Viewpoints for Viral Genome Sequencing in Clinical and Biological Field

Posted by kiko on December 18th, 2018

Thanks to Whole-genome sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research, thus, we are experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data. Besides, whole-genome sequencing of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. Viral genome sequencing is significant for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral Whole-genome sequencing, this technique provides important insights into virus transmission, evolution and pathogenesis.  

What is a viral genome?

Viral genome means gene or generic material of virus, it may be DNA or RNA furthermore that RNA can directly give to protein or it first goes to DNA and then make RNA. The interesting fact of viral genome is that it contains information for only replication and synthesis of its cot protein. All other Information like that for polymerases and other protein is used of the host, so it is very small genome.

Why we sequence viruses’ Genome in the clinical field? —Taking HIV as an example

Viruses represent the greatest source of biological diversity on Earth. For small viruses such as human immunodeficiency virus (HIV), influenza virus, hepatitis B virus (HBV) and hepatitis C virus (HCV), sequencing of partial genomes has been widely used for research, but it also has important clinical applications. One of the main reasons and applications to sequence viruses is the detection of drug resistance. For example, the management of highly active antiretroviral therapy (HAART) for HIV relies on viral sequencing for the detection of drug resistance variants. HAART has dramatically improved survival of patients with HIV, but successful therapy requires long-term suppression of viral replication with antiretroviral drugs, which may be prevented by impaired host immunity, sub-optimal drug penetration in certain tissue compartments and incomplete adherence of patients to therapy. When viral replication continues despite treatment the high mutation rate of HIV enables resistance variants to develop.

Why do we need deep viral genome sequencing?

Modern methods, which make use of massively parallel sequencing, allow better examination of diversity and analysis of viral populations that contain nucleotide variants or haplotypes at low frequencies (less than 50% of the consensus sequence). Minority variant analysis is particularly powerful for RNA viruses, retro-transcribing DNA viruses and retroviruses, because they typically show high diversity, even in a single host. HIV is the classic example; the HIV reverse transcriptase is error-prone and introduces mutations at an extremely high rate (4.1 ± 1.7 × 10−3 per base per cell). Not one, but many closely related but subtly different viral variants, exist in a single patient. These variants are sometimes described as a quasispecies or a cloud of intra-host viral diversity. The presence of a mixed population of viruses introduces problems for determining the true consensus ‘majority’ sequence, but these minority (nonconsensus) variants may also change the clinical phenotype of the virus, and can predict changes in genotype, tropism or drug resistance.

Obstacles and challenges encountered

Except for some technical challenges of viral WGS we mentioned above, there are a number of other roadblocks which may slow the advance of viral genome sequencing in the clinical. They may be considered in three groups: ethical issues, including incidental host and microbiological findings; regulatory issues, such as the establishment of standards, good laboratory practice and sensitivity and specificity thresholds for sequencing; and analytical issues regarding data interpretation and the numerous choices of analysis options.

Conclusion on development of viral WGS

Viral genome sequencing is of growing clinical importance for diagnosis, disease management, molecular epidemiology and infection control. There are a number of methods available to achieve WGS of viruses from clinical samples, amplicon sequencing, target enrichment or metagenomics. Currently the choice of method is specific to both the virus and the clinical question.