Nucleic acid-based viral diagnostic is a gold standard approach for the detection of number of viral pathogens offering exceptional sensitivity and specificity. Clinical laboratories use recent technologies such as sequencing and quantitative polymerase chain reaction for fast and precise identification of number of viruses. The rapid advancement in high-throughput technology has transformed nucleic acid based viral diagnostics and frequently utilized in laboratory testing nowadays. Among them, next generation sequencing (NGS) has evolved from a research instrument to a sophisticated diagnostic method for accurate, high-throughput, cost-effective DNA and RNA sequencing. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) technology has revolutionized diagnostics and employed in viral identification. Digital PCR is now frequently utilized for the absolute quantification of viral nucleic acid in a sample. Advancements in NGS, CRISPR technology, and digital PCR have greatly influenced viral diagnosis nowadays. This chapter explores the significant developments and application of NGS, CRISPR-based diagnostics, and digital PCR in viral diagnosis. Additionally, artificial intelligence (AI) is now integrated with large data set of viral genomic sequences to offer deep insight. Ongoing advancements in AI, demonstrate potential for enhancing the precision and promptness of viral infection identification.