Dan Ross/Wellcome Sanger Institute

Human respiratory pathogens will be tracked in new initiative

Data generated will lead to better understanding of common pathogens, act as an early warning system for new viruses and support public health responses

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A new initiative to better understand respiratory viruses has been launched today by the Wellcome Sanger Institute. The new Respiratory Virus & Microbiome Initiative will lay the groundwork for large-scale genomic surveillance of respiratory viruses, building on the Institute’s genomics expertise and the experience gained sequencing millions of SARS-CoV-2 genomes during the pandemic1.

The initiative aims to develop the capability for routine genomic surveillance of respiratory viruses, including influenza virus, respiratory syncytial virus (RSV), adenovirus and rhinovirus. It will also monitor for emerging pathogens.

Led by researchers working in genomic surveillance of pathogens at the Wellcome Sanger Institute, the initiative will work closely with partners at the UK Health and Security Agency (UKHSA), other public health bodies and UK academic institutions.

The data generated by the initiative will lead to a better understanding of common pathogens present in the UK, act as an early warning system for new viruses, support public health responses, and enable research into the transmission and evolution of respiratory microorganisms. Better understanding of which pathogen strains are in circulation will help to generate new vaccines and ensure existing ones are likely to be protective.

The Respiratory Virus & Microbiome Initiative (RVI) team will initially establish combined genome sequencing of SARS-CoV-2, influenza, respiratory syncytial virus (RSV) and other common respiratory viruses in a single test. However, the ultimate goal is to determine all of the genes and all of the species – including viral, bacterial and fungal species – present in a single nose swab sample, using a metagenomic approach2.

These techniques will be developed using residual material from diagnostic swab samples. The results will give a baseline of respiratory virus dynamics in the UK, and will generate an extensive viral genome dataset that will be made publicly available.

“Genomic sequencing offers incredible opportunity to track viruses globally. It can give researchers and policy-makers a finger on the pulse of where and how they are circulating. This is vital information for preparing healthcare and research systems. This Wellcome Sanger Institute initiative is a really important step in building monitoring systems in the UK, and could help track outbreaks of viruses such as influenza and RSV. This approach is an example of how science can be used to detect rising levels of infectious diseases and identify it’s sources and drivers. It could also become a blueprint to strengthen virus tracking in other countries. Preventing future pandemics depends on countries around the world working together to ensure early intervention on infectious disease rise and spread.”

Gordon Dougan Director of Infectious Disease, Wellcome

The team will also develop the methodology required to enable a routine surveillance programme for respiratory pathogens, with the capability to provide actionable data to inform public health decisions. This will initially be for the UK, with a view to making the methodology available for use elsewhere.

Alongside genomic surveillance, researchers at the Sanger Institute and collaborators will study the data to better understand the transmission and evolution of respiratory viruses, as well as seeking to identify new viruses and potential pandemic threats.

“This initiative is an exciting development in expanding the UK pathogen genomics capability that has been so vital to our health protection activity in recent years. Genomic sequencing has been crucial in the response to the COVID-19 pandemic and will continue to be pivotal in global efforts to address all kinds of threats to health in the future. We look forward to working closely with the Wellcome Sanger Institute in the future as we develop our understanding of the transmission and evolution of respiratory viral pathogens and build upon existing genomic surveillance capacity in the UK and around the world.”

Professor Susan Hopkins Chief Medical Advisor, UK Health and Security Agency (UKHSA)

Scientists will also undertake work into the dynamics of the respiratory microbiome: all the organisms that reside in our nose, throat and lungs. The team will study how the microbiome changes during infection and how this relates to illness severity. The metagenomic data generated will enable researchers to track antimicrobial resistance, for example in methicillin-resistant Staphylococcus aureus (MRSA).

The data, protocols and methods generated by this project will be made freely and publicly available. Over time, the aim is to scale up and adapt the platforms, technologies and methodology developed by the initiative so they can be used globally for pathogen genomic surveillance programmes.

“The Respiratory Virus & Microbiome Initiative is an exciting opportunity to build on the technology and methodology that has been developed for genomic surveillance of SARS-CoV-2 during the pandemic. We aim to help answer some of the most pressing public health questions, while at the same time addressing some of the gaps in our basic knowledge about respiratory infection and health. Ultimately, we hope to contribute to global efforts to further establish pathogen genomics for routine public health and research, and as part of pandemic preparedness.”

Dr Ewan Harrison Head of the Respiratory Virus & Microbiome Initiative, Wellcome Sanger Institute

More information

1 This work builds on the Sanger Institute’s expertise in genomic surveillance, and extensive knowledge gained by undertaking large-scale, nationwide sequencing of SARS-CoV-2 during the pandemic as part of the COVID-19 Genomics UK (COG-UK) consortium. The Sanger Institute’s SARS-CoV-2 whole genome sequencing work continues in partnership with UKHSA.

2 Metagenomics is the study of the structure and function of genetic material gathered from all the organisms present in a single sample. One of its primary uses is to study communities of organisms, such as the human microbiome.


This project is funded by Wellcome.