Viewpoints from for Viral Genome Sequencing in Clinical and Biological

Field

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Thanks to Whole-genome sequencing technologies, genome sequencing has become a Commented [A1]: 首行不需要缩进
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
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sequencing , this technique provides important insights into virus transmission, evolution and
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pathogenesis.
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What is a viral genome?
Viral genome means gene or generic material of virus, it may be DNA or RNA furthermore Formatted: Font: Bold

that RNA can directly give to protein or it first goes to DNA and then make RNA. The interesting Formatted: Font: Bold
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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?—field? —Taking HIV as Formatted: Font: Bold
an example Formatted: Font: Bold
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? Commented [A3]: 小标题都粗体
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.