Section 3.4. Whole Viral Genome Sequencing (from DOI: 10.3390/v12020211)

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Article	Current Trends in Diagnostics of Viral Infections of Unknown Etiology (DOI: 10.3390/v12020211)
Sections in this Publication
Section	Section 1. Introduction (from DOI: 10.3390/v12020211)
Section	Section 2. Traditional Methods of Diagnosing Infections (from DOI: 10.3390/v12020211)
Section	Section 3. Studying Viral Pathogens with High Throughput Sequencing (HTS) (from DOI: 10.3390/v12020211)
Section	Section 3.1. Metagenomic Approach (from DOI: 10.3390/v12020211)
Section	Section 3.2. Problems of Metagenomic Approach (from DOI: 10.3390/v12020211)
Section	Section 3.3. Methods for Improving Sequencing Output (from DOI: 10.3390/v12020211)
Section	Section 3.3.1. Nucleic Acids Depletion (from DOI: 10.3390/v12020211)
Section	Section 3.3.2. Hybridization-Based Enrichment (from DOI: 10.3390/v12020211)
Section	Section 3.3.3. Target Amplification (from DOI: 10.3390/v12020211)
Section	Section 3.4. Whole Viral Genome Sequencing (from DOI: 10.3390/v12020211)
Section	Section 3.5. Methods of Sequencing Data Analysis (from DOI: 10.3390/v12020211)
Section	Section 4. Long Read Sequencing (from DOI: 10.3390/v12020211)
Section	Section 5. Obstacles to Overcome in the Nearest Future (from DOI: 10.3390/v12020211)
Section	Section 6. Conclusions (from DOI: 10.3390/v12020211)
Section	Author Contributions (from DOI: 10.3390/v12020211)
Section	Funding (from DOI: 10.3390/v12020211)
Section	Conflicts of Interest (from DOI: 10.3390/v12020211)
Section	References (from DOI: 10.3390/v12020211)
Named Entities in this Section

From publication: "Current Trends in Diagnostics of Viral Infections of Unknown Etiology" published as Viruses; 2020 Feb 14 ; 12 (2); DOI: https://doi.org/10.3390/v12020211

Section 3.4. Whole Viral Genome Sequencing

Once a pathogen is identified, whole genome sequencing can be engaged for further research into its genome. This could prove beneficial for the knowledge of its genetic patterns, drug resistance and possible targets for antiviral therapy.

Comparatively small genomes, like those of human immunodeficiency virus (HIV), influenza virus, hepatitis B virus (HBV) and hepatitis C virus (HCV), are frequently sequenced in research purposes, and attempts are being made to integrate this procedure into clinical practice. Until recently, detection of drug-resistant strains required sequencing of only certain parts of viral genome. Whole genome sequencing (WGS) was considered far too expensive for this purpose; however, we are obtaining more data on evolving mechanisms of drug resistance, including genetic mutations that define it, and with the cost of WGS steadily decreasing, the use of this method becomes justified.

Routine use of NGS for diagnostic purposes is expected to hold great advantages over existing techniques. For instance, the genotyping of Coronavirus virus, which has been drawing attention of epidemiologists worldwide, is already influencing decision-making in healthcare. Additionally, genomes of drug-resistant HIV strains are used to study the evolution of the virus and complex genotype/phenotype associations between the virus and the host.

At present, WGS remains costly, even for small viral genomes, compared to the price of target sequencing. Nevertheless, additional data produced using WGS might supplement our knowledge of genetic substrates for drug resistance and uncover complex intergenic associations at its core.