infecting potatoes which are a problem for the quality and the quantity of global potato production. Some of the most common in potato crops and most economically important viruses are Potato virus Y (PVY), Potato leaf roll virus (PLRV), Potato virus X (PVX), Potato Virus A (PVA), Potato virus S (PVS), and Potato virus M (PVM). The identification and characterization of these viruses is crucial for the diagnosis, prevention, and control for potato growers around the world. Selection of resistant to viruses on potato cultivars, introduction of certification schemes for virus-free planting material, and different control measures are irreplaceable and obligatory for guaranteeing the quality and yield of potato production.

Tobacco mosaic virus (TMV) was the first virus discovered (1898) and the first virus ever purified. Since then, TMV became an object of intense scientific investigation, and discoveries made on TMV have marked the development of molecular virology and modern biology. As a result, an unprecedented amount of data is available on the molecular biology of the TMV and its structure, which led to the exploitation of TMV and its constituent sequences/parts for the development of vectors for the expression of heterologous genes in planta as well as virus-induced gene silencing (VIGS) in plants, for the generation of transgenic virus-resistant plants and as a novel tool in the virus-based bio-nanotechnology for a plethora of applications. This book chapter will focus on TMV molecular biology and its management strategies.

In general, viruses are able to encode a limited number of proteins, and therefore, they recruit many different host components to produce viral proteins. Eukaryotic translation initiation factors play a major role in the infectious cycle of viruses, and they emerge as a key target for the control of viral diseases. Resistance against plant viruses is mostly recessive in nature, and eukaryotic translation initiation factors are one such class of recessive resistant genes that confer resistance to many plant RNA viruses, especially potyviruses. The viral genome-linked protein (VPg) of potyviruses interacts directly with the plant eukaryotic initiation factors, and any mutations or alterations in VPg may lead to resistance to viruses. Eukaryotic initiation factor-based resistant alleles are found naturally in many crops, and these genes are the main target for developing resistance in many economically important crop plants infected by potyviruses through either genetic engineering or gene editing technologies in the absence of natural resistant alleles.

The genus Polerovirus is currently ascribed to the family Solemoviridae. Cucurbit aphid-borne yellows virus (CABYV) was the first cucurbit-infecting polerovirus recorded in the world from France in 1988 infecting cucumber, melon, and zucchini squash plants. Subsequently, this has been documented worldwide infecting various cucurbits within a span of 30 years from its first documentation, indicating its rapid global distribution, hence gaining the status of an “emerging virus.” Globally, eight Polerovirus species have been documented to cause economically important diseases in cucurbit crops. However, the occurrence of these viruses was not known in India until the first report of CABYV in 2017. In the recent past, the incidences of cucurbit-infecting poleroviruses have been increasing worldwide in different hosts and geographic locations causing 10%–100% crop losses in several crops. However, their impact on different crops has remained to be estimated in India. This book chapter documents the up-to-date information available on the occurrence and distribution, biology, molecular biology, detection and diagnosis, epidemiology, and management aspects of the cucurbit-infecting poleroviruses in terms of global and Indian contexts as well as the future thrust areas of research investigations.

Viruses are unique pathogens of agriculturally important crops. Transmission of plant viruses via insect vectors is an interesting mechanism in the life cycle of viruses and insects as well. Virus-vector interaction develops the understanding of the transmission mechanisms involved. Plant viruses spread horizontally and vertically through insects depending on the transmission mode. Plant viruses interact with their vectors in different ways for their survival and spread. Different proteins in viruses, hosts, and insects are involved in the transmission and acquisition of plant viruses from different sources, although insect proteins are involved in virus transmission but are poorly characterized. Hitherto, insect proteins involved in virus transmission have been poorly characterized. Identification of different proteins and their role involved in molecular mechanisms in virus acquisition and transmission through insects are the key areas in the research gap and recent advances. Among the other proteins, cuticular proteins have been emerged as the vital molecules in plant virus transmission. This chapter will describe the role of insects in the life cycles of viruses and hosts. The interaction of virus-vector-host will also be elaborated through the role of different proteins and molecular mechanisms in this chapter. These understanding and interactions and mechanisms will be helpful to formulate the management strategies for plant viruses in agricultural crops.