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Why viral genome sequencing is important

Article highlighting the applications of sequencing to investigate viruses
Illustrative image of a blue DNA molecule on a white background with sequences of letters A, C, T, G representing a DNA sequence
© COG-Train

Viruses are the most abundant biological entities on Earth, and they significantly impact living organisms by causing diseases and shaping their immune systems. The study of viral infectious diseases in terms of etiopathogenesis and the development of new therapeutics is undergoing rapid changes.

The year 2020 was a turning point in history and in global health. The COVID-19 pandemic, as well as being an enormous human tragedy costing millions of lives, has opened great scientific opportunities and capitalised on them. A technological revolution, building over the past decade, has enabled new ways to respond to a pandemic: genomic sequencing of pathogens and rapid development of vaccines. The genome sequencing of SARS-CoV-2 has been established as a powerful supplementary tool to diagnostics.

A genome – an organism’s genetic material – is essentially its instruction manual, which contains all the information needed to make and maintain it. Coronaviruses are RNA viruses, and therefore have a single RNA strand that is 30,000 letters long. These letters can be ‘read’ one by one, using a technique called sequencing. Although certain technologies now allow for the direct sequencing of RNA, most require the generation of cDNA first, before the code can be read. Virus genomes constantly alter (mutate), changing a few letters at a time as they divide and spread by infecting more people. These changes can be exploited to track the spread of the virus by sequencing, recording and analysing genomes.

We all have heard about COVID-19 sequencing in many ways and through many sources. Most people know that COVID-19 genome sequencing is ongoing in their countries. In this article, we will focus on why genome sequencing of SARS-CoV-2 is important.

Why is viral genome sequencing important?

These sequences have valuable information that scientists use to:

1) Characterise the genome of the virus.
2) Estimate a particular variant’s prevalence in a population.
3) Evaluate how effective medical treatments, such as monoclonal antibodies, are against variants.
4) Investigate the spread of a virus in outbreaks.
5) Genome sequences play a critical role in our understanding of viral evolution, disease epidemiology, surveillance, diagnosis, and countermeasure development. They, therefore, represent valuable resources which must be properly documented and curated to ensure future utility.

WGS informs mitigation strategies

Whole-genome sequencing provides the most high-resolution data and allows for the efficient relatedness analysis that is instrumental to outbreak investigations at all levels, ranging from within a small community to intercontinental spread during a pandemic. Investigators have been able to determine relatedness between different SARS-CoV-2 virus sequences from various patients, concluding that pre-symptomatic patients most likely contributed to transmission. This information also helps us to understand how a pathogen spreads in a certain geographical area, for example between countries or across continents.

Tweaking COVID-19 diagnostics and developing therapeutics with WGS data

SARS-CoV-2 sequence data allow scientists to develop new targets for molecular assays and track the trends of mutations that may lead to reduced sensitivity of existing assays. The availability of SARS-CoV-2 sequence data allows researchers to identify potential therapeutic targets and provides a basis for epitope mapping and modelling, along with the prediction of immune response to the virus, all of which could help guide therapeutics and vaccine development.

WGS Uncovers Fundamental Virus Biology:

In order to understand the pathogenesis and immune response in COVID-19, scientists may analyse SARS-CoV-2 genome sequence data in an effort to explain the mechanism behind their observations.

SARS-CoV-2 genome sequencing may also help in the diagnosis of COVID-19 when the nature of infection is unique or complicated. This is well-demonstrated by the use of WGS to determine whether individuals who got sick twice within a short period of time had relapsed or been reinfected with a different strain of SARS-CoV-2. Evidence suggesting that reinfection is possible has been reported in several countries including Hong Kong, the United States, India and the Netherlands.

In summary, WGS data for SARS-CoV-2 are invaluable to our disease control and prevention efforts. As we learn more about the biology and transmission dynamics of the virus, we come closer to finding sustainable and effective strategies to put a stop to this pandemic.

References

How does virus genome sequencing help the response to COVID-19?

What is Genomic Surveillance?

Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health

How COVID-19 transformed genomics and changed the handling of disease outbreaks forever

Have you performed viral whole genome sequencing? What other organisms have you sequenced? Share with us in the comments.

© COG-Train
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A Practical Guide for SARS-CoV-2 Whole Genome Sequencing

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