A detailed look at the benefits of rapid SARS-CoV-2 genomic sequencing to inform infection control decisions

The COVID-19 pandemic has highlighted the need for large-scale genomic sequencing that can be delivered at a pace to inform public health and infection control decisions. We spoke to Dr Hayley Colton from the University of Sheffield, Department of Infection, Immunity and Cardiovascular Disease, about how she and her team set out to understand the barriers to rapid sequencing and its onward use for action and impact.

When the COVID-19 pandemic hit, research teams around the world worked tirelessly to set up genomic sequencing capabilities for the SARS-CoV-2 virus. Fast turnaround time of positive sample-to-viral sequence was a key goal, with the aim of increasing the likelihood that viral genome data could contribute towards pandemic control. Sequence information was used nationally to track the spread of variants of concern, as well as establishing their rate of transmissibility, and properties of disease severity and immune evasion. It was also an opportunity to use sequence data to better understand more localised viral spread in places such as in hospitals, and to explore whether this information could help infection prevention and control teams (IPC) in the management of virus spread to vulnerable hospitalised patients.

Evaluating the utility of genomics to track virus spread in hospitals was of major importance and the focus of the COG-UK Hospital-Onset COVID-19 Infection (HOCI) study. Specifically, this defined the potential benefits of rapid COVID-19 genomic sequencing in preventing spread of the virus in UK NHS hospitals. Hayley and her team ran a sub-analysis of this study, which focused on turnaround time at 14 COG-UK sequencing centres across the country. “The research aimed to identify any differences between the sequencing centres and the reasons for variability, which would inform potential solutions,” Hayley tells us.

To enrich the information, they gathered on timing of sequencing, the team also conducted in-depth structured interviews with staff at sequencing centres on their processes. This provided the team with detailed responses to some of the variability of the data and the reasons behind delays where these occurred.

In summary, Hayley and her team found that there was a notable uniformity in timing across all labs, starting from the point of collecting the sample through to the generation of the diagnostic PCR result. This was a surprise given the differences in size of labs and variation in the high number of samples being received. The main difference observed was the delay time between receipt of the diagnostic PCR result and when the sequencing report was generated. This led the research team to take a closer look at the underlying cause of the delays between these points, which they found related to the logistics of getting the positive sample to the sequencing centre.

This finding demonstrates the value of integrating sequencing facilities into the same labs where diagnostic testing is taking place or of ensuring short geographic distances between diagnostic and sequencing facilities. Hayley recognises that increased staff flexibility and ensuring available training for those working in the labs to optimise turnaround time in the future can be key to fighting future outbreaks in hospitals. “Although simple, these are practical and actionable steps that could help speed up future sequencing efforts, enhancing the tangible value of sequencing to IPC practice and other interventions,” says Hayley.

Hayley is passionate about driving collaboration and promoting sequencing for future pandemic preparedness.  “We hope that our research will inspire others and provide valuable learning around the barriers to rapid sequencing turnaround to those starting their career within sequencing or setting up a sequencing lab,” adds Hayley.

Hayley reiterates the importance of being able to upscale sequencing in the future. “Genomic sequencing is part of our technological future, and the COVID-19 pandemic was the catalyst to a rapid uptake of genomic sequencing worldwide,” concludes Hayley.

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