**1.2. Viral sequencing methods**

The distinction of complete genome ever to be sequenced belongs to bacteriophage ΦX174 with a genome size of 5,386 bases and was achieved through the Sanger's shotgunsequencing approach [5]. The major aim of early sequencing projects was to characterize the genomic content of an organism in terms of its coding potential. Over the last few years, the unprecedented growth in the area of sequencing technologies has had a huge impact on the way viral genomes are being addressed. The scale of generating and handling data, which was unimaginable previously, has become a reality today due to the advent of Next-Generation Sequencing (NGS) technologies. Advantages of NGS over the conventional Sanger sequencing approach are the rapid generation of sequencing data on a very massive scale and at affordable cost. NGS also provides scope for wide range of studies that include transcriptomics, gene expression and regulation (DNA–protein interaction), single-nucleo‐ tide polymorphism (SNP) and RNA profiling. Sequencing of viruses, in particular, has been important to understand the spread of epidemics, the circulating viral particles and the improvement of strains for vaccine design. Different technologies such as Roche 454 [6], Illumina [7], Ion Torrent [8] and more recently the fourth-generation sequencing methodol‐ ogies popularly called single-cell sequencing, *viz.* Oxford Nanopore [9] and Pacific Biosciences [10], are available for sequencing.

Sample preparation and enrichment are the prerequisites for sequencing the viromes. Filtration and centrifugation on caesium chloride density gradient have proved to enrich the virus-like particles. A strategy like depletion of host rRNAs is also known to increase the virus fraction and has been attributed to the discovery of several novel RNA viruses [11]. In plant virology, use of CF11 cellulose spin column is routinely used for deep sequencing of dsRNA.

There exist several scenarios for sequencing viral genomes such as sequencing of individual strains or population [12]. Sequencing of individual genomes helps to catalogue the genes encoded in a particular strain and is a vital step for in-depth characterization studies. Se‐ quencing of multiple isolates/strains/species enables understanding of the factors responsible for varying virulence using comparative genomic approaches [13]. For understanding the coevolution of viral and host genomes, in particular, archaea and bacteria, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacer sequencing is used [14]. CRISPR are found in archaea and bacteria that serve as an antiviral mechanism in which viral genomic sequences are integrated as CRISPR spacers into the host, thereby making it immune to viral infection [15]. Understanding complex dynamics of virus–host interactions in higher organ‐ isms using sequencing provides valuable insights into transmission between animal reservoirs [16]. Sequencing of 'Auxiliary metabolic genes', which are involved in processes like motility and transcriptional repression, enables to unravel the viral genes that influence host machinery in diverse ways [17].
