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Using rapid viral sequencing to understand COVID-19 transmission in hospitals

Rapid viral sequencing information was provided to infection, prevention and control teams in hospitals to discover whether this would allow them to implement control measures more accurately and faster to reduce spread of COVID.

Joint working across the eight organisations that make up our Academic Health Science Centre has been central to delivering a more effective response to the challenges of the pandemic. Here we show how collaboration among our member organisations, building on relationships and networks fostered by the AHSC, has enabled the rapid translation of health research into practice as part of the COVID response.


In the early stages of the COVID-19 pandemic in the UK , large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing COVID-19, was underway to provide understanding of viral transmission and evolution. This provided evidence that a high percentage of inpatients with COVID-19 had acquired their infection in hospital.

There was an opportunity to use rapid whole-genome sequencing to identify linked and unlinked infections quickly to inform infection prevention control practices.

A rapid response

In September 2020, as part of the Urgent Public Health supported COVID-19 Genomics UK Consortium (COG-UK) Hospital Onset COVID-19 Infection (HOCI) study, rapid viral sequencing information was provided to infection, prevention and control (IPC) teams in hospitals to discover whether this would allow them to implement control measures more accurately and faster to reduce spread. This work was conducted across 14 hospitals across the UK served by 11 sequencing hubs.

Standard-of-care IPC was compared with IPC augmented by rapidly generated viral sequence data to identify patients with known linkage of their SARS-CoV-2 sequences, indicating possible transmission originating in a hospital. Two main outcomes were measured: whether the availability of rapidly delivered SARS-CoV-2 sequence to IPC teams a) reduced the numbers of healthcare-acquired infection and b) reduced the size of outbreaks when they did occur. 

More than 2,000 patients with possible healthcare-acquired infection were included in the study. To help teams interpret the sequence data, a sequence reporting tool was developed, producing a simple one-page report identifying the likelihood that the patient’s SARS-CoV-2 was acquired in hospital (high/medium/low) and providing a list of case numbers of patients with potentially linked infections.

A sub-study analysed viral sequences collected over an eight-week period during which the Alpha variant swept through the UK. In contrast to data from community studies, the sub-study found no increased mortality or evidence of disease severity among more than 1,117 inpatients with Alpha compared with 1,234 cases of the previous B.1 variant.

Using study findings to inform pandemic planning

The final analyses of this study will be reported in summer 2021. These will include the main outcomes as well as qualitative analyses of the acceptability of sequencing for IPC and the steps that would be needed for sequencing to be introduced for routine use in NHS hospitals. A health economic study will provide the cost benefits of sequencing. 

The results from this study will be critical to planning what is needed to harness genomic data linked to patient data for controlling hospital outbreaks and managing individual patients. They will also inform what is needed for trusts to use sequence data to manage infection control. 

All of the sequencing carried out in this study was run by the Pathogens Genomics Unit (PGU) at UCL. The PGU is jointly funded by both UCLH and GOSH Biomedical Research Centres (BRCs). Having the structures and governance already in place allowed the work on COVID to begin immediately, providing significant support to clinical activities at UCLH and GOSH. Furthermore, the PGU provided support to the Royal Free and Barts Hospital as well as others around London. The relationships and networks supported and fostered by the AHSC were essential to enable these working relationships at a time of crisis. 

Impact Report 2020/21

Our impact report 2020/21 shares how we have worked in collaboration with those across our partnership to accelerate research and innovation into practice during the COVID-19 pandemic.

Read the report