17 Nov 2020

The COG-UK Project Hospital-Onset COVID-19 Infections (HOCI) Study


The COG-UK Project Hospital-Onset COVID-19 Infections (HOCI) Study

The COG-UK HOCI study is investigating how integrating rapid, real-time COVID-19 genomic sequencing can impact decision-making by infection control teams to prevent the spread of the SARS-CoV-2 virus in NHS hospitals.

What is the COG-UK HOCI study?

Hospitals have been shown to play a major role in the spread of SARS-CoV-2. While rapid and repeated testing of patients and staff for the presence of the virus is key to identifying potential hospital outbreaks, it cannot tell us which infections are actually linked, and where to focus infection prevention and control (IPC) measures.

Sequencing of virus genomes to identify closely matched sequences has been repeatedly shown to better identify hospital outbreaks as compared to standard IPC measures alone (Ref 1Ref 2 and Ref 3). For SARS-CoV-2 in particular, COVID-19 Genomics UK (COG-UK) consortium researchers have shown that rapid genome sequencing enables the identification of sources of hospital outbreaks fast enough to inform changes in IPC practices and reduce further spread of the virus (Ref 4).

The COG-UK HOCI study aims to evaluate the benefits of rapid COVID-19 genomic sequencing on infection control in preventing the spread of the virus in UK NHS hospitals.

2,000 patients will be recruited to the study at approximately 15 NHS hospitals across the UK. The study is funded by COG-UK and benefits from the extensive network of existing sequencing partners across the UK. COG-UK HOCI is sponsored by University College London (UCL), with Professor Judith Breuer as Chief Investigator.


What are the aims of the research?

The study involves the delivery of a SARS-CoV-2 genomic sequencing data report to IPC teams, either within 5–10 days (‘standard’ sequencing time, typical at a national centralised laboratory) or within 24–48 hours (‘rapid’ local sequencing).

The goal of COG-UK HOCI is to determine the impact that integrating ‘rapid’ real-time genomic sequencing can have on decision-making by IPC teams in hospitals.

Determining whether the ‘rapid’ availability of SARS-CoV-2 sequence data (within 24–48 hours) reduces the rate of hospital-onset infections, compared with ‘standard’ availability of sequencing data (within 5–10 days) would have important implications for how genomic sequencing is used in healthcare settings.

Incidence rates of IPC-defined virus outbreaks will be compared to that of IPC-defined with sequence-supported hospital outbreaks. The health-economic benefit of both rapid and standard sequencing is also being investigated.


Where is the study taking place?

The COG-UK HOCI study is being conducted at the following NHS trial sites —Glasgow (Glasgow Royal Infirmary), Guys and St Thomas’ NHS Foundation Trust, Imperial Healthcare NHS trust, Liverpool Foundation Trust, Manchester Royal Infirmary, Newcastle (Freeman Hospital and Royal Victoria Infirmary), Nottingham (Queens Medical Centre), Royal Free Hospital, Sandwell General Hospital, Sheffield Teaching Hospitals NHS Foundation Trust, Southampton General Hospital, Barts Health NHS Trust (The Royal London Hospital), and University College London Hospitals (UCLH).

All hospitals are linked to a sequencing lab where the genomic sequencing takes place.


When does the study start/finish?

Phase 1 covers baseline data collection to understand current practice at the participating NHS hospitals and will last approximately one month.

Phases 2 and 3 are the interventional aspects to the study. Virus samples will be sequenced to provide SARS-CoV-2 genome data, either on a 24–48 hour turnaround or 5–10 day basis, and a summary report with probabilities of linkages within the hospital generated. The report will be returned to Infection Control/Prevention teams to help inform their practice. Approximately half the participating hospitals will be entering into the ‘standard’ speed of sequencing first, and the other half the ‘rapid’ phase first, prior to switching at the end of the initial intervention phase.

Phase 4 will only be completed if/where insufficient HOCI baseline data was collected during Phase 1. This may be due to very limited or no nosocomial (within hospital) transmission of the virus during Phase 1.

COG-UK will be reporting on the outcomes of the COG-UK HOCI study in summer 2021. It is anticipated that the study will be of critical importance for future integration of real-time pathogen genomic sequencing into the clinic.



  1. Roy S, Hartley J, Dunn H, Williams R, Williams CA, Breuer J. Whole-genome Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza A. Clin Infect Dis. 2019;69(10):1649-1656.
  2. Brown JR, Roy S, Shah D, et al. Norovirus Transmission Dynamics in a Pediatric Hospital Using Full Genome Sequences. Clin Infect Dis. 2019;68(2):222-228.
  3. Houldcroft CJ, Roy S, Morfopoulou S, et al. Use of Whole-Genome Sequencing of Adenovirus in Immunocompromised Pediatric Patients to Identify Nosocomial Transmission and Mixed-Genotype Infection. J Infect Dis. 2018;218(8):1261-1271.
  4. Meredith LW, Hamilton WL, Warne B, et al. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect Dis. 2020.


COVID-19 Genomics UK (COG-UK)

The current COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents a major threat to health. The COVID-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here:

COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. For more information, visit:

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.