3 Nov 2020

Software tool will help doctors identify and prevent hospital transmission of SARS-CoV-2

University of Cambridge Press Release

Software tool will help doctors identify and prevent hospital transmission of SARS-CoV-2

A new software tool developed in Cambridge will help doctors identify where cases of COVID-19 were caused by transmission within a hospital, helping them to prevent further spread of the disease

The new software package, A2B-Covid, has been designed by a team of doctors and scientists at Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, NIHR Cambridge Biomedical Research Campus, and the MRC Biostatistics Unit at the University of Cambridge.

Addenbrooke’s cares for coronavirus patients from Cambridge and across the East of England. As the virus is highly infectious, an important part of care is preventing the spread of the virus within the hospital grounds.  However, with patients coming in and out of the hospital every day it can be hard to tell whether new infections come from the local community or from transmission in the hospital itself.

The software combines knowledge about infection dynamics, data describing the movements of individuals, and genome sequence data to assess whether or not coronavirus has been transmitted between people in the hospital environment. As the virus replicates and spreads, small changes occur in the viral genome.  Genome sequencing – reading the genomes of a sample of viruses taken from a patient – helps researchers to work out whether cases are linked.  Other factors, such as the difference in time between people reporting symptoms, also inform the analysis. Knowing where different people stayed or worked in the hospital gives an idea of who was in the same place at the same time so as to potentially transmit the virus.

COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.