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The genetic basis of invasive meningococcal disease

Lead Research Organisation: IMPERIAL COLLEGE LONDON
Department Name: Infectious Disease

Abstract

Invasive meningococcal disease (IMD) is a rare disease affecting children and young adults due to bacterial infection by Neisseria meningitidis. Life-threatening infection of the blood, and/or brain lead to IMD. Although most people carry this bacteria in their nose, the majority do not develop IMD. We know that genetic mutations of specific immune pathways make individuals more susceptible to IMD. Patients with these mutations are unable to produce factors that help kill the bacteria. These mutations however are only present in a small number of IMD patients. We thus put forward the idea that other genetic mutations may exist in IMD patients. To identify new genes in IMD, we sequenced DNA from ~700 children with life-threatening bacterial infections, including 250 IMD patients. The sequences from these patients revealed mutations in other protective immune signaling pathways known to be involved in sensing invading bacteria. Here, we propose to test whether these new mutations affect the way a cell responds to the bacteria in an experimental infection. We will use cells from the lining of the airway, and blood cells. We chose to carry out these experiments in these cell types as airway cells are important for the entry of bacteria into the nose, and the blood cells will model the 'invasive' stage of disease when the bacteria replicates in the blood leading to life-threatening infection. Finally, we will test some of these mutations in a zebrafish model of bacterial infection where we may visualize how the body responds to infection in real-time. Understanding the role of
these genes will improve our understanding of why certain individuals develop life-threatening infections and may lead to better treatment and prevention of childhood infections.

Publications

10 25 50
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Andreakos E (2025) The seven enigmas of SARS-CoV-2: from the past to the future. in Journal of human immunity

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Bellos E (2025) Genetic determinants of the complement and coagulation pathways in invasive meningococcal disease. in The Journal of allergy and clinical immunology

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Callaby H (2025) Monkeypox virus isolation from longitudinal samples in 11 hospitalised patients. in The Lancet. Infectious diseases

 
Title Front cover of JEM - gene burden analysis circular Manhattan plot 
Description Front cover of JEM - gene burden analysis circular Manhattan plot -figure from our paper in this issue on the discovery of BTNL8 underlying MIS-C 
Type Of Art Image 
Year Produced 2024 
Impact Front cover of JEM journal 
URL https://rupress.org/jem/issue/221/12
 
Description Multisystem Inflammatory Syndrome in Children (MIS-C) is a rare but serious condition that typically arises several weeks after exposure to the SARS-CoV-2 virus, responsible for COVID-19. This syndrome leads to widespread inflammation affecting multiple organ systems, including the heart, lungs, kidneys, brain, skin, eyes, and gastrointestinal tract. Early recognition and prompt medical attention are crucial, as MIS-C can rapidly progress to life-threatening conditions such as shock and organ failure. Treatment typically involves supportive care and medications to reduce inflammation, including intravenous immunoglobulin (IVIG) and corticosteroids. With timely intervention, most children recover fully. Ongoing research is exploring potential genetic factors contributing to MIS-C. A recent study identified variants in the BTNL8 gene among affected individuals, suggesting a possible genetic predisposition.Multisystem Inflammatory Syndrome in Children (MIS-C) is a rare condition following COVID-19, often involving gut issues. Researchers found a genetic link, identifying rare variants in the BTNL8 gene in MIS-C patients. This gene helps regulate immune cells in the gut, and mutations may lead to inflammation and intestinal damage. These genetic changes were found only in MIS-C cases, not in other infections. The findings suggest that disrupted gut health may play a role in MIS-C, helping scientists better understand and potentially improve treatments for affected children.

We have also published a paper on the identificaiton of complement and coagulation genes underlying severe presetnations of invasive mningococcal disease - published in PMID: 40987388 .
Exploitation Route help identify more patients with mutations in BTNL8, complement genes which can help us understand the mechanism of pathology better
Sectors Healthcare

 
Description UK Paediatric Encephalitis Guidelines
Geographic Reach Europe 
Policy Influence Type Contribution to a national consultation/review
Impact it has yet to be finalized so no impact yet
 
Description BSI Travel Award
Amount £500 (GBP)
Organisation British Society For Immunology 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2016 
End 09/2016
 
Description Departmental studentship
Amount £30,000 (GBP)
Organisation Imperial College London 
Sector Academic/University
Country United Kingdom
Start 12/2015 
End 06/2019
 
Description ESPID Master class travel award
Amount £500 (GBP)
Organisation European Society for Paediatric Infectious Diseases (ESPID) 
Sector Charity/Non Profit
Country Netherlands
Start 04/2015 
End 05/2015
 
Description Genomic and transcriptomic determinants of host susceptibility, protection, and viral mutation in experimental SARS CoV-2 infection
Amount £1,870,596 (GBP)
Funding ID 224530/Z/21/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2022 
End 12/2024
 
Description ISARIC - Coronavirus Clinical Characterisation Consortium (ISARIC-4C)
Amount £5,958,870 (GBP)
Funding ID MC_PC_19059 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 03/2020 
End 09/2021
 
Description Immunologic and Predictive Features of MIS-C
Amount £169,136 (GBP)
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 06/2022 
End 06/2027
 
Description PaeCH Travel Fund
Amount £500 (GBP)
Funding ID https://www.imperial.ac.uk/centre-for-paediatrics-child-health/research/ 
Organisation Imperial College London 
Sector Academic/University
Country United Kingdom
Start 09/2024 
End 10/2024
 
Description The Great Britain Sasakawa Foundation Butterfield Award
Amount £7,400 (GBP)
Funding ID B133 
Organisation The Great Britain Sasakawa Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2021 
End 02/2024
 
Description UNDINE - The human genetic and immunological determinants of the clinical manifestations of SARS-CoV-2 infection: Towards personalized medicine
Amount £179,366 (GBP)
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 05/2022 
End 05/2026
 
Title BurdenMC 
Description burdenMC is a framework that generates empirical estimates for the burden of rare variants in patient sequencing cohorts. To achieve this, we take advantage of existing large-scale population sequencing databases that capture the breadth of human genomic variation across different populations. The main contributing database is gnomAD (Gudmundsson et al., 2022), which contains whole genome and whole exome sequences of >140,000 individuals from around the globe. burdenMC is a Monte Carlo sampling method that iteratively simulates control datasets from gnomAD using only the summary statistics that are publicly available. 
Type Of Material Data analysis technique 
Year Produced 2024 
Provided To Others? Yes  
Impact Identifed enrichment of rare variatns in BTNL8 in MIS-C patients. Allows for gene enrichment studies in small population cohorts lacking sequenced controls, and accounting for diverse populations. 
URL https://rupress.org/jem/article/221/12/e920240699/277108/Heterozygous-BTNL8-variants-in-individuals-...
 
Description Bogunovic Lab Collaboration 
Organisation Icahn School of Medicine at Mount Sinai
Country United States 
Sector Academic/University 
PI Contribution I have contributed our expertise on autophagy analysis, patient-based cell analysis, and contribution of select infectious disease patients to understand the molecular and immunological basis to disease.
Collaborator Contribution The Bogunovic lab have access to patients with various immune dysregulation and expertise in deep immunophenotyping leading to the identification of new inborn errors of immunity.
Impact This has resulted in the following outcomes; PMID: 34363755
Start Year 2021
 
Description COVID Human Genetic Effort 
Organisation Imagine Institute
Country France 
Sector Hospitals 
PI Contribution I am part of the steering committee as well as a member in this international consortium studying the genetics of COVID19 disease. I also am a co-lead on a subcommittee focusing on the genetics of multisytem inflamatorry disorder in children (MIS-C).
Collaborator Contribution This is led by my collaborators JL Casanova (Rockefeller U, USA) and Helen Su (NIAID, US) and 80 other consortia members globally who contribute patients, DNA and data.
Impact additional PMIDs 33904890 34413139 34413140 34524075 35090163 35104687 Publications: 1. Alessia David, Nicholas Parkinson, Thomas P Peacock, Erola Pairo-Castineira, Tarun Khanna, Aurelie Cobat, Albert Tenesa, Vanessa Sancho-Shimizu, GenOMICC Investigators, ISARIC4C Investigators, Jean-Laurent Casanova, Laurent Abel, Wendy S. Barclay, J. Kenneth Baillie, Michael JE Sternberg. A common TMPRSS2 variant protects against severe COVID-19. medRxiv March 8, 2021. doi: https://doi.org/10.1101/2021.03.04.21252931 2. Zhang, Q., P. Bastard, Z. Liu, J. Le Pen, M. Moncada-Velez, J. Chen, M. Ogishi, I.K.D. Sabli, S. Hodeib, C. Korol, J. Rosain, K. Bilguvar, J. Ye, A. Bolze, B. Bigio, R. Yang, A.A. Arias, Q. Zhou, Y. Zhang, F. Onodi, S. Korniotis, L. Karpf, Q. Philippot, M. Chbihi, L. Bonnet-Madin, K. Dorgham, N. Smith, W.M. Schneider, B.S. Razooky, H.H. Hoffmann, E. Michailidis, L. Moens, J.E. Han, L. Lorenzo, L. Bizien, P. Meade, A.L. Neehus, A.C. Ugurbil, A. Corneau, G. Kerner, P. Zhang, F. Rapaport, Y. Seeleuthner, J. Manry, C. Masson, Y. Schmitt, A. Schluter, T. Le Voyer, T. Khan, J. Li, J. Fellay, L. Roussel, M. Shahrooei, M.F. Alosaimi, D. Mansouri, H. Al-Saud, F. Al-Mulla, F. Almourfi, S.Z. Al-Muhsen, F. Alsohime, S. Al Turki, R. Hasanato, D. van de Beek, A. Biondi, L.R. Bettini, M. D'Angio, P. Bonfanti, L. Imberti, A. Sottini, S. Paghera, E. Quiros-Roldan, C. Rossi, A.J. Oler, M.F. Tompkins, C. Alba, I. Vandernoot, J.C. Goffard, G. Smits, I. Migeotte, F. Haerynck, P. Soler-Palacin, A. Martin-Nalda, R. Colobran, P.E. Morange, S. Keles, F. Colkesen, T. Ozcelik, K.K. Yasar, S. Senoglu, S.N. Karabela, C. Rodriguez-Gallego, G. Novelli, S. Hraiech, Y. Tandjaoui-Lambiotte, X. Duval, C. Laouenan, C.-S. Clinicians, C. Clinicians, C.G. Imagine, C.C.S.G. French, V.C.C. Co, U.M.C.C.-B. Amsterdam, C.H.G. Effort, N.-U.T.C.I. Group, A.L. Snow, C.L. Dalgard, J.D. Milner, D.C. Vinh, T.H. Mogensen, N. Marr, A.N. Spaan, B. Boisson, S. Boisson-Dupuis, J. Bustamante, A. Puel, M.J. Ciancanelli, I. Meyts, T. Maniatis, V. Soumelis, A. Amara, M. Nussenzweig, A. Garcia-Sastre, F. Krammer, A. Pujol, D. Duffy, R.P. Lifton, S.Y. Zhang, G. Gorochov, V. Beziat, E. Jouanguy, V. Sancho-Shimizu, C.M. Rice, L. Abel, L.D. Notarangelo, A. Cobat, H.C. Su and J.L. Casanova, Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science, 2020. 370(6515). *co-second to last author 3. 14. Bastard, P., L.B. Rosen, Q. Zhang, E. Michailidis, H.H. Hoffmann, Y. Zhang, K. Dorgham, Q. Philippot, J. Rosain, V. Beziat, J. Manry, E. Shaw, L. Haljasmagi, P. Peterson, L. Lorenzo, L. Bizien, S. Trouillet-Assant, K. Dobbs, A.A. de Jesus, A. Belot, A. Kallaste, E. Catherinot, Y. Tandjaoui-Lambiotte, J. Le Pen, G. Kerner, B. Bigio, Y. Seeleuthner, R. Yang, A. Bolze, A.N. Spaan, O.M. Delmonte, M.S. Abers, A. Aiuti, G. Casari, V. Lampasona, L. Piemonti, F. Ciceri, K. Bilguvar, R.P. Lifton, M. Vasse, D.M. Smadja, M. Migaud, J. Hadjadj, B. Terrier, D. Duffy, L. Quintana-Murci, D. van de Beek, L. Roussel, D.C. Vinh, S.G. Tangye, F. Haerynck, D. Dalmau, J. Martinez-Picado, P. Brodin, M.C. Nussenzweig, S. Boisson-Dupuis, C. Rodriguez-Gallego, G. Vogt, T.H. Mogensen, A.J. Oler, J. Gu, P.D. Burbelo, J.I. Cohen, A. Biondi, L.R. Bettini, M. D'Angio, P. Bonfanti, P. Rossignol, J. Mayaux, F. Rieux-Laucat, E.S. Husebye, F. Fusco, M.V. Ursini, L. Imberti, A. Sottini, S. Paghera, E. Quiros-Roldan, C. Rossi, R. Castagnoli, D. Montagna, A. Licari, G.L. Marseglia, X. Duval, J. Ghosn, H. Lab, N.-U.I.R.t.C. Group, C. Clinicians, C.-S. Clinicians, C.G. Imagine, C.C.S.G. French, C. Milieu Interieur, V.C.C. Co, U.M.C.C.-B. Amsterdam, C.H.G. Effort, J.S. Tsang, R. Goldbach-Mansky, K. Kisand, M.S. Lionakis, A. Puel, S.Y. Zhang, S.M. Holland, G. Gorochov, E. Jouanguy, C.M. Rice, A. Cobat, L.D. Notarangelo, L. Abel, H.C. Su and J.L. Casanova, Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science, 2020. 370(6515). 4. Casanova, J.L., H.C. Su, and C.H.G. Effort, A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection. Cell, 2020. 181(6): p. 1194-1199. Talk 1. WFI Infection and Immunity Seminar. Imperial College London, 26 January, 2021 2. COVID-19: Biomedical Insights Into An Evolving Epidemic (One Year Later) National University Singapore, 25 January, 2021
Start Year 2020
 
Description COVID Human Genetic Effort 
Organisation National Institutes of Health (NIH)
Department National Institute of Allergy and Infectious Diseases (NIAID)
Country United States 
Sector Public 
PI Contribution I am part of the steering committee as well as a member in this international consortium studying the genetics of COVID19 disease. I also am a co-lead on a subcommittee focusing on the genetics of multisytem inflamatorry disorder in children (MIS-C).
Collaborator Contribution This is led by my collaborators JL Casanova (Rockefeller U, USA) and Helen Su (NIAID, US) and 80 other consortia members globally who contribute patients, DNA and data.
Impact additional PMIDs 33904890 34413139 34413140 34524075 35090163 35104687 Publications: 1. Alessia David, Nicholas Parkinson, Thomas P Peacock, Erola Pairo-Castineira, Tarun Khanna, Aurelie Cobat, Albert Tenesa, Vanessa Sancho-Shimizu, GenOMICC Investigators, ISARIC4C Investigators, Jean-Laurent Casanova, Laurent Abel, Wendy S. Barclay, J. Kenneth Baillie, Michael JE Sternberg. A common TMPRSS2 variant protects against severe COVID-19. medRxiv March 8, 2021. doi: https://doi.org/10.1101/2021.03.04.21252931 2. Zhang, Q., P. Bastard, Z. Liu, J. Le Pen, M. Moncada-Velez, J. Chen, M. Ogishi, I.K.D. Sabli, S. Hodeib, C. Korol, J. Rosain, K. Bilguvar, J. Ye, A. Bolze, B. Bigio, R. Yang, A.A. Arias, Q. Zhou, Y. Zhang, F. Onodi, S. Korniotis, L. Karpf, Q. Philippot, M. Chbihi, L. Bonnet-Madin, K. Dorgham, N. Smith, W.M. Schneider, B.S. Razooky, H.H. Hoffmann, E. Michailidis, L. Moens, J.E. Han, L. Lorenzo, L. Bizien, P. Meade, A.L. Neehus, A.C. Ugurbil, A. Corneau, G. Kerner, P. Zhang, F. Rapaport, Y. Seeleuthner, J. Manry, C. Masson, Y. Schmitt, A. Schluter, T. Le Voyer, T. Khan, J. Li, J. Fellay, L. Roussel, M. Shahrooei, M.F. Alosaimi, D. Mansouri, H. Al-Saud, F. Al-Mulla, F. Almourfi, S.Z. Al-Muhsen, F. Alsohime, S. Al Turki, R. Hasanato, D. van de Beek, A. Biondi, L.R. Bettini, M. D'Angio, P. Bonfanti, L. Imberti, A. Sottini, S. Paghera, E. Quiros-Roldan, C. Rossi, A.J. Oler, M.F. Tompkins, C. Alba, I. Vandernoot, J.C. Goffard, G. Smits, I. Migeotte, F. Haerynck, P. Soler-Palacin, A. Martin-Nalda, R. Colobran, P.E. Morange, S. Keles, F. Colkesen, T. Ozcelik, K.K. Yasar, S. Senoglu, S.N. Karabela, C. Rodriguez-Gallego, G. Novelli, S. Hraiech, Y. Tandjaoui-Lambiotte, X. Duval, C. Laouenan, C.-S. Clinicians, C. Clinicians, C.G. Imagine, C.C.S.G. French, V.C.C. Co, U.M.C.C.-B. Amsterdam, C.H.G. Effort, N.-U.T.C.I. Group, A.L. Snow, C.L. Dalgard, J.D. Milner, D.C. Vinh, T.H. Mogensen, N. Marr, A.N. Spaan, B. Boisson, S. Boisson-Dupuis, J. Bustamante, A. Puel, M.J. Ciancanelli, I. Meyts, T. Maniatis, V. Soumelis, A. Amara, M. Nussenzweig, A. Garcia-Sastre, F. Krammer, A. Pujol, D. Duffy, R.P. Lifton, S.Y. Zhang, G. Gorochov, V. Beziat, E. Jouanguy, V. Sancho-Shimizu, C.M. Rice, L. Abel, L.D. Notarangelo, A. Cobat, H.C. Su and J.L. Casanova, Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science, 2020. 370(6515). *co-second to last author 3. 14. Bastard, P., L.B. Rosen, Q. Zhang, E. Michailidis, H.H. Hoffmann, Y. Zhang, K. Dorgham, Q. Philippot, J. Rosain, V. Beziat, J. Manry, E. Shaw, L. Haljasmagi, P. Peterson, L. Lorenzo, L. Bizien, S. Trouillet-Assant, K. Dobbs, A.A. de Jesus, A. Belot, A. Kallaste, E. Catherinot, Y. Tandjaoui-Lambiotte, J. Le Pen, G. Kerner, B. Bigio, Y. Seeleuthner, R. Yang, A. Bolze, A.N. Spaan, O.M. Delmonte, M.S. Abers, A. Aiuti, G. Casari, V. Lampasona, L. Piemonti, F. Ciceri, K. Bilguvar, R.P. Lifton, M. Vasse, D.M. Smadja, M. Migaud, J. Hadjadj, B. Terrier, D. Duffy, L. Quintana-Murci, D. van de Beek, L. Roussel, D.C. Vinh, S.G. Tangye, F. Haerynck, D. Dalmau, J. Martinez-Picado, P. Brodin, M.C. Nussenzweig, S. Boisson-Dupuis, C. Rodriguez-Gallego, G. Vogt, T.H. Mogensen, A.J. Oler, J. Gu, P.D. Burbelo, J.I. Cohen, A. Biondi, L.R. Bettini, M. D'Angio, P. Bonfanti, P. Rossignol, J. Mayaux, F. Rieux-Laucat, E.S. Husebye, F. Fusco, M.V. Ursini, L. Imberti, A. Sottini, S. Paghera, E. Quiros-Roldan, C. Rossi, R. Castagnoli, D. Montagna, A. Licari, G.L. Marseglia, X. Duval, J. Ghosn, H. Lab, N.-U.I.R.t.C. Group, C. Clinicians, C.-S. Clinicians, C.G. Imagine, C.C.S.G. French, C. Milieu Interieur, V.C.C. Co, U.M.C.C.-B. Amsterdam, C.H.G. Effort, J.S. Tsang, R. Goldbach-Mansky, K. Kisand, M.S. Lionakis, A. Puel, S.Y. Zhang, S.M. Holland, G. Gorochov, E. Jouanguy, C.M. Rice, A. Cobat, L.D. Notarangelo, L. Abel, H.C. Su and J.L. Casanova, Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science, 2020. 370(6515). 4. Casanova, J.L., H.C. Su, and C.H.G. Effort, A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection. Cell, 2020. 181(6): p. 1194-1199. Talk 1. WFI Infection and Immunity Seminar. Imperial College London, 26 January, 2021 2. COVID-19: Biomedical Insights Into An Evolving Epidemic (One Year Later) National University Singapore, 25 January, 2021
Start Year 2020
 
Description COVID Human Genetic Effort 
Organisation Rockefeller University
Country United States 
Sector Academic/University 
PI Contribution I am part of the steering committee as well as a member in this international consortium studying the genetics of COVID19 disease. I also am a co-lead on a subcommittee focusing on the genetics of multisytem inflamatorry disorder in children (MIS-C).
Collaborator Contribution This is led by my collaborators JL Casanova (Rockefeller U, USA) and Helen Su (NIAID, US) and 80 other consortia members globally who contribute patients, DNA and data.
Impact additional PMIDs 33904890 34413139 34413140 34524075 35090163 35104687 Publications: 1. Alessia David, Nicholas Parkinson, Thomas P Peacock, Erola Pairo-Castineira, Tarun Khanna, Aurelie Cobat, Albert Tenesa, Vanessa Sancho-Shimizu, GenOMICC Investigators, ISARIC4C Investigators, Jean-Laurent Casanova, Laurent Abel, Wendy S. Barclay, J. Kenneth Baillie, Michael JE Sternberg. A common TMPRSS2 variant protects against severe COVID-19. medRxiv March 8, 2021. doi: https://doi.org/10.1101/2021.03.04.21252931 2. Zhang, Q., P. Bastard, Z. Liu, J. Le Pen, M. Moncada-Velez, J. Chen, M. Ogishi, I.K.D. Sabli, S. Hodeib, C. Korol, J. Rosain, K. Bilguvar, J. Ye, A. Bolze, B. Bigio, R. Yang, A.A. Arias, Q. Zhou, Y. Zhang, F. Onodi, S. Korniotis, L. Karpf, Q. Philippot, M. Chbihi, L. Bonnet-Madin, K. Dorgham, N. Smith, W.M. Schneider, B.S. Razooky, H.H. Hoffmann, E. Michailidis, L. Moens, J.E. Han, L. Lorenzo, L. Bizien, P. Meade, A.L. Neehus, A.C. Ugurbil, A. Corneau, G. Kerner, P. Zhang, F. Rapaport, Y. Seeleuthner, J. Manry, C. Masson, Y. Schmitt, A. Schluter, T. Le Voyer, T. Khan, J. Li, J. Fellay, L. Roussel, M. Shahrooei, M.F. Alosaimi, D. Mansouri, H. Al-Saud, F. Al-Mulla, F. Almourfi, S.Z. Al-Muhsen, F. Alsohime, S. Al Turki, R. Hasanato, D. van de Beek, A. Biondi, L.R. Bettini, M. D'Angio, P. Bonfanti, L. Imberti, A. Sottini, S. Paghera, E. Quiros-Roldan, C. Rossi, A.J. Oler, M.F. Tompkins, C. Alba, I. Vandernoot, J.C. Goffard, G. Smits, I. Migeotte, F. Haerynck, P. Soler-Palacin, A. Martin-Nalda, R. Colobran, P.E. Morange, S. Keles, F. Colkesen, T. Ozcelik, K.K. Yasar, S. Senoglu, S.N. Karabela, C. Rodriguez-Gallego, G. Novelli, S. Hraiech, Y. Tandjaoui-Lambiotte, X. Duval, C. Laouenan, C.-S. Clinicians, C. Clinicians, C.G. Imagine, C.C.S.G. French, V.C.C. Co, U.M.C.C.-B. Amsterdam, C.H.G. Effort, N.-U.T.C.I. Group, A.L. Snow, C.L. Dalgard, J.D. Milner, D.C. Vinh, T.H. Mogensen, N. Marr, A.N. Spaan, B. Boisson, S. Boisson-Dupuis, J. Bustamante, A. Puel, M.J. Ciancanelli, I. Meyts, T. Maniatis, V. Soumelis, A. Amara, M. Nussenzweig, A. Garcia-Sastre, F. Krammer, A. Pujol, D. Duffy, R.P. Lifton, S.Y. Zhang, G. Gorochov, V. Beziat, E. Jouanguy, V. Sancho-Shimizu, C.M. Rice, L. Abel, L.D. Notarangelo, A. Cobat, H.C. Su and J.L. Casanova, Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science, 2020. 370(6515). *co-second to last author 3. 14. Bastard, P., L.B. Rosen, Q. Zhang, E. Michailidis, H.H. Hoffmann, Y. Zhang, K. Dorgham, Q. Philippot, J. Rosain, V. Beziat, J. Manry, E. Shaw, L. Haljasmagi, P. Peterson, L. Lorenzo, L. Bizien, S. Trouillet-Assant, K. Dobbs, A.A. de Jesus, A. Belot, A. Kallaste, E. Catherinot, Y. Tandjaoui-Lambiotte, J. Le Pen, G. Kerner, B. Bigio, Y. Seeleuthner, R. Yang, A. Bolze, A.N. Spaan, O.M. Delmonte, M.S. Abers, A. Aiuti, G. Casari, V. Lampasona, L. Piemonti, F. Ciceri, K. Bilguvar, R.P. Lifton, M. Vasse, D.M. Smadja, M. Migaud, J. Hadjadj, B. Terrier, D. Duffy, L. Quintana-Murci, D. van de Beek, L. Roussel, D.C. Vinh, S.G. Tangye, F. Haerynck, D. Dalmau, J. Martinez-Picado, P. Brodin, M.C. Nussenzweig, S. Boisson-Dupuis, C. Rodriguez-Gallego, G. Vogt, T.H. Mogensen, A.J. Oler, J. Gu, P.D. Burbelo, J.I. Cohen, A. Biondi, L.R. Bettini, M. D'Angio, P. Bonfanti, P. Rossignol, J. Mayaux, F. Rieux-Laucat, E.S. Husebye, F. Fusco, M.V. Ursini, L. Imberti, A. Sottini, S. Paghera, E. Quiros-Roldan, C. Rossi, R. Castagnoli, D. Montagna, A. Licari, G.L. Marseglia, X. Duval, J. Ghosn, H. Lab, N.-U.I.R.t.C. Group, C. Clinicians, C.-S. Clinicians, C.G. Imagine, C.C.S.G. French, C. Milieu Interieur, V.C.C. Co, U.M.C.C.-B. Amsterdam, C.H.G. Effort, J.S. Tsang, R. Goldbach-Mansky, K. Kisand, M.S. Lionakis, A. Puel, S.Y. Zhang, S.M. Holland, G. Gorochov, E. Jouanguy, C.M. Rice, A. Cobat, L.D. Notarangelo, L. Abel, H.C. Su and J.L. Casanova, Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science, 2020. 370(6515). 4. Casanova, J.L., H.C. Su, and C.H.G. Effort, A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection. Cell, 2020. 181(6): p. 1194-1199. Talk 1. WFI Infection and Immunity Seminar. Imperial College London, 26 January, 2021 2. COVID-19: Biomedical Insights Into An Evolving Epidemic (One Year Later) National University Singapore, 25 January, 2021
Start Year 2020
 
Description EUCLIDS 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution EUCLIDS is an FP7 funded multi EU center study that commenced in 2011 with the aim of understanding the genetics underlying life threatening infection of childhood. Over 6000 patients have been recruited and large scale genomic analysis underway to characterize severe pediatric infections focusing primarily on bacterial infections. I was in charge of WP7: Extreme phenotype cohort genomic analysis for clinical biomarker discovery for which we have sequenced 750 patients with various bacterial infections. Specifically, i contributed to the design, selection and analysis of the sequenced patients. Although this study ended in 2016 the collaboration is still ongoing as we have only just received the sequence results from this study, and hence we expect output in terms of papers in the very near future.
Collaborator Contribution This multi center study was led by Prof Levin at Imperial College London and 14 other partners (University of Newcastle upon Tyne, Novarits Vaccine and Diagnostics, MRC Gambia, Micropathology, Oxford Gene Technology, Genome Institute of Singapore, Medical University Graz, Radboud University Nijmegen, Erasmus University Medical Center, AMC University Amsterdam, University of Oxford, University of Liverpool) whose role was mainly to recruit patients into the study and to carry out different aspects of the large EU grant.
Impact doi: 10.1038/srep35842 doi: 10.1186/s13054-018-2052-7.
Start Year 2011
 
Description HSE cohort collaboration 
Organisation Imagine Institute
Country France 
Sector Hospitals 
PI Contribution I have contributed by revealing a new role for autophagy in the development of herpes encephalitis as well as in the identification of other candidate genes. Furthermore I am interrogating the role of herpes infection in the development of NMDAR autoimmune encephalitis.
Collaborator Contribution Prof Jean Laurent Casanova has a collection of chlidhood herpes encephalitis patients including biobanked samples and exome sequences that he has agreed to share for my research. He also contributes his expertise in the field of primary immunodeficiencies to our research. This is an ongoing collaboration.
Impact doi: 10.1016/j.cell.2017.01.039 doi: 10.1016/j.molmed.2016.04.006 doi: 10.1016/j.jaci.2013.01.008. doi: 10.1084/jem.20111316.
Start Year 2011
 
Description HSE cohort collaboration 
Organisation Rockefeller University
Country United States 
Sector Academic/University 
PI Contribution I have contributed by revealing a new role for autophagy in the development of herpes encephalitis as well as in the identification of other candidate genes. Furthermore I am interrogating the role of herpes infection in the development of NMDAR autoimmune encephalitis.
Collaborator Contribution Prof Jean Laurent Casanova has a collection of chlidhood herpes encephalitis patients including biobanked samples and exome sequences that he has agreed to share for my research. He also contributes his expertise in the field of primary immunodeficiencies to our research. This is an ongoing collaboration.
Impact doi: 10.1016/j.cell.2017.01.039 doi: 10.1016/j.molmed.2016.04.006 doi: 10.1016/j.jaci.2013.01.008. doi: 10.1084/jem.20111316.
Start Year 2011
 
Description Hayday collaboration 
Organisation Francis Crick Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Identfifed BTNL8 variants underlying MIS-C
Collaborator Contribution Assisted with functional validation of BTNL8 variants.
Impact J Exp Med (2024) 221 (12): e920240699. https://doi.org/10.1084/jem.20240699
Start Year 2023
 
Description ISARI-4C 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution We will study the rare genetic variation underlying critical COVID19 disease
Collaborator Contribution The study is led by Kenny Baillie (Univ Edinbourgh) Calum Semple (Univ Liverpool) and Peter Oppenshaw (Imperial College London) and they are leading the recruitment of all COVID19 infected individuals as well as studies around transmission, immune response, and genetics susceptbitly.
Impact Additional PMIDs 35081335, 34911741, 34812731, 34810237, 34729465, 34686560, 34661677, 34619109, 34274064, 34237774, 34170486, 34107928, 34100002, 34000238, 33997800, 33676593, 33444539, PUblications: 1. Davies, N.G., R.C. Barnard, C.I. Jarvis, T.W. Russell, M.G. Semple, M. Jit, W.J. Edmunds, C.-W.G. Centre for Mathematical Modelling of Infectious Diseases, and I.C. investigators, Association of tiered restrictions and a second lockdown with COVID-19 deaths and hospital admissions in England: a modelling study. Lancet Infect Dis, 2020. 2. Docherty, A.B., E.M. Harrison, C.A. Green, H.E. Hardwick, R. Pius, L. Norman, K.A. Holden, J.M. Read, F. Dondelinger, G. Carson, L. Merson, J. Lee, D. Plotkin, L. Sigfrid, S. Halpin, C. Jackson, C. Gamble, P.W. Horby, J.S. Nguyen-Van-Tam, A. Ho, C.D. Russell, J. Dunning, P.J. Openshaw, J.K. Baillie, M.G. Semple, and I.C. investigators, Features of 20 133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study. BMJ, 2020. 369: p. m1985. 3. Drake, T.M., A.B. Docherty, E.M. Harrison, J.K. Quint, H. Adamali, S. Agnew, S. Babu, C.M. Barber, S. Barratt, E. Bendstrup, S. Bianchi, D.C. Villegas, N. Chaudhuri, F. Chua, R. Coker, W. Chang, A. Crawshaw, L.E. Crowley, D. Dosanjh, C.A. Fiddler, I.A. Forrest, P.M. George, M.A. Gibbons, K. Groom, S. Haney, S.P. Hart, E. Heiden, M. Henry, L.P. Ho, R.K. Hoyles, J. Hutchinson, K. Hurley, M. Jones, S. Jones, M. Kokosi, M. Kreuter, L.S. MacKay, S. Mahendran, G. Margaritopoulos, M. Molina-Molina, P.L. Molyneaux, A. O'Brien, K. O'Reilly, A. Packham, H. Parfrey, V. Poletti, J.C. Porter, E. Renzoni, P. Rivera-Ortega, A.M. Russell, G. Saini, L.G. Spencer, G.M. Stella, H. Stone, S. Sturney, D. Thickett, M. Thillai, T. Wallis, K. Ward, A.U. Wells, A. West, M. Wickremasinghe, F. Woodhead, G. Hearson, L. Howard, J.K. Baillie, P.J.M. Openshaw, M.G. Semple, I. Stewart, R.G. Jenkins, and I.C. Investigators, Outcome of Hospitalization for COVID-19 in Patients with Interstitial Lung Disease. An International Multicenter Study. Am J Respir Crit Care Med, 2020. 202(12): p. 1656-1665. 4. Gupta, R.K., E.M. Harrison, A. Ho, A.B. Docherty, S.R. Knight, M. van Smeden, I. Abubakar, M. Lipman, M. Quartagno, R. Pius, I. Buchan, G. Carson, T.M. Drake, J. Dunning, C.J. Fairfield, C. Gamble, C.A. Green, S. Halpin, H.E. Hardwick, K.A. Holden, P.W. Horby, C. Jackson, K.A. McLean, L. Merson, J.S. Nguyen-Van-Tam, L. Norman, P.L. Olliaro, M.G. Pritchard, C.D. Russell, J. Scott-Brown, C.A. Shaw, A. Sheikh, T. Solomon, C. Sudlow, O.V. Swann, L. Turtle, P.J.M. Openshaw, J.K. Baillie, M.G. Semple, M. Noursadeghi, and I.C. Investigators, Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study. Lancet Respir Med, 2021. 5. Huls, A., A.C.S. Costa, M. Dierssen, R.A. Baksh, S. Bargagna, N.T. Baumer, A.C. Brandao, A. Carfi, M. Carmona-Iragui, B.A. Chicoine, S. Ghosh, M. Lakhanpaul, C. Manso, M.A. Mayer, M.D.C. Ortega, D.R. de Asua, A.S. Rebillat, L.A. Russell, G. Sgandurra, D. Valentini, S.L. Sherman, A. Strydom, and T.R.C.-. Initiative, Medical vulnerability of individuals with Down syndrome to severe COVID-19-data from the Trisomy 21 Research Society and the UK ISARIC4C survey. EClinicalMedicine, 2021: p. 100769. 6. Knight, S.R., A. Ho, R. Pius, I. Buchan, G. Carson, T.M. Drake, J. Dunning, C.J. Fairfield, C. Gamble, C.A. Green, R. Gupta, S. Halpin, H.E. Hardwick, K.A. Holden, P.W. Horby, C. Jackson, K.A. McLean, L. Merson, J.S. Nguyen-Van-Tam, L. Norman, M. Noursadeghi, P.L. Olliaro, M.G. Pritchard, C.D. Russell, C.A. Shaw, A. Sheikh, T. Solomon, C. Sudlow, O.V. Swann, L.C. Turtle, P.J. Openshaw, J.K. Baillie, M.G. Semple, A.B. Docherty, E.M. Harrison, and I.C. investigators, Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score. BMJ, 2020. 370: p. m3339. 7. Pairo-Castineira, E., S. Clohisey, L. Klaric, A.D. Bretherick, K. Rawlik, D. Pasko, S. Walker, N. Parkinson, M.H. Fourman, C.D. Russell, J. Furniss, A. Richmond, E. Gountouna, N. Wrobel, D. Harrison, B. Wang, Y. Wu, A. Meynert, F. Griffiths, W. Oosthuyzen, A. Kousathanas, L. Moutsianas, Z. Yang, R. Zhai, C. Zheng, G. Grimes, R. Beale, J. Millar, B. Shih, S. Keating, M. Zechner, C. Haley, D.J. Porteous, C. Hayward, J. Yang, J. Knight, C. Summers, M. Shankar-Hari, P. Klenerman, L. Turtle, A. Ho, S.C. Moore, C. Hinds, P. Horby, A. Nichol, D. Maslove, L. Ling, D. McAuley, H. Montgomery, T. Walsh, A.C. Pereira, A. Renieri, O.I. Gen, I.C. Investigators, C.-H.G. Initiative, I. andMe, B. Investigators, C.I. Gen, X. Shen, C.P. Ponting, A. Fawkes, A. Tenesa, M. Caulfield, R. Scott, K. Rowan, L. Murphy, P.J.M. Openshaw, M.G. Semple, A. Law, V. Vitart, J.F. Wilson, and J.K. Baillie, Genetic mechanisms of critical illness in COVID-19. Nature, 2021. 591(7848): p. 92-98. 8. Peng, Y., A.J. Mentzer, G. Liu, X. Yao, Z. Yin, D. Dong, W. Dejnirattisai, T. Rostron, P. Supasa, C. Liu, C. Lopez-Camacho, J. Slon-Campos, Y. Zhao, D.I. Stuart, G.C. Paesen, J.M. Grimes, A.A. Antson, O.W. Bayfield, D. Hawkins, D.S. Ker, B. Wang, L. Turtle, K. Subramaniam, P. Thomson, P. Zhang, C. Dold, J. Ratcliff, P. Simmonds, T. de Silva, P. Sopp, D. Wellington, U. Rajapaksa, Y.L. Chen, M. Salio, G. Napolitani, W. Paes, P. Borrow, B.M. Kessler, J.W. Fry, N.F. Schwabe, M.G. Semple, J.K. Baillie, S.C. Moore, P.J.M. Openshaw, M.A. Ansari, S. Dunachie, E. Barnes, J. Frater, G. Kerr, P. Goulder, T. Lockett, R. Levin, Y. Zhang, R. Jing, L.P. Ho, T.c.C. Oxford Immunology Network Covid-19 Response, I.C. Investigators, R.J. Cornall, C.P. Conlon, P. Klenerman, G.R. Screaton, J. Mongkolsapaya, A. McMichael, J.C. Knight, G. Ogg, and T. Dong, Broad and strong memory CD4(+) and CD8(+) T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat Immunol, 2020. 21(11): p. 1336-1345. 9. Swann, O.V., K.A. Holden, L. Turtle, L. Pollock, C.J. Fairfield, T.M. Drake, S. Seth, C. Egan, H.E. Hardwick, S. Halpin, M. Girvan, C. Donohue, M. Pritchard, L.B. Patel, S. Ladhani, L. Sigfrid, I.P. Sinha, P.L. Olliaro, J.S. Nguyen-Van-Tam, P.W. Horby, L. Merson, G. Carson, J. Dunning, P.J.M. Openshaw, J.K. Baillie, E.M. Harrison, A.B. Docherty, M.G. Semple, and I.C. Investigators, Clinical characteristics of children and young people admitted to hospital with covid-19 in United Kingdom: prospective multicentre observational cohort study. BMJ, 2020. 370: p. m3249. 10. Thompson, C.P., N.E. Grayson, R.S. Paton, J.S. Bolton, J. Lourenco, B.S. Penman, L.N. Lee, V. Odon, J. Mongkolsapaya, S. Chinnakannan, W. Dejnirattisai, M. Edmans, A. Fyfe, C. Imlach, K. Kooblall, N. Lim, C. Liu, C. Lopez-Camacho, C. McInally, A.L. McNaughton, N. Ramamurthy, J. Ratcliff, P. Supasa, O. Sampson, B. Wang, A.J. Mentzer, M. Turner, M.G. Semple, K. Baillie, I.C. Investigators, H. Harvala, G.R. Screaton, N. Temperton, P. Klenerman, L.M. Jarvis, S. Gupta, and P. Simmonds, Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020. Euro Surveill, 2020. 25(42). 11. Thomson, E.C., L.E. Rosen, J.G. Shepherd, R. Spreafico, A. da Silva Filipe, J.A. Wojcechowskyj, C. Davis, L. Piccoli, D.J. Pascall, J. Dillen, S. Lytras, N. Czudnochowski, R. Shah, M. Meury, N. Jesudason, A. De Marco, K. Li, J. Bassi, A. O'Toole, D. Pinto, R.M. Colquhoun, K. Culap, B. Jackson, F. Zatta, A. Rambaut, S. Jaconi, V.B. Sreenu, J. Nix, I. Zhang, R.F. Jarrett, W.G. Glass, M. Beltramello, K. Nomikou, M. Pizzuto, L. Tong, E. Cameroni, T.I. Croll, N. Johnson, J. Di Iulio, A. Wickenhagen, A. Ceschi, A.M. Harbison, D. Mair, P. Ferrari, K. Smollett, F. Sallusto, S. Carmichael, C. Garzoni, J. Nichols, M. Galli, J. Hughes, A. Riva, A. Ho, M. Schiuma, M.G. Semple, P.J.M. Openshaw, E. Fadda, J.K. Baillie, J.D. Chodera, I.C. Investigators, C.-G.U. Consortium, S.J. Rihn, S.J. Lycett, H.W. Virgin, A. Telenti, D. Corti, D.L. Robertson, and G. Snell, Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 2021. 184(5): p. 1171-1187 e20. 12. Bloom, C.I., T.M. Drake, A.B. Docherty, B.J. Lipworth, S.L. Johnston, J.S. Nguyen-Van-Tam, G. Carson, J. Dunning, E.M. Harrison, J.K. Baillie, M.G. Semple, P. Cullinan, P.J.M. Openshaw, and I. investigators, Risk of adverse outcomes in patients with underlying respiratory conditions admitted to hospital with COVID-19: a national, multicentre prospective cohort study using the ISARIC WHO Clinical Characterisation Protocol UK. Lancet Respir Med, 2021. Press engagements • Times radio Breakfast morning show- Genetics of COVID19 (Live interview Dec 19,2020) • Nature Briefing - https://www.nature.com/articles/d41586-020-03589-3; Dec 15,2020 • BBC 10oclock news - https://youtu.be/iDRP_zbdixU ;Dec 11, 2020 • BBC news (online) - https://www.bbc.co.uk/news/health-54832563 Dec 11,2020 Talks 1. Critical Care Reviews Editorial Presentation on the GENOMICC Study. January 22, 2021. https://criticalcarereviews.com/index.php/eccr21
Start Year 2020