Sequencing and Tracking Of Phylogeny in Covid-19 study (STOP Covid-19) [COVID-19]
Research type
Research Study
Full title
Sequencing and Tracking Of Phylogeny in Covid-19 study (STOP Covid-19)
IRAS ID
282394
Contact name
Samuel Robson
Contact email
Sponsor organisation
Portsmouth Hospital NHS Trust
Duration of Study in the UK
2 years, 0 months, 1 days
Research summary
Research Summary
The current Covid-19 pandemic has had an unprecedented effect on our way of life. The UK is currently in a Government-mandated lock-down to enforce social isolation of individuals in order to quell the spread of a particularly virulent strain of a coronavirus (SARS-CoV-2) causing severe acute respiratory syndrome (SARS). Following shutdown of labs at the University of Portsmouth, we have redeployed our lab equipment and expertise in whole-genome sequencing data analysis in a strategic attempt to further understand the virus and help to track, predict and ultimately stop the spread of the virus throughout the globe. \n\nQueen Alexandra Hospital (QAH) in the Wessex region have recently begun to test patients for Covid-19, by extracting viral RNA from swab samples. We propose to use surplus extracts of these viral RNA samples to generate whole genome sequences for the virus from those that have tested positive. This will allow identification of distinct groups of the virus that have arisen as the pandemic has evolved, epidemiological tracing of the virus by linking with anonymous patient information, and near real-time monitoring of adaptations of the virus. \n\nAs the pandemic continues to grow, understanding the evolution of the virus and its spread across the globe will help researchers to (1) predict the future spread of the virus (2) estimate the number of worldwide cases, and (3) aid in the development of epidemiological models for estimating a potential end point to the pandemic crisis. In addition, the ability to track mutations in real time allows researchers access to a large body of data to explore in order to identify potential targets for cures and vaccines. We will work with the Covid-19 Genomics UK Consortium and other groups across the globe, with whom we will collaborate in order to contribute at a national and international level. [Study relying on COPI notice]
Summary of Results
Throughout the COVID-19 pandemic, whole genome sequencing of SARS-CoV-2 virus samples collected from patients with COVID-19 was used to help to understand how the virus spread. As the virus passes from person to person, small errors can occur during replication (both at random and due to evolutionary selective pressures), resulting in small mutations. Mutations occur infrequently, and can be used as a kind of fingerprint to identify cases that are part of a shared infection chain, since cases with identical genome sequences, or with fewer mutations than expected by chance, are likely to be linked.
Researchers at the University of Portsmouth began working with Portsmouth Hospitals University NHS Trust early on in the pandemic, in order to use this approach of ‘genomic epidemiology’ to help understand outbreaks throughout the hospital. In addition, this project became a major part of the COG-UK program, providing whole genome sequencing to NHS Trusts across the south coast of the UK.
These data helped to understand the transmission of the virus locally, nationally, and globally, as well as allowing for the identification of novel variants of concern, such as Alpha, Delta and Omicron. Data from the COG-UK consortium greatly impacted the global understanding of the virus, and allowed for rapid development of vaccines against the virus.
As well as impacting more generally on the national level, this project aimed to help understand the virus at the local level. We used whole genome sequencing of viral samples collected for COVID-19 testing to disentangle complex hospital infection clusters and influence local infection prevention and control procedures, and internal hospital policies on testing, isolation of patients, PPE use, etc. We found that the Alpha variant, which resulted in rapid spread and increased prevalence in the community, also resulted in outbreaks of all non-Alpha variants circulating in the hospital at the time, due to pressure on the NHS service. Such hospital-acquired infections were enriched amongst older and more vulnerable patients more likely to be in hospital for longer periods, but had no impact on disease severity. Study of healthcare workers over this time period also identified a significant role for the vaccine in reducing infection rates, with around 4-time fewer vaccinated staff showing infections than non-vaccinated staff.
REC name
North West - Haydock Research Ethics Committee
REC reference
20/NW/0217
Date of REC Opinion
15 Apr 2020
REC opinion
Favourable Opinion