Leveraging the Power of Genomics To Detect and Track SARS-CoV-2 Variants – Technology Networks

Monitoring changes in the viral genome is continuing to play a crucial role in shaping the response to the COVID-19 pandemic.The COVID-19 pandemic has caused over 4.5 million deaths worldwide, with more than 200 million people having been infected with the novel coronavirus, SARS-CoV-2. Since the virus first emerged in China in December 2019, the analysis of genetic sequencing data from millions of positive samples has revealed how the virus has evolved.Changes in the SARS-CoV-2 genome occur at a rate of around one or two mutations per month, says Dr. Alessandro Carabelli, Research Associate at COG-UK, University of Cambridge, UK.Most mutations have little or no effect on the biology of SARS-CoV-2 and persist in the descendants of that virus providing useful tags for tracking its spread.By understanding viral transmission pathways within a certain setting, such as a workplace or prison, this can help inform decisions on what actions are needed to contain an outbreak, says Patricia Brennan, director of Science Product Management at Chan Zuckerberg Initiative, San Francisco, USA.But some mutations can alter the biological behavior of SARS-CoV-2, such as improved transmissibility or ability to evade the immune system. Detecting and tracking the emergence of these changes is vital as they may threaten the performance of vaccines, therapies, diagnostic tools or other public health and social measures.

While coronaviruses, like SARS-CoV-2, have evolved some proofreading mechanisms to maintain their genomes, random errors can still occur.

As mutations accumulate, this leads to numerous differences in the virus population over time, explains Carabelli.But some mutations can change the behavior of the virus and these will persist if they confer an advantage, such as altering its ability to cause disease or transmit from one person to another. Changes that occur in the gene encoding the spike protein are of particular interest, as it is involved in the virus entering human cells and is the target for most COVID-19 vaccines.A concern is that mutations may arise that lead to lower vaccine efficacy, says Carabelli. The most numerically important mutation to date is the spike protein variant D614G, which was not present when the virus first emerged but is now almost ubiquitous.Accurate SARS-CoV-2 Surveillance With Resilience to Genomic Variation

As a result of persistent transmission, there are now several mutational variants of SARS-CoV-2. These variants have emerged and rapidly changed the viral dynamics, thus threatening ongoing public health efforts to limit the transmission of SARS-CoV-2. Download this app note to discover a surveillance assay that will remain effective as new variants emerge while offering high sensitivity and capture efficiency.

New variants will continue to emerge, and it is important we understand the phenotypes of emerging variants in terms of infectivity, transmissibility and antigenicity as soon as possible, says Carabelli.

Tracking mutations in the virus is an essential surveillance partner to vaccine roll-out and it likely to be needed for as long as the vaccine is required, states Carabelli.

COVID-19 vaccines might have to be periodically updated to reflect any changes in the virus.Whats great about many of the latest technologies used to develop COVID-19 vaccines such as mRNA vaccines is that they can be updated quickly to target those emerging variants, says Ayscue.Where Do We Go From Here: A Reflection of COVID-19

In less than two years, much has been discovered about SARS-CoV-2 and its variants, and to date several vaccines have been created. Capitalizing on several decades of progress on new vaccine technologies, viral immunology, structural biology and protein engineering research, along with clinical trial operations, seven vaccines have undergone the process of rapid development, evaluation, manufacturing and deployment. Download this app note to explore various solutions designed to improve COVID-19 detection and the development of vaccines and therapeutics.

Genomic data is great for understanding transmission pathways it can tease out whether a cluster of infections is associated with people getting infected within that setting or bringing it in from outside, explains Ayscue. Its essentially giving you breadcrumbs to follow those mutations and work out where viral transmission is happening providing the evidence to inform what measures are needed to disrupt it.

But the COVID-19 pandemic has exposed huge disparities in the current capacity of public health systems to perform genomic surveillance of circulating pathogens both at a national and international level.

Public health systems are extremely fragmented in many countries, including the US, says Brennan. This means that the frontline work is often being done by people who dont have the necessary skills and infrastructure to carry out these analyses.The development of an open-source free software tool, called Aspen, is one step towards democratizing the technology enabling individual public health laboratories to conduct genomic analyses and interpret the data independently.People can load their data and do the analysis so they can see where the mutations have occurred, says Brennan. They can look at those in terms of the population they came from and work out where they need to take action.

Genomic surveillance and the use of pathogen genomes on this scale to track the spread of the virus, study local outbreaks and inform public health policy signifies a new age in virus genomic investigations, says Carabelli.

The global community will need to work together to put the necessary infrastructure in place to be ready for future pandemics.

If COVID-19 has taught us anything, its that borders and boundaries dont exist as long as people are moving around, says Brennan. We need to get the tools that researchers have developed to places where they can be applied and used more readily as a society, I hope we can tend to that more diligently than we have in the last many decades.

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Leveraging the Power of Genomics To Detect and Track SARS-CoV-2 Variants - Technology Networks