**6. Conclusion and future directions**

RNA-seq has become an indispensable diagnostic tool of clinically important RNA viruses. It has taken the research community almost 20 years to sequence a complete HIV viral genome, but it took a little over 2 months to sequence a near complete SARS-CoV-2 genome and identify its origin! With an improved understanding of the genomic structures of virus populations, RNA-seq can be used to track the origins, genetic diversity, and global monitoring of transmission patterns. In a public health context, RNA-Seq is an indispensable tool to be utilized in the assessment of risks and the emergence of future outbreaks. Additionally, assessment of transcriptomic profiles, during host responses to infection improved the understanding of disease pathogenesis and identify patients at risk for severe outcomes. To overcome drug resistance, novel viral genotype-guided agents based on antisense RNAs (e.g., aptamers, peptide nucleic acids oligomers, ribozymes, and RNAi silencing therapies) are being developed to specifically inhibit viral replication. Complex bioinformatics approaches enabled vaccines to be designed with high probabilities of intercepting viral escape [143]. Much work awaits the global scientific community, including the establishment of unified reference standards and the adoption of a single nomenclature for SARS-CoV-2. Additionally, the assessment of long-term vaccination efficacy by RNA-Seq in the clinical laboratory is necessary to fully understand its benefits [144].

## **Abbreviations**


*Diagnostic Applications for RNA-Seq Technology and Transcriptome Analyses in Human… DOI: http://dx.doi.org/10.5772/intechopen.99156*
