Singleplex tests have demonstrated the ability of Cas13- and Cas12-based diagnostics to sensitively identify a variety of viral targets. SHERLOCK’s capacity to recognise small amounts of ZIKV in artificial lentivirus samples at known concentrations and in patient samples with a variety of viral titres was first proven during the Zika epidemic [81]. In a collection of 25 patient samples, DETECTR was initially utilised to identify the DNA of HPV16 and HPV18. With the exception of two samples, DETECTR produced concordant results when compared to the gold-standard qPCR [73]. Since then, a growing number of CRISPR-based assays have been created and approved for use with human viruses, including the ones that cause Lassa fever, the Epstein–Barr virus, the Powassan virus, the H7N9 influenza virus, the hantavirus, the Ebola virus, and the Japanese encephalitis virus (JEV) [85,86,87]. CRISPR-based tests could be created for any viral pathogen given enough genomic data due to the adaptability of these platforms [88,89]. Once a new virus’ genomic sequence is known, CRISPR-based detection techniques can be quickly tested and validated for it. The advent of SARS-CoV-2 in late 2019 served as a prime example of this. New assays were being created and posted on social media and preprint servers soon after the first SARS-CoV-2 genomes were released [90,91,92,93], and soon after that, peer-reviewed papers. The DETECTR approach was used to create a SARS-CoV-2 assay, which was then validated on more than 70 patient samples, demonstrating how quickly these assays can be created [90]. Similar to this, a SHERLOCK test with excellent agreement with RT-qPCR was validated on more than 150 patient samples in Thailand [94]. Soon after, many more publications appeared [95,96,97]. The FDA’s emergency use authorisation (EUA) process for CRISPR-based SARS-CoV-2 diagnostics was also facilitated by the COVID-19 pandemic. The first FDA authorizations of a CRISPR-based diagnostic came from Mammoth Biosciences and SHERLOCK Biosciences shortly after these CRISPR-based detection technologies were published, underscoring the future potential of CRISPR-based diagnostics for becoming a standard selection of molecular assays for viral diagnosis [98].The field of viral infection is the one where CRISPR-based diagnostic methods have received the greatest attention [99]. The CRISPR/Cas12a and Cas13a families have inspired the development of several research techniques called DETECTR and SHERLOCK, respectively (Figure 3) [100]. In a three-step procedure, DETECTR employs the Type V Cas12a enzyme to connect directly to DNA targets [101]. Usually, a guide RNA drives the Cas12a enzyme to a highly sensitive and specific genome’s double-stranded DNA sequence [73]. Once coupled to its viral genetic target, the Cas12a enzyme indiscriminately cleaves a single-stranded DNA molecule connected to a quencher molecule and a reporter fluorescence [100]. This “collateral” cleavage is recognized by the release of a fluorescent signal from the fluorophore and quencher [73]. The DETECTR method’s main benefit is its great sensitivity, which allows it to identify a single viral particle molecule inside a microliter of the sample [100]. The Type VI Cas13a enzyme is used in the SHERLOCK method to bind and cleave RNA indiscriminately using targets that are crRNAs. When certain sequences are present, target RNA is bound by a target-specific molecule with an attached fluorophore, which then cleaves it collaterally, producing a fluorescence signal that can be recognized and studied to determine the presence of viral nucleic acid [102]. Since its inception, For use in recognizing and diagnosing viruses, SHERLOCK has undergone significant research [75]. Researchers have further improved the approach, creating a more straightforward and focused SHERLOCKv2 protocol [75]. The additional CRISPR-associated Csm6 enzyme was paired with Cas13 enzymes, which more than tripled sensitivity [75]. In both laboratory and clinical settings, viruses can be identified using the DETECTR and SHERLOCK procedures (Figure 3). Although it can be used to diagnose any virus, the DETECTR technique has been widely used to diagnose HPV [102]. Recombinase polymerase amplification (RPA) can enhance highly contagious component multiplication and detection when combined with the SHERLOCK and DETECTR methods. [102]. Additionally, the “SHERLOCK” methodology can be improved for the analysis of HIV, a viral disease that is still a major problem for the entire world [100]. According to HUDSON protocol researchers, universal-flavivirus RPA and crRNAs unique to a particular viral species can both be used to pinpoint conserved sections in these viruses’ genetic material [103]. Although any virus can be detected using SHERLOCK and HUDSON protocols, earlier research concentrated on the detection of flaviviruses such as Dengue, Zika, West Nile, and yellow fever viruses [88,89]. How CRISPR techniques can be used to diagnose the new coronavirus (SARS-CoV-2), an emerging pathogen that has infected over 12.9 million individuals and killed over 500,000 people thus far [104], is of great acute interest to scientists at the moment [22]. The lengthy incubation period is also concerning, as a person with the virus may go up to two weeks without signs before exposure to the disease [105]. In the applications presented, the DETECTR approach has been employed to detect this virus and emphasises determining the occurrence of the N and E gene variations unique to SARS-CoV-2 [106]. If both genes are found, a positive result is produced, and the process has been refined to eliminate false positives brought on by related coronaviruses [93]. Several kits have been created by the CRISPR-associated nucleases Cas9, Cas12, or Cas13, including CASLFA, FELUDA, DETECTR, HOLMES, SHERLOCK, and others [107].