Routine genome sequencing of infectious respiratory viruses for better treatment and vaccines

Genome sequencing of organisms has been in practice for half a century. Bacteriophage MS2 was the first virus to be sequenced entirely by 1976. Even though viral genome sequencing has become more convenient since then, it was only during the COVID-19 pandemic that routine sequencing of viral samples was conducted. Sequencing of thousands of samples revealed that the SARS-CoV-2 virus was evolving at a fast rate, and subsequently, omicron variants were detected. Based on the sequencing data, researchers predicted that the variant had the potential to cause severe cases around the globe. This further helped the government and decision-makers to plan and warn the public about the pandemic.

Routine sequencing of complete viral genomes can reveal their evolutionary patterns. It can help to plan effective treatments, develop better vaccines, and predict new outbreaks. Realizing the utility of viral sequencing, a team led by Ewan Harrison at the Wellcome Sanger Institute in Cambridge, UK, plans to conduct routine DNA sequencing of virus samples from people with severe respiratory infections such as flu and Respiratory Syncytial Virus (RSV).

The team, called the Respiratory Virus and Microbiome Initiative, will begin trials on stored COVID-19 test swabs and sequence all the genetic materials, including virus, bacteria, and fungi, present in the samples. This approach is called metagenomics and will allow the researchers to study the complete microbiome of the respiratory tract of infected persons. The team plans to optimize the test using stored swabs to make it cheaper, faster, and more convenient. After that, in collaboration with the UK Health Security Agency, they plan to run more extensive sequencing of fresh swabs from affected respiratory patients by 2024.

Genome sequencing of the entire viral genome will help to characterize the virus and provide knowledge about its constituent proteins. Once the sequence data is available, doctors can optimize their treatments based on the detected variant. Similarly, vaccine development can be more targeted to provide adequate protection against several variants.

While no such plans are apparent elsewhere in the world, the team hopes similar approaches will be adopted by other countries and wish to make all their data freely available. An integrated global effort will help in curbing COVID-19-like pandemics in the future and prevent severe outbreaks.


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