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Currently accepted at: JMIR Public Health and Surveillance

Date Submitted: Mar 7, 2020
Open Peer Review Period: Mar 7, 2020 - Mar 18, 2020
Date Accepted: Mar 24, 2020
(closed for review but you can still tweet)

This paper has been accepted and is currently in production.

It will appear shortly on 10.2196/18606

The final accepted version (not copyedited yet) is in this tab.

Emergence of a Novel Coronavirus (COVID-19): A Protocol for Extending Surveillance Used by the Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) and Public Health England (PHE)

  • Simon de Lusignan; 
  • Jamie Lopez Bernal; 
  • Maria Zambon; 
  • Oluwafunmi Akinyemi; 
  • Gayatri Amirthalingam; 
  • Nick Andrews; 
  • Ray Borrow; 
  • Rachel Byford; 
  • André Charlett; 
  • Gavin Dabrera; 
  • Joanna Ellis; 
  • Alex Elliot; 
  • Michael Feher; 
  • Filipa Ferreira; 
  • Else Krajenbrink; 
  • Jonathan Leach; 
  • Ezra Linley; 
  • Harshana Liyanage; 
  • Cecilia Okusi; 
  • Mary Ramsay; 
  • Gillian Smith; 
  • Julian Sherlock; 
  • Nicholas Thomas; 
  • Manasa Tripathy; 
  • John Williams; 
  • Gary Howsam; 
  • Mark Joy; 
  • Richard Hobbs; 



The Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) and Public Health England (PHE) have successfully worked together on surveillance of influenza and other infectious diseases for over 50 years, including three previous pandemics. With the emergence of the international outbreak of Coronavirus infection (COVID-19), a UK national approach to containment has been established to test people suspected of exposure to COVID-19. At the same time and separately, the RCGP RSC surveillance has been extended to monitor the temporal and geographical distribution of COVID-19 infection in the community as well as assess the effectiveness of the containment strategy.


Surveillance of COVID-19 in both the well population and also ambulatory cases with respiratory infections, to ascertain both rate and pattern of COVID-19 spread, and to assess the effectiveness of the containment policy.


The RCGP RSC, a network of over 500 general practices in England extract pseudonymised data weekly. This extended surveillance comprises of five components: 1. Recording in medical record of anyone suspected to have or exposed to COVID-19. Computerised Medical Records (CMR) suppliers have within a week of request created new codes to support this. 2. Extension of current virological surveillance and testing people with influenza like–illness or lower respiratory tract infections. With the caveat, that people suspected to have, or who have been exposed to COVID-19 should be referred to the national containment pathway and not seen in primary care. 3. Serology sample collection across all age groups. This will be an extra blood sample taken from people who are attending their general practice for a scheduled blood test. The 100 general practices currently undertaking annual influenza virology surveillance will be involved in the extended virological and serological surveillance. 4. Collecting convalescent serum samples. 5. Data curation We have the opportunity to escalate the data extraction to twice weekly if needed. Swabs and sera will be analysed in PHE reference laboratories.


General Practice (GP) clinical system providers have introduced an emergency new set of clinical codes to support COVID-19 surveillance. Additionally, practices participating in current virology surveillance are now taking samples for COVID-19 surveillance from low risk patients presenting with lower respiratory tract infection (LRTI). Within the first two weeks of set up of this surveillance, we have identified 3 cases; one through the new coding system, the other two through the extended virology sampling.


We have rapidly converted the established national RCGP RSC influenza surveillance system into one that can test the effectiveness of the COVID-19 containment policy. The extended surveillance has already seen the use of new codes with 3 cases reported. Rapid sharing of this protocol should enable scientific critique and shared learning.


Please cite as:

de Lusignan S, Lopez Bernal J, Zambon M, Akinyemi O, Amirthalingam G, Andrews N, Borrow R, Byford R, Charlett A, Dabrera G, Ellis J, Elliot A, Feher M, Ferreira F, Krajenbrink E, Leach J, Linley E, Liyanage H, Okusi C, Ramsay M, Smith G, Sherlock J, Thomas N, Tripathy M, Williams J, Howsam G, Joy M, Hobbs R

Emergence of a Novel Coronavirus (COVID-19): A Protocol for Extending Surveillance Used by the Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) and Public Health England (PHE)

DOI: 10.2196/18606


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