Table 1.

Current approaches for virus detection and characterization.

The target of detection and application		Methods	Advantages	Limitations
Viral proteins and nucleic acids detection	Rapid known virus detection with known invariable portions of the genome	Amplification-based [1]	Fast, cheap, highly sensitive detection	Detection of the presence/absence of a viral nucleic acid; false-positive results, difficulty detecting viruses with highly variable genomes; detection of only known viruses, requires knowledge of the nucleotide sequence; inability to differentiate between infectious and noninfectious viruses
		Methods related to CRISPR/Cas use [2,3]	Can be used in the field, relatively short time to obtain results, high sensitivity	Detection of the presence/absence of a viral nucleic acid; detection of only known viruses, requires knowledge of the nucleotide sequence
		Southern/northern hybridization	Sensitive detection. Many types of specimens can be used (Blood, cerebrospinal fluid, urine, bronchoalveolar lavage, etc.)	Requires knowledge of the virus nucleotide sequence
	Searching for new viruses	NGS [4]	Determination of the nucleotide sequence of viruses	Difficulty of identifying RNA viruses in patient samples due to additional stages of sample preparation and, as a consequence, a decrease in the viral RNA to host RNA ratio. Difficulties in data processing
	Rapid detection of known viruses with known viral proteins	Immunoassays [5] (direct determination of viral proteins and indirect determination of IgG and IgM)	For proteins, the ability to detect previous exposure.	Likelihood of false-positive results; possible cross-reactivity with closely related viruses
Detection of viable viral particles	Extraction and study of live viral particles	Cell-based approach with CPE detection [6]	Determination of live virus particles in clinical material, studying their pathogenicity and transmission mechanisms. Detection of viruses with a highly variable genome that cannot be determined by PCR methods.	The main problem is the long time period (up to several weeks) required for a result to be available. Cell cultures are also very susceptible to bacterial contamination and toxic substances in the clinical virus specimen. Additionally, many viruses will not grow in cell culture (Epstein-Barr virus, hepatitis B, hepatitis C, parvovirus, etc.)
		Cell-based reporter [7,8]		It is necessary to develop different approaches to study specific viruses. Suitable for viruses with annotated genomes.