The U.K.’s Wellcome Sanger Institute has been tracking the genome of the SARS-CoV-2 virus since the start of the pandemic, charting its millions of mutations using samples from patients across the country as variants rise and fall. Now, the research institution hopes to do the same for other respiratory pathogens—and is developing a test that can detect more than one virus in a single patient sample.
“Genomic sequencing offers incredible opportunity to track viruses globally. It can give researchers and policymakers a finger on the pulse of where and how they are circulating,” Gordon Dougan, Ph.D., director of infectious disease at Wellcome, said in a release. “This is vital information for preparing healthcare and research systems.”
The goal of the new program, called the Respiratory Virus and Microbiome Initiative, is to set up the infrastructure to analyze the genomes of influenza, respiratory syncytial virus (RSV) and others from patient samples on a massive scale, which will also enable the institute to monitor for emerging pathogens.
The researchers are particularly interested in co-infections between viruses and other microbes. Co-infection with other pathogens is common in severe respiratory disease, and COVID-19 was no different: Hospitals in India, for example, were reportedly overrun with dual infections of SARS-CoV-2 and the deadly mucormycosis or "black fungus" during the country’s delta wave.
To track multiple microbes in a single sample, the researchers will need to leverage metagenomics, or the study of all the organisms present in a single sample from the clinic or the environment. They will specifically use shotgun metagenomic sequencing, a technique that sequences the genome of every pathogen in a sample and compares it to reference genomes for identification. This contrasts with the sequencing tools in common use, which sequence only one genome at a time to detect the presence of an individual microbe.
A timeline for the technology’s development has not been released, though Ewan Harrison, Ph.D., head of the initiative, told The Guardian that some iteration of it could be available by fall. The first version will combine the ability to sequence SARS-CoV-2, influenza, RSV and other common respiratory viruses from one swab. The scientists are using “residual material” from diagnostic swab samples to build the technology, and the results will give “a baseline of respiratory virus dynamics in the UK” along with a publicly available viral genome data set, according to the release.
The institute will collaborate with the government's UK Health Security Agency, nonprofit Health Data Research UK, the COVID-19 Genomics UK Consortium and the University of Cambridge on the initiative. It is being funded by Wellcome, a charitable trust based in London focused on biomedical research.