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.

“Doctors collect lots of information to identify cases of transmission. The dates on which people got sick, and where they were in the hospital, are all useful information. In addition, new advances in genomics mean that doctors can read the genome sequence of a virus cheaply and easily. More similar sequences suggest that two cases are more likely to be linked. Our program combines all of the data in one to identify cases of possible transmission.”

Dr Chris Illingworth from the MRC Biostatistics Unit at the University of Cambridge, one of the developers of the code

Flagging up possible cases of transmission is a first step in taking action. Looking at the details of a case, doctors can make a judgement about whether transmission has happened, and if so, how that took place. Early identification can prevent the spread of coronavirus through a ward. Where transmission has happened, lessons can be learnt, taking steps to make the hospital a safer place for patients and healthcare workers alike.

A2B-Covid will be available for free to doctors and clinicians across the UK and worldwide. Details of the package have been published in a pre-print article in MedRxiv, prior to being peer-reviewed, at

“Infection control is a vital part of keeping people safe and well in hospital. In a busy hospital environment this tool will make it simpler and easier to identify cases of concern, so as to minimise incidence of hospital-based viral transmission.”

Dr Will Hamilton, an infectious diseases clinician at Addenbrooke’s and author of the study

The project has been funded by the COVID-19 Genomics UK Consortium, a Cambridge-led nationwide initiative to deliver large-scale, rapid sequencing of the cause of the disease and share intelligence with hospitals, regional NHS centres and the Government. It is an example of the increasing use of genomic technologies in a clinical setting.

“This work is a great example of how genome sequence data, rapidly collected and made available to clinicians, can make a real difference to clinical practice and patient safety. From the nurses who collected samples, through to the sequencing team, medics and statisticians, this has been a case of experts across multiple disciplines coming together to combat COVID-19.”

Dr Estee Torok, from the Department of Medicine at the University of Cambridge and senior author of the paper