Integrated Pathogens and Mobile Elements GeCIP Domain


The Integrated Pathogens and Mobile Elements GeCIP domain is split into three different sub-domains: endogenous retroviruses; Identification of pathogens; and COVID‐19 Susceptibility and Response. During the 2020 pandemic this third sub-domain was set up specifically to look at the genomic factors influencing COVID-19 infection. Any GeCIP members who intend to work with Genomics England on the COVID data Genomics England is gathering should register to join the Integrated Pathogens and Mobile Elements GeCIP Domain, using the form here.

To register as a participant in the Genomics England COVID-19 study, being conducted in partnership with GenOMICC, or to learn more about this please see our page on this here.

Endogenous Retroviruses

More than 10 years have passed since the first high quality, complete version of the human genome was published. The most-­studied part is the one that encodes for proteins (known as the exome) and accounts for 2‐3% of the total human genetic code. The rest of the genome is less understood.

Around half is composed of repetitive elements; one category of these, known as Endogenous Retroviruses (ERVs), is a remnant of ancient retroviral  infections of our ancient ancestors’ germ-cells, and make up around 5­‐8% of the human genome.

Our research explores potential health effects of human ERVs by combining bioinformatics and wet-lab approaches, with particular focus on trying to understand whether an association between particular ERV make up and incidence of disease can be found.

Identification of pathogens

Over 30 research groups at the Norwich Research Park carry out research on bacteria. This work, linked to the BBSRC-funded The Genome Analysis Centre (TGAC), is generating discoveries that have applications in the fields of human health, pharmaceuticals, agriculture, food processing and environmental monitoring. We will apply our combined expertise to the identification of human pathogens using whole genome DNA sequence (WGS) data. As part of the Pan-Cancer ICGC  (International  Cancer  Genome Consortium) Project, a bioinformatics analysis pipeline (SEPATH) has already been set up within TGAC to carry out this work, demonstrating proof of principle.

Covid‐19 Susceptibility and Response

Covid‐19 is a novel coronavirus strain with no vaccine and limited treatment options. Global attempts to prevent the virus overwhelming healthcare services centre on social distancing/ isolation, at considerable cost to global productivity and to the health and wellbeing of many. However, in most cases, infection by Covid‐19 produces only a mild response. The ability to identify and specifically protect those individuals who are most likely to develop severe illness would allow those at low risk of severe illness to continue to live as usual, and could help us to ensure that the most vulnerable are protected. Additionally, identification of gene variants that change the likelihood of getting infected or the severity of response may offer clues as to the biological systems underlying the body’s response to COVID‐19, which could help in the development of vaccines and/ or novel treatments.

Detailed Research Plan

You can see the full scope of the research this domain has been approved to perform in the Detailed Research Plan here. If you feel that your research is not covered by your domain’s detailed research plan please contact your domain lead to review this. You can find all of the Detailed Research Plans for approved GeCIP domains on this page.

The lead(s) of this domain are Colin Cooper and co-lead Gkikas Magiorkinis. You can find the full list of domain leads and their contact details on our page here.

Below are the current subdomains for this domain. You can find the full details of the research proposed by this domain in the Integrated Pathogens and Mobile Elements DRP.

Sub-domain leads

Endogenous retroviruses, retrotransposonsGkikas Magiorkinis
Identification of PathogensColin Cooper
COVID‐19 Susceptibility and ResponseGkikas Magiorkinis

Other Projects