Citrus are cultivated in a vast area worldwide and many countries grow it. Citrus fruits are delicious and everybody can eat it easily so many farmers like to grow them because of the good market. This plant has many diseases that induce various kinds of agents like fungi, bacteria, nematodes, and viruses. In this chapter, we discussed some citrus viral diseases that are very important and dangerous for fields. First, the Citrus Tristeza virus is explained that exists around the world. After that, you will know about other viruses like the Citrus psorosis virus. Viroids are another agent that causes diseases and reduces the amount of production. You learn some of them in this chapter like Hop stunt viroid, Citrus exocortis viroid, etc. The significant point of knowing citrus viral diseases is in the management of diseases. The control of viral diseases is difficult because there are no poisons or combinations to remove viruses from infected plants. If farmers or experts know about symptoms that cause viruses or viroids, they can report it to the related office and do some work to control it and it is important to the agriculture industry.

Citrus tristeza virus (CTV) is one of the economically destructive viruses affecting citrus trees worldwide, causing significant losses in fruit production. Comparative genomic studies have shown genetic diversity in various regions of the genome of CTV isolates, which has classified the virus into several genotypes. In recent years, some orange citrumelo-tolerant rootstocks showed yellowing, decline, and vein clearing in northern Iran (Mazandaran province, Sari). We confirmed the presence of CTV in the symptomatic trees by reverse transcription PCR (RT-PCR). The complete genome of a Sari isolate of CTV (Sari isolate) was sequenced using next-generation sequencing (NGS) technology. In addition, phylogenetic analysis, differential gene expression of the virus and identification of its variants in a population were studied. We obtained the final contigs of the virus (nt) and annotated all genomes to viral ORFs, untranslated regions (UTRs), intergenic regions, and 5’ and 3’ ends of the genome. Phylogenetic analysis of the Sari isolate and other genotypes of CTV showed that the Sari isolates were placed in a distinct cluster without a sister group. Based on the number of specific transcripts (TPM) in CTV RNA -Seq, P13 was the most highly expressed gene related to the host range of the virus and its systemic infection. The ORFs of the polyprotein, P33, and P18 showed variation in a single population of the sari isolate. The CTV has a potential for variation in a population in a host, and these variations may contribute to the best fit of the CTV in different situations. In Iran, whole genome sequencing of the CTV was performed for the first time, and we gained new insights into CTV variation in a population.