Professor Thushan de Silva

MBChB BSc (Hons) DTM&H MRCP FRCPath PhD

School of Medicine and Population Health

Professor of Infectious Diseases

Honorary Consultant Physician in Infectious Diseases

t.desilva@sheffield.ac.uk
+44 114 215 9532

The Medical School

Full contact details

Professor Thushan de Silva
School of Medicine and Population Health
The Medical School
Beech Hill Road
Sheffield
S10 2RX

Profile

I am an Infectious Diseases Clinician Scientist with a programme of research centred around clinical discovery science in the UK and Africa. Our group applies a broad range of methods including human immunology, epidemiology, molecular diagnostics and genomics, to establish how pathogens interact with human hosts at population and individual levels. We work primarily on respiratory viruses such as influenza and SARS-CoV-2, and Streptococcus pyogenes (Group A Streptococcus), investigating the natural history of infection and immunity to inform the design of diagnostic tools, vaccines, and other preventative measures. A specific area of interest is also how immunocompromising conditions such as HIV and haematopoietic stem cell transplantation impact the clinical risk and vaccine-induced immunity to respiratory viruses.

I am part of the Clinical Infection Research Group (CIRG) in the Medical School at the University of Sheffield and am an Honorary Consultant Physician in Infectious Diseases in the South Yorkshire Regional Department of Infection and Tropical Medicine in Sheffield. I am co-director of the Florey Institute of Infection and lead the host-pathogen interactions theme. I am also a Principal Investigator in the Vaccines and Immunity Theme at the Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine.

I completed my undergraduate medical training at the University of Bristol in 2000. Following postgraduate clinical training in General Internal Medicine, Infectious Diseases and HIV in Oxford and London, I moved to Sheffield for higher specialist training in Infectious Diseases & Microbiology in 2004. After relocating to The MRC Unit The Gambia in 2007, I was awarded a British Infection Society Research Fellowship (2007-8), followed by a MRC Clinical Research Training Fellowship and PhD (2008 – 11) under the supervision of Professor Sarah Rowland-Jones and Professor Robin Weiss, to study the pathogenesis of HIV-2 infection and the molecular epidemiology of HIV-1 and HIV-2 in West Africa.

I joined the University of Sheffield in 2013 as an NIHR Academic Clinical Lecturer in Infectious Diseases & Microbiology. I was awarded a Wellcome Trust Intermediate Clinical Fellowship (2016 -2021), based between Imperial College London and the MRC Unit The Gambia, to study the immunogenicity of intranasal Live Attenuated Influenza Vaccine in children and bidirectional interactions with nasopharyngeal microbiota. I returned to the University of Sheffield as a Senior Clinical Lecturer in 2020 and led a programme of SARS-CoV-2 research through the COVID-19 pandemic, including roles as lead PI in Sheffield for the COG-UK consortium and the PITCH study. I was awarded an MBE in 2021 for services to COVID-19 research.

Publications

Show: Featured publications All publications

Featured publications

Journal articles

Colton H, Barratt N, Temperton N, Hornsby H, Angyal A, Grouneva I, Lindsey BB, Kearns P, Barnes E, Goodyear CS , Richter A et al (2024) Greater preservation of SARS‐CoV‐2 neutralising antibody responses following the ChAdOx1‐S (AZD1222) vaccine compared with mRNA vaccines in haematopoietic cell transplant recipients. British Journal of Haematology. View this article in WRRO
Jarju S, Wenlock RD, Danso M, Jobe D, Jagne YJ, Darboe A, Kumado M, Jallow Y, Touray M, Ceesay EA , Gaye H et al (2024) High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia. Nature Communications, 15(1). View this article in WRRO
Armitage EP, de Crombrugghe G, Keeley AJ, Senghore E, Camara FE, Jammeh M, Bittaye A, Ceesay H, Ceesay I, Samateh B , Manneh M et al (2024) Streptococcus pyogenes carriage and infection within households in The Gambia: a longitudinal cohort study. The Lancet Microbe.
Hornsby H, Nicols AR, Longet S, Liu C, Tomic A, Angyal A, Kronsteiner B, Tyerman JK, Tipton T, Zhang P , Gallis M et al (2023) Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history. Nature Communications, 14(1). View this article in WRRO
Barnes E, Goodyear CS, Willicombe M, Gaskell C, Siebert S, I de Silva T, Murray SM, Rea D, Snowden JA, Carroll M , Pirrie S et al (2023) SARS-CoV-2-specific immune responses and clinical outcomes after COVID-19 vaccination in patients with immune-suppressive disease. Nature Medicine, 29(7), 1760-1774. View this article in WRRO
Asante IA, Hsu SN, Boatemaa L, Kwasah L, Adusei-Poku M, Odoom JK, Awuku-Larbi Y, Foulkes BH, Oliver-Commey J, Asiedu EK , Parker MD et al (2023) Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis. The Lancet Global Health, 11(7), e1075-e1085.
Keeley AJ, Groves D, Armitage EP, Senghore E, Jagne YJ, Sallah HJ, Drammeh S, Angyal A, Hornsby H, de Crombrugghe G , Smeesters PR et al (2023) Streptococcus pyogenes colonization in children aged 24–59 months in the Gambia: impact of live attenuated influenza vaccine and associated serological responses. The Journal of Infectious Diseases, 228(7), 957-965. View this article in WRRO
Moore SC, Kronsteiner B, Longet S, Adele S, Deeks AS, Liu C, Dejnirattisai W, Reyes LS, Meardon N, Faustini S , Al-Taei S et al (2023) Evolution of long-term vaccine-induced and hybrid immunity in healthcare workers after different COVID-19 vaccine regimens. Med, 4(3), 191-215.e9.
Kanteh A, Jallow HS, Manneh J, Sanyang B, Kujabi MA, Ndure SL, Jarju S, Sey AP, Damilare K D, Bah Y , Sambou S et al (2023) Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022. The Lancet Global Health, 11(3), e414-e424.
Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, de Silva TI, Peacock SJ, Barclay WS, Towers GJ & Robertson DL (2023) SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature Reviews Microbiology, 21(3), 162-177.
Miller PDE, Patel SR, Skinner R, Dignan F, Richter A, Jeffery K, Khan A, Heath PT, Clark A, Orchard K , Snowden JA et al (2023) Joint consensus statement on the vaccination of adult and paediatric haematopoietic stem cell transplant recipients: Prepared on behalf of the British society of blood and marrow transplantation and cellular therapy (BSBMTCT), the Children's cancer and Leukaemia Group (CCLG), and British Infection Association (BIA). Journal of Infection, 86(1), 1-8.
Longet S, Hargreaves A, Healy S, Brown R, Hornsby HR, Meardon N, Tipton T, Barnes E, Dunachie S, Duncan CJA , Klenerman P et al (2022) mRNA vaccination drives differential mucosal neutralizing antibody profiles in naïve and SARS-CoV-2 previously-infected individuals. Frontiers in Immunology, 13. View this article in WRRO
Costa-Martins AG, Mane K, Lindsey BB, Ogava RLT, Castro IC, Jagne YJ, Sallah HJ, Armitage EP, Jarju S, Ahadzie B , Ellis-Watson R et al (2022) Prior upregulation of interferon pathways in the nasopharynx impacts viral shedding following live attenuated influenza vaccine challenge in children. Cell Reports Medicine, 3(2), 100516-100516.
Lindsey BB, Villabona-Arenas CJ, Campbell F, Keeley AJ, Parker MD, Shah DR, Parsons H, Zhang P, Kakkar N, Gallis M , Foulkes BH et al (2022) Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves. Nature Communications, 13(1). View this article in WRRO
Angyal A, Longet S, Moore SC, Payne RP, Harding A, Tipton T, Rongkard P, Ali M, Hering LM, Meardon N , Austin J et al (2022) T-cell and antibody responses to first BNT162b2 vaccine dose in previously infected and SARS-CoV-2-naive UK health-care workers: a multicentre prospective cohort study. The Lancet Microbe, 3(1), e21-e31. View this article in WRRO
Payne RP, Longet S, Austin JA, Skelly DT, Dejnirattisai W, Adele S, Meardon N, Faustini S, Al-Taei S, Moore SC , Tipton T et al (2021) Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine. Cell, 184(23), 5699-5714.e11.
de Silva TI, Liu G, Lindsey BB, Dong D, Moore SC, Hsu NS, Shah D, Wellington D, Mentzer AJ, Angyal A , Brown R et al (2021) The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells. iScience, 103353-103353.
Peno C, Armitage EP, Clerc M, Balcazar Lopez C, Jagne YJ, Drammeh S, Jarju S, Sallah H, Senghore E, Lindsey BB , Camara J et al (2021) The effect of live attenuated influenza vaccine on pneumococcal colonisation densities among children aged 24–59 months in The Gambia: a phase 4, open label, randomised, controlled trial. The Lancet Microbe, 2(12), e656-e665.
Weissman D, Alameh M-G, de Silva T, Collini P, Hornsby H, Brown R, LaBranche CC, Edwards RJ, Sutherland L, Santra S , Mansouri K et al (2020) D614G Spike mutation increases SARS CoV-2 susceptibility to neutralization. Cell Host & Microbe.
Minter A, Hoschler K, Jagne YJ, Sallah H, Armitage E, Lindsey B, Hay JA, Riley S, de Silva TI & Kucharski A (2020) Estimation of seasonal influenza attack rates and antibody dynamics in children using cross-sectional serological data. The Journal of Infectious Diseases. View this article in WRRO
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B , Hastie KM et al (2020) Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. View this article in WRRO
Armitage EP, Senghore E, Darboe S, Barry M, Camara J, Bah S, Marks M, Cerami C, Roca A, Antonio M , Turner CE et al (2019) High burden and seasonal variation of paediatric scabies and pyoderma prevalence in the Gambia : a cross-sectional study. PLOS Neglected Tropical Diseases, 13(10). View this article in WRRO
de Lima DS, Cardozo LE, Maracaja-Coutinho V, Suhrbier A, Mane K, Jeffries D, Silveira ELV, Amaral PP, Rappuoli R, de Silva TI & Nakaya HI (2019) Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. Proceedings of the National Academy of Sciences, 116(34), 17121-17126. View this article in WRRO
Lindsey BB, Jagne YJ, Armitage EP, Singanayagam A, Sallah HJ, Drammeh S, Senghore E, Mohammed NI, Jeffries D, Höschler K , Tregoning JS et al (2019) Effect of a Russian-backbone live-attenuated influenza vaccine with an updated pandemic H1N1 strain on shedding and immunogenicity among children in The Gambia : an open-label, observational, phase 4 study. The Lancet Respiratory Medicine. View this article in WRRO
Lindsey BB, Armitage EP, Kampmann B & de Silva TI (2018) The efficacy, effectiveness, and immunogenicity of influenza vaccines in Africa: a systematic review. The Lancet Infectious Diseases. View this article in WRRO
de Silva TI, Gould V, Mohammed NI, Cope A, Meijer A, Zutt I, Reimerink J, Kampmann B, Hoschler K, Zambon M & Tregoning JS (2017) Comparison of mucosal lining fluid sampling methods and influenza-specific IgA detection assays for use in human studies of influenza immunity. Journal of Immunological Methods.
de Silva TI, Peng Y, Leligdowicz A, Zaidi I, Li L, Griffin H, Blais M-E, Vincent T, Saraiva M, Yindom L-M , van Tienen C et al (2013) Correlates of T-cell–mediated viral control and phenotype of CD8+ T cells in HIV-2, a naturally contained human retroviral infection. Blood, 121(21), 4330-4339.
de Silva TI, Aasa-Chapman M, Cotten M, Hue S, Robinson J, Bibollet-Ruche F, Sarge-Njie R, Berry N, Jaye A, Aaby P , Whittle H et al (2012) Potent Autologous and Heterologous Neutralizing Antibody Responses Occur in HIV-2 Infection across a Broad Range of Infection Outcomes. Journal of Virology, 86(2), 930-946.

All publications

Journal articles

Carreño JM, Meade P, Sogodogo NF, Sano K, Tcheou J, Raskin A, Singh G, Fried M, Loganathan M, Francis B , Bielak D et al (2025) Induction of hemagglutinin stalk reactive antibodies by administration of a live-attenuated influenza virus vaccine to children. iScience, 112893-112893.
Saso A, Kanteh E, Jeffries D, Okoye M, Mohammed N, Kumado M, Roetynck S, Jobe H, Faal A, Roberts E , Gageldonk P et al (2025) The effect of pertussis vaccination in pregnancy on the immunogenicity of acellular or whole-cell pertussis vaccination in Gambian infants (GaPS): a single-centre, randomised, controlled, double-blind, phase 4 trial. The Lancet Infectious Diseases.
Locke TE, Keeley AJ, Laundy N, Keil C, Hamilton J, Pandor A, I de Silva T & Darton TC (2025) Prevalence and risk factors for Staphylococcus aureus colonisation among healthy individuals in low- and middle-income countries: a systematic review and meta-analysis. Journal of Infection. View this article in WRRO
Massai L, Carducci M, Rovetini L, Paterson A, Whitcombe A, McGregor R, Lorenz N, Keeley AJ, de Silva TI, Bennett J , Berlanda Scorza F et al (2025) Characterization of an IL-8 cleavage inhibition assay to determine the functionality of anti-SpyCEP antibodies in human sera. Journal of Immunological Methods, 536, 113786-113786.
Locke T, Siribaddana S, Jayaweera JAAS, Suligoy CM, de Silva TI, Corrigan RM & Darton TC (2024) A prospective cohort study to investigate the transmission and burden of Staphylococcus aureus in Sri Lanka. Microbial Genomics, 10(12).
Colton H, Barratt N, Temperton N, Hornsby H, Angyal A, Grouneva I, Lindsey BB, Kearns P, Barnes E, Goodyear CS , Richter A et al (2024) Greater preservation of SARS‐CoV‐2 neutralising antibody responses following the ChAdOx1‐S (AZD1222) vaccine compared with mRNA vaccines in haematopoietic cell transplant recipients. British Journal of Haematology. View this article in WRRO
Saville TJ, Colton H, Jarju S, Armitage EP, Drammeh S, Tazzyman S, Jagne YJ, Sallah HJ, Senghore E, Evans CM , Darton TC et al (2024) Microfluidic qPCR for detection of 21 common respiratory viruses in children with influenza-like illness. Scientific Reports, 14(1). View this article in WRRO
Wiseman JP, Scarrott JM, Alves-Cruzeiro J, Saffari A, Böger C, Karyka E, Dawes E, Davies AK, Marchi PM, Graves E , Fernandes F et al (2024) Pre-clinical development of AP4B1 gene replacement therapy for hereditary spastic paraplegia type 47. EMBO Molecular Medicine. View this article in WRRO
Galgut O, Ashford F, Deeks A, Ghataure A, Islam M, Sambhi T, Ker YW, Duncan CJA, de Silva TI, Hopkins S , Hall V et al (2024) COVID-19 vaccines are effective at preventing symptomatic and severe infection among healthcare workers: A clinical review. Vaccine: X, 20, 100546-100546.
Hall JN, Bah SY, Khalid H, Brailey A, Coleman S, Kirk T, Hussain N, Tovey M, Chaudhuri RR, Davies S , Tilley L et al (2024) Molecular characterization of Streptococcus pyogenes (StrepA) non-invasive isolates during the 2022–2023 UK upsurge. Microbial Genomics, 10(8).
Sanyang B, de Silva TI, Camara B, Beloum N, Kanteh A, Manneh J, de Steenhuijsen Piters WAA, Bogaert D, Sesay AK & Roca A (2024) Effect of intra-partum azithromycin on gut microbiota development in early childhood: a post hoc analysis of a double-blind randomized trial. iScience, 110626-110626.
Goodyear CS, Patel A, Barnes E, Willicombe M, Siebert S, de Silva TI, Snowden JA, Lim SH, Bowden SJ, Billingham L , Richter A et al (2024) Immunogenicity of third dose COVID-19 vaccine strategies in patients who are immunocompromised with suboptimal immunity following two doses (OCTAVE-DUO): an open-label, multicentre, randomised, controlled, phase 3 trial. The Lancet Rheumatology, 6(6), e339-e351.
Jarju S, Wenlock RD, Danso M, Jobe D, Jagne YJ, Darboe A, Kumado M, Jallow Y, Touray M, Ceesay EA , Gaye H et al (2024) High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia. Nature Communications, 15(1). View this article in WRRO
Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI , Ritter TG et al (2024) A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. Cell Reports Medicine, 101553-101553.
Armitage EP, de Crombrugghe G, Keeley AJ, Senghore E, Camara FE, Jammeh M, Bittaye A, Ceesay H, Ceesay I, Samateh B , Manneh M et al (2024) Streptococcus pyogenes carriage and infection within households in The Gambia: a longitudinal cohort study. The Lancet Microbe.
Liew F, Efstathiou C, Fontanella S, Richardson M, Saunders R, Swieboda D, Sidhu JK, Ascough S, Moore SC, Mohamed N , Nunag J et al (2024) Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease. Nature Immunology, 25(4), 607-621.
Suau Sans M, Manneh M, Ceesay I, Bittaye A, de Crombrugghe G, Keeley AJ, de Silva TI, Palmer J, Armitage EP & Marks M (2024) Health-seeking behaviour and beliefs around sore throat in The Gambia: A qualitative study. PLOS Global Public Health, 4(3). View this article in WRRO
Brittain G, Petrie J, Duffy KEM, Glover R, Hullock K, Papaioannou D, Roldan E, Beecher C, Bursnall M, Ciccarelli O , Coles AJ et al (2024) Efficacy and safety of autologous haematopoietic stem cell transplantation versus alemtuzumab, ocrelizumab, ofatumumab or cladribine in relapsing remitting multiple sclerosis (StarMS): protocol for a randomised controlled trial. BMJ Open, 14(2), e083582-e083582.
Carducci M, Whitcombe A, Rovetini L, Massai L, Keeley AJ, de Silva TI, Bennett J, Berlanda Scorza F, Iturriza M, Moreland NJ , Moriel DG et al (2024) Development and characterization of a hemolysis inhibition assay to determine functionality of anti-Streptolysin O antibodies in human sera. Journal of Immunological Methods, 526, 113618-113618.
Sidhu JK, Siggins MK, Liew F, Russell CD, Uruchurtu ASS, Davis C, Turtle L, Moore SC, Hardwick HE, Oosthuyzen W , Thomson EC et al (2024) Delayed Mucosal Antiviral Responses Despite Robust Peripheral Inflammation in Fatal COVID-19. The Journal of Infectious Diseases, 230(1), e17-e29.
Hall J, Angyal A, Armitage E, Senghore E, Darboe S, Barry M, Camara J, Bah S, Keeley A, McCarthy J , Turner C et al (2023) 44 Quantitative PCR demonstrates the underestimated burden of Streptococcus pyogenes as a cause of paediatric pyoderma in The Gambia. Clinical Infection in Practice, 20, 100304-100304.
Armitage EP, Keeley AJ, de Crombrugghe G, Senghore E, Camara FE, Jammeh M, Bittaye A, Ceesay H, Ceesay I, Samateh B , Manneh M et al (2023) Streptococcus pyogenes carriage acquisition, persistence and transmission dynamics within households in The Gambia (SpyCATS): protocol for a longitudinal household cohort study. Wellcome Open Research, 8. View this article in WRRO
Hornsby H, Nicols AR, Longet S, Liu C, Tomic A, Angyal A, Kronsteiner B, Tyerman JK, Tipton T, Zhang P , Gallis M et al (2023) Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history. Nature Communications, 14(1). View this article in WRRO
Barnes E, Goodyear CS, Willicombe M, Gaskell C, Siebert S, I de Silva T, Murray SM, Rea D, Snowden JA, Carroll M , Pirrie S et al (2023) SARS-CoV-2-specific immune responses and clinical outcomes after COVID-19 vaccination in patients with immune-suppressive disease. Nature Medicine, 29(7), 1760-1774. View this article in WRRO
Asante IA, Hsu SN, Boatemaa L, Kwasah L, Adusei-Poku M, Odoom JK, Awuku-Larbi Y, Foulkes BH, Oliver-Commey J, Asiedu EK , Parker MD et al (2023) Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis. The Lancet Global Health, 11(7), e1075-e1085.
Panca M, Blackstone J, Stirrup O, Cutino-Moguel M-T, Thomson E, Peters C, Snell LB, Nebbia G, Holmes A, Chawla A , Machin N et al (2023) Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals. Journal of Hospital Infection.
Williams DM, Hornsby HR, Shehata OM, Brown R, Gallis M, Meardon N, Newman TAH, Plowright M, Zafred D, Shun-Shion ASM , Hodder AJ et al (2023) Establishing SARS-CoV-2 membrane protein-specific antibodies as a valuable serological target via high-content microscopy. iScience, 26(7), 107056-107056.
Keeley AJ, Groves D, Armitage EP, Senghore E, Jagne YJ, Sallah HJ, Drammeh S, Angyal A, Hornsby H, de Crombrugghe G , Smeesters PR et al (2023) Streptococcus pyogenes colonization in children aged 24–59 months in the Gambia: impact of live attenuated influenza vaccine and associated serological responses. The Journal of Infectious Diseases, 228(7), 957-965. View this article in WRRO
Dijokaite-Guraliuc A, Das R, Zhou D, Ginn HM, Liu C, Duyvesteyn HME, Huo J, Nutalai R, Supasa P, Selvaraj M , de Silva TI et al (2023) Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Cell Reports, 42(4).
Goldswain H, Dong X, Penrice-Randal R, Alruwaili M, Shawli GT, Prince T, Williamson MK, Raghwani J, Randle N, Jones B , Donovan-Banfield I et al (2023) The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection. Genome Biology, 24(1).
Moore SC, Kronsteiner B, Longet S, Adele S, Deeks AS, Liu C, Dejnirattisai W, Reyes LS, Meardon N, Faustini S , Al-Taei S et al (2023) Evolution of long-term vaccine-induced and hybrid immunity in healthcare workers after different COVID-19 vaccine regimens. Med, 4(3), 191-215.e9.
Kanteh A, Jallow HS, Manneh J, Sanyang B, Kujabi MA, Ndure SL, Jarju S, Sey AP, Damilare K D, Bah Y , Sambou S et al (2023) Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022. The Lancet Global Health, 11(3), e414-e424.
Turtle L, Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A , de Silva TI et al (2023) Outcome of COVID-19 in hospitalised immunocompromised patients: an analysis of the WHO ISARIC CCP-UK prospective cohort study. PLoS Medicine, 20(1).
Armitage EP, Keeley AJ, de Crombrugghe G, Senghore E, Camara FE, Jammeh M, Bittaye A, Ceesay H, Ceesay I, Samateh B , Manneh M et al (2023) Streptococcus pyogenes carriage acquisition, persistence and transmission dynamics within households in The Gambia (SpyCATS): protocol for a longitudinal household cohort study. Wellcome Open Research, 8.
Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, de Silva TI, Peacock SJ, Barclay WS, Towers GJ & Robertson DL (2023) SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature Reviews Microbiology, 21(3), 162-177.
Liew F, Talwar S, Cross A, Willett BJ, Scott S, Logan N, Siggins MK, Swieboda D, Sidhu JK, Efstathiou C , Moore SC et al (2023) SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination. eBioMedicine, 87.
Miller PDE, Patel SR, Skinner R, Dignan F, Richter A, Jeffery K, Khan A, Heath PT, Clark A, Orchard K , Snowden JA et al (2023) Joint consensus statement on the vaccination of adult and paediatric haematopoietic stem cell transplant recipients: Prepared on behalf of the British society of blood and marrow transplantation and cellular therapy (BSBMTCT), the Children's cancer and Leukaemia Group (CCLG), and British Infection Association (BIA). Journal of Infection, 86(1), 1-8.
Huo J, Dijokaite-Guraliuc A, Liu C, Zhou D, Ginn HM, Das R, Supasa P, Selvaraj M, Nutalai R, Tuekprakhon A , Duyvesteyn HME et al (2022) A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75. Cell Reports, 111903-111903.
Colton H, Parker MD, Stirrup O, Blackstone J, Loose M, McClure CP, Roy S, Williams C, McLeod J, Smith D , Taha Y et al (2022) Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: Analysis of data from the COG-UK HOCI study. Journal of Hospital Infection.
Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K , Saluja T et al (2022) Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study. eLife, 11.
Longet S, Hargreaves A, Healy S, Brown R, Hornsby HR, Meardon N, Tipton T, Barnes E, Dunachie S, Duncan CJA , Klenerman P et al (2022) mRNA vaccination drives differential mucosal neutralizing antibody profiles in naïve and SARS-CoV-2 previously-infected individuals. Frontiers in Immunology, 13. View this article in WRRO
Boswell MT, Nazziwa J, Kuroki K, Palm A, Karlson S, Månsson F, Biague A, da Silva ZJ, Onyango CO, de Silva TI , Jaye A et al (2022) Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS. Virus Evolution, 8(2).
Sanyang B, de Silva TI, Kanteh A, Bojang A, Manneh J, de Steenhuijsen Piters WAA, Peno C, Bogaert D, Sesay AK & Roca A (2022) Effect of intra-partum azithromycin on the development of the infant nasopharyngeal microbiota: a post hoc analysis of a double-blind randomized trial. eBioMedicine, 83.
Wilkinson SAJ, Richter A, Casey A, Osman H, Mirza JD, Stockton J, Quick J, Ratcliffe L, Sparks N, Cumley N , Poplawski R et al (2022) Recurrent SARS-CoV-2 mutations in immunodeficient patients. Virus Evolution, 8(2).
Smallman-Raynor MR & Cliff AD (2022) Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021. Epidemiology and Infection, 150.
Parker MD, Stewart H, Shehata OM, Lindsey BB, Shah DR, Hsu S, Keeley AJ, Partridge DG, Leary S, Cope A , State A et al (2022) Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections.. Commun Biol, 5(1), 666.
Colton H, Hodgson D, Hornsby H, Brown R, Mckenzie J, Bradley KL, James C, Lindsey BB, Birch S, Marsh L , Wood S et al (2022) Risk factors for SARS-CoV-2 seroprevalence following the first pandemic wave in UK healthcare workers in a large NHS Foundation Trust. Wellcome Open Research, 6, 220.
Relph KA, Russell CD, Fairfield CJ, Turtle L, de Silva TI, Siggins MK, Drake TM, Thwaites RS, Abrams S, Moore SC , Hardwick HE et al (2022) Procalcitonin Is Not a Reliable Biomarker of Bacterial Coinfection in People With Coronavirus Disease 2019 Undergoing Microbiological Investigation at the Time of Hospital Admission. Open Forum Infectious Diseases, 9(5).
Blackstone J, Stirrup O, Mapp F, Panca M, Copas A, Flowers P, Hockey L, Price J, Partridge D, Peters C , de Silva T et al (2022) Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals. BMJ Open, 12(4), e052514-e052514.
Locke T, Parsons H, Briffa N, Stott M, de Silva TI & Darton TC (2022) A bundle of infection control measures reduces post-operative sternal wound infection due to Staphylococcus aureus but not Gram-negative bacteria: a retrospective analysis of 6,903 patient episodes. Journal of Hospital Infection.
Tomic A, Skelly DT, Ogbe A, O’Connor D, Pace M, Adland E, Alexander F, Ali M, Allott K, Azim Ansari M , Belij-Rammerstorfer S et al (2022) Divergent trajectories of antiviral memory after SARS-CoV-2 infection. Nature Communications, 13(1).
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van Tienen C, McConkey SJ, de Silva TI, Cotten M, Kaye S, Sarge-Njie R, da Costa C, Gonçalves N, Parker J, Vincent T , Jaye A et al (2011) Maternal proviral load and vertical transmission of Human T cell Lymphotropic Virus type 1 in Guinea-Bissau. Retrovirology, 8(S1).
de Silva T & Weiss RA (2010) HIV-2 goes global: An unaddressed issue in Indian anti-retroviral programmes. Indian Journal of Medical Research, 132(12), 660-662.
de Silva TI, Turner R, Hué S, Trikha R, van Tienen C, Onyango C, Jaye A, Foley B, Whittle H, Rowland-Jones SL & Cotten M (2010) HIV-1 subtype distribution in the Gambia and the significant presence of CRF49_cpx, a novel circulating recombinant form. Retrovirology, 7(1). View this article in WRRO
Onyango CO, Leligdowicz A, Yokoyama M, Sato H, Song H, Nakayama EE, Shioda T, de Silva T, Townend J, Jaye A , Whittle H et al (2010) HIV-2 capsids distinguish high and low virus load patients in a West African community cohort. Vaccine, 28, B60-B67.
de Silva TI, van Tienen C, Rowland-Jones SL & Cotten M (2010) Dual infection with HIV-1 and HIV-2: double trouble or destructive interference?. HIV Therapy, 4(3), 305-323.
Jallow S, Vincent T, Leligdowicz A, De Silva T, Van Tienen C, Alabi A, Sarge‐Njie R, Aaby P, Corrah T, Whittle H , Jaye A et al (2009) Presence of a Multidrug‐Resistance Mutation in an HIV‐2 Variant Infecting a Treatment‐Naive Individual in Caio, Guinea Bissau. Clinical Infectious Diseases, 48(12), 1790-1793.
de Silva TI, Cotten M & Rowland-Jones SL (2008) HIV-2: the forgotten AIDS virus. Trends in Microbiology, 16(12), 588-595.
Stone B, Patel TG, De Silva TI, Green ST & Chapman ALN (2008) Successful treatment of actinomyces brain abscesses using once daily parenteral ceftriaxone in an outpatient setting: a case series. Journal of Infection, 57(5), 426-427.
Rowland-Jones S & de Silva T (2008) Resisting Immune Exhaustion in HIV-1 Infection. PLoS Medicine, 5(5), 721-724. View this article in WRRO
de Silva T, Kudesia G, Joall A, Whittaker D, Ryan C & Davies S (2007) The significance of low-positive MOTA scoresin the BD-ProbeTec-Strand Displacement Amplification test for the detection of Neisseria gonorrhoeae. Journal of Infection, 55(3), e67-e68.
de Silva TI, Post FA, Griffin MD & Dockrell DH (2007) HIV-1 Infection and the Kidney: An Evolving Challenge in HIV Medicine. Mayo Clinic Proceedings, 82(9), 1103-1116. View this article in WRRO
de Silva T, Thickett K & Winstanley T (2007) Screening for Extended-Spectrum Beta Lactamase producing gram-negative organisms: can the sensitivity and specificity of current guidance be improved?. Journal of Infection, 55(3), e58-e58.
de Silva TI, Cope A, Goepel J & Greig JM (2007) The use of adjuvant granulocyte-macrophage colony-stimulating factor in HIV-related disseminated atypical mycobacterial infection. Journal of Infection, 54(4), e207-e210.
de Silva T, Kudesia G, Joall A, Whittaker D, Davies S & Ryan C (2006) Significance of Low Positive Scores Obtained with a Method Other than Acceleration in the BDProbeTec-Strand Displacement Amplification Test for Detection of Neisseria gonorrhoeae. Journal of Clinical Microbiology, 44(12), 4628-4629.
Raychaudhuri M, de Silva T, Connor S & Poulton M (2006) Haemorrhagic acute disseminated encephalomyelitis: an unusual case of blindness in an HIV-infected patient. International Journal of STD & AIDS, 17(7), 495-497.
Chapman AL, Kudesia G, McKendrick MW & de Silva TI (2006) WITHDRAWN: Ongoing queries: Interpretation of serology in asymptomatic or atypical chronic Q fever. Journal of Infection.
Evans CM, Mudhar H, Rennie I, Green ST & de Silva TI (2006) WITHDRAWN: Spontaneous resolution of endophthalmitis due to nocardia species. Journal of Infection.
de Silva T, Chapman A, Kudesia G & McKendrick M (2006) Ongoing queries: Interpretation of serology in asymptomatic or atypical chronic Q fever. Journal of Infection, 52(4), e113-e116.
de Silva T (2005) Ventriculitis and hydrocephalus: an unusual presentation of toxoplasmosis in an adult with human immunodeficiency virus. Journal of Neurology, Neurosurgery & Psychiatry, 76(8), 1074-1074.
de Silva T (2005) HIV infection associated with Strongyloides stercoralis colitis resulting in Streptococcus bovis bacteraemia and meningitis. Sexually Transmitted Infections, 81(3), 276-277.
Jagne YJ, Jobe D, Darboe A, Danso M, Barratt N, Gomez M, Wenlock R, Jarju S, Sylva EL, Touray AF , Toure F et al () Compartmentalised mucosal and blood immunity to SARS-CoV-2 is associated with high seroprevalence before the Delta wave in Africa. Communications Medicine, 5(1).
de Crombrugghe G, Armitage EP, Keeley AJ, Senghore E, Camara F, Jammeh M, Bittaye A, Ceesay H, Ceesay I, Samateh B , Manneh M et al () Household molecular epidemiology of Streptococcus pyogenes carriage and infection in The Gambia. The Journal of Infectious Diseases.
Chen J-L, Wang B, Lu Y, Antoun E, Bird O, Drennan PG, Yin Z, Liu G, Yao X, Pidoux M , Bates A et al () T cell memory response to MPXV infection exhibits greater effector function and migratory potential compared to MVA-BN vaccination. Nature Communications, 16(1).
Mellors J, Dhaliwal R, Longet S, Tipton T, McInnes I, Siebert S, Kearns P, Rea D, Cook G, Willicombe M , Thomas D et al () Complement-mediated enhancement of SARS-CoV-2 antibody neutralisation potency in vaccinated individuals. Nature Communications, 16(1).
Hall JN, Armitage EP, Senghore E, Darboe S, Barry M, Camara J, Bah S, Keeley AJ, McCarthy JS, Smeesters P , Turner CE et al () Molecular methods enhance the detection of pyoderma-related Streptococcus pyogenes and emm-type distribution in children. The Journal of Infectious Diseases.
Brudenell EL, Pohare MB, Zafred D, Phipps J, Hornsby HR, Darby J, Dai J, Liggett E, Cain K, Barran P , de Silva TI et al () Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in Escherichia coli. Biochemical Journal.
Ali M, Longet S, Neale I, Rongkard P, Chowdhury FUH, Hill J, Brown A, Laidlaw S, Tipton T, Hoque A , Hassan N et al () Obesity differs from diabetes mellitus in antibody and T-cell responses post-COVID-19 recovery. Clinical and Experimental Immunology.
Michael BD, Dunai C, Needham EJ, Tharmaratnam K, Williams R, Huang Y, Boardman SA, Clark JJ, Sharma P, Subramaniam K , Wood GK et al () Author Correction: Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses. Nature Communications, 15(1).
Gupta V, Kariotis S, Rajab MD, Errington N, Alhathli E, Jammeh E, Brook M, Meardon N, Collini P, Cole J , Wild JM et al () Unsupervised machine learning to investigate trajectory patterns of COVID-19 symptoms and physical activity measured via the MyHeart Counts App and smart devices. npj Digital Medicine, 6(1).
Neale I, Ali M, Kronsteiner B, Longet S, Abraham P, Deeks AS, Brown A, Moore SC, Stafford L, Dobson SL , Plowright M et al () CD4+ and CD8+ T cells and antibodies are associated with protection against Delta vaccine breakthrough infection: a nested case-control study within the PITCH study. mBio.
Bah SY, Kujabi MA, Darboe S, Kebbeh N, Kebbeh BFK, Kanteh A, Bojang R, Lawn JE, Kampmann B, Sesay AK , de Silva TI et al () Acquisition and carriage of genetically diverse multi-drug resistant gram-negative bacilli in hospitalised newborns in The Gambia. Communications Medicine, 3(1).
Jarju S, Senghore E, Brotherton H, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM , Saidy B et al () Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Research, 6, 148-148.
Bah SY, Keeley AJ, Armitage EP, Khalid H, Chaudhuri RR, Senghore E, Manneh J, Tilley L, Marks M, Darboe S , Sesay AK et al () Genomic Characterization of Skin and Soft Tissue Streptococcus pyogenes Isolates from a Low-Income and a High-Income Setting. mSphere.
Jarju S, Senghore E, Brotherton H, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM , Saidy B et al () Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Research, 6, 148-148.
Keeley AJ, Carducci M, Massai L, Pizza M, de Silva TI, G. Moriel D & Rossi O () Development and Characterisation of a Four-Plex Assay to Measure Streptococcus pyogenes Antigen-Specific IgG in Human Sera. Methods and Protocols, 5(4), 55-55.
Shankar S, Beckett J, Tipton T, Ogbe A, Kasanyinga M, Dold C, Lumley S, Dengu F, Rompianesi G, Elgilani F , Longet S et al () SARS-CoV-2-Specific T Cell Responses Are Not Associated with Protection against Reinfection in Hemodialysis Patients. Journal of the American Society of Nephrology, ASN.2021121587-ASN.2021121587.
Wright DW, Harvey WT, Hughes J, Cox M, Peacock TP, Colquhoun R, Jackson B, Orton R, Nielsen M, Hsu NS , Harrison EM et al () Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer. Virus Evolution.
Colton H, Hodgson D, Hornsby H, Brown R, Mckenzie J, Bradley KL, James C, Lindsey BB, Birch S, Marsh L , Wood S et al () Risk factors for SARS-CoV-2 seroprevalence following the first pandemic wave in UK healthcare workers in a large NHS Foundation Trust. Wellcome Open Research, 6, 220-220.
Jabang S, Erhart A, Darboe S, Baldeh A-K, Delforge V, Watson G, Foster-Nyarko E, Salaudeen R, Lawal B, Mackenzie G , Botteaux A et al () Molecular Epidemiology of Group A Streptococcus Infections in The Gambia. Vaccines, 9(2), 124-124.
Peng Y, Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C , Lopez-Camacho C et al () Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients.
Lindsey B, Jagne YJ, Armitage E, Singanayagam A, Sallah H, Drammeh S, Senghore E, Mohammed N, Jeffries D, Höschler K , Tregoning J et al () The impact of an updated pandemic H1N1 strain on shedding and immunogenicity to Russian-backbone live attenuated influenza vaccine among children in The Gambia: an open-label, observational, phase 4 study.. The Lancet Respiratory Medicine.
Rowland-Jones S & de Silva T () Correction: Resisting Immune Exhaustion in HIV-1 Infection. PLoS Medicine, 5(6), e134-e134.
de Silva T, Evans C, Mudhar HS, Rennie I & Green ST () Isolated endogenous endophthalmitis secondary to Nocardia spp in an immunocompetent adult. Journal of Clinical Pathology, 59(11), 1226-1226.
Parker MD, Lindsey BB, Leary S, Gaudieri S, Chopra A, Wyles M, Angyal A, Green LR, Parsons P, Tucker RM , Brown R et al () periscope: sub-genomic RNA identification in SARS-CoV-2 ARTIC Network Nanopore Sequencing Data.
Williams EJ, Mair L, de Silva TI, Green DJ, House P, Cawthron K, Gillies C, Wigfull J, Parsons H & Partridge DG () Routine measurement of serum procalcitonin allows antibiotics to be safely withheld in patients admitted to hospital with SARS-CoV-2 infection.. View this article in WRRO
Lindsey BB, Höschler K & de Silva TI () Complexities in predicting the immunogenicity of live attenuated influenza vaccines. Clinical Infectious Diseases. View this article in WRRO
Jeewandara C, Jayathilaka D, Ranasinghe D, Hsu NS, Ariyaratne D, Jayadas TT, Panambara Arachchige DM, Lindsey BB, Gomes L, Parker MD , Wijewickrama A et al () Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka. Frontiers in Microbiology, 12.
Shankar S, Beckett J, Tipton T, Ogbe A, Kasanyinga M, Dold C, Lumley S, Dengu F, Rompianesi G, Elgilani F , Longet S et al () Poor Antibody Responses to SARS-CoV-2 Infection or Vaccination Are Associated With High Re-Infection Rates in Haemodialysis and Renal Transplant Patients.
Kearns P, Siebert S, willicombe M, Gaskell C, Kirkham A, Pirrie S, Bowden S, Magwaro S, Hughes A, Lim Z , Dimitriadis S et al () Examining the Immunological Effects of COVID-19 Vaccination in Patients with Conditions Potentially Leading to Diminished Immune Response Capacity – The OCTAVE Trial.
Russell CD, Fairfield CJ, Drake TM, Turtle L, Seaton RA, Wootton DG, Sigfrid L, Harrison EM, Docherty A, de Silva TI , Egan C et al () Co-Infections, Secondary Infections, and Antimicrobial Usage in Hospitalised Patients with COVID-19 from the ISARIC WHO CCP-UK Study: A Prospective, Multicentre Cohort Study.
Costa-Martins AG, Mane K, Lindsey BB, Ogava RLT, Castro Í, Jagne YJ, Sallah H, Armitage E, Ahadzie B, Ellis-Watson R , Tregoning JS et al () Pre-Existing Upregulation of Interferon Pathways in the Nasopharynx Impacts Viral Shedding Following Live Attenuated Influenza Vaccine Challenge in Children.
Williams DM, Hornsby H, Shehata OM, Brown R, Gallis M, Meardon N, Newman TAH, Plowright M, Zafred D, Shun-Shion ASM , Hodder AJ et al () Characterisation of SARS-CoV-2 Membrane Protein-Specific Antibodies as an Additional Serological Target Following COVID-19 Infections Identified Through a High Content Microscopy-Based Platform.
Peno C, Jagne YJ, Clerc M, Balcazar CL, Armitage E, Sallah H, Drammeh S, Senghore E, Goderski G, von Tol S , Meijer A et al () Interactions between Live Attenuated Influenza Vaccine and the Nasopharyngeal Microbiota Among Children Aged 24-59 Months in the Gambia: A Phase IV Open Label, Randomised Controlled Clinical Trial.
Armitage E, de Crombrugghe G, Keeley AJ, Senghore E, Camara FE, Jammeh M, Bittaye A, Ceesay H, Ceesay I, Samateh B , Manneh M et al () Streptococcus Pyogenes Carriage and Infection within Households in the Gambia: A Longitudinal Cohort Study.
Jarju S, Wenlock R, Danso M, Jobe D, Jagne YJ, Darboe A, Kumado M, Jallow Y, Touray M, Ceesay EA , Gaye H et al () SARS-CoV-2 Incidence and Re-Infection During Delta and Omicron Ba.1 Waves in the Gambia: Results from a Prospective Household Cohort Study in a Population with Low SARS-CoV-2 Vaccine Coverage.
Goodyear CS, Patel A, Barnes E, willicombe M, Siebert S, de Silva TI, Snowden JA, Lim S, Bowden S, Billingham LJ , Richter AG et al () Immunogenicity of SARSCoV2 Third Dose Vaccine Strategies in Immunocompromised Patients with Suboptimal Immunity Following Two Doses (OCTAVE-DUO): An Open-Label, Multi-Centre, Randomised, Controlled Phase III Trial.
Armitage E, Senghore E, Camara FE, Jarju S, Jagne S, Ceesay E, Fornah Darboe F, de Crombrugghe G, Keeley AJ, Hall JN , Angyal A et al () Evaluating Clinical Decision Rules and Rapid Diagnostic Tests for the Diagnosis of Streptococcus Pyogenes Pharyngitis in Gambian Children: A Diagnostic Accuracy Study.

Chapters

Abrahamian FM, Aldape MJ, Aldasoro E, Allen UD, Al-Sum H, Anadkat MJ, Anders K, Angelakis E, Angus BJ, Antoniadou A , Arena F et al (2017) List of Contributors, Infectious Diseases (pp. xv-xxxvi). Elsevier
De Silva TI & Green ST (2017) Managing the Patient with Recurring Skin Infections, Infectious Diseases (pp. 133-135.e1). Elsevier
Moysi E, de Silva T & Rowland-Jones S (2012) Immune Mechanisms of Viral Control in HIV-2 Infection, Models of Protection Against HIV/SIV (pp. 293-315). Elsevier
Ball TB, Barré-Sinoussi F, Biasin M, Blankson JN, Broliden K, Buckheit RW, Card CM, Clerici M, de Silva T, Fellay J , Fowke KR et al (2012) Contributors, Models of Protection Against HIV/SIV (pp. xi-xii). Elsevier

Conference proceedings papers

Miller PDE, de Silva T, Leonard H, Goddard K, Anthias C, Hoschler K, Peggs K, Madrigal A & Snowden JA (2017) Viral microneutralization assay to determine seasonal influenza vaccine immunogenicity in the first year post reduced intensity conditioning allogeneic HSCT. BONE MARROW TRANSPLANTATION, Vol. 52 (pp S269-S270)
Miller PDE, de Silva T, Skinner R, Gilleece M, Peniket A, Hamblin A, Greenfield D, Anthias C, Peggs K, Madrigal A , Snowden JA et al (2016) Routine Vaccination Programme (RVP) Practice after Adult and Paediatric Allogeneic Haematopoietic Stem Cell Transplant (HSCT): A British Society of Blood and Marrow Transplantation (BSBMT) Survey of UK NHS-Based Programmes. BONE MARROW TRANSPLANTATION, Vol. 51 (pp S400-S401)
Meiring J, De Silva T & Snowden J (2015) A study of adherence to a vaccination schedule following adult allogenic haematopoietic stem cell transplants in UK transplant centre. BONE MARROW TRANSPLANTATION, Vol. 50 (pp S203-S204)

Preprints

Hodgson D, Hay J, Jarju S, Jobe D, Wenlock R, de Silva TI & Kucharski AJ (2025) serojump: A Bayesian tool for inferring infection timing and antibody kinetics from longitudinal serological data, Cold Spring Harbor Laboratory.
Keeley AJ, Camara FE, Armitage E, de Crombrugghe G, Sillah J, Fofana ML, Rollinson V, Senghore E, Jammeh M, Whitcombe AL , Bittaye A et al (2025) Early life serological profiles and the development of natural protective humoral immunity toStreptococcus pyogenesin a high burden setting, Cold Spring Harbor Laboratory.
Hao S, Tomic I, Lindsey BB, Jagne YJ, Hoschler K, Meijer A, Carreno Quiroz JM, Meade P, Sano K, Peno C , Costa Martins AG et al (2025) Integrative Mapping of Pre-existing Immune Landscapes for Vaccine Response Prediction, Cold Spring Harbor Laboratory.
JAGNE YJ, Jobe D, Darboe A, Danso M, Barratt N, Gomez M, Wenlock R, Jarju S, Sylva E, Touray AF , Toure F et al (2024) Compartmentalised mucosal and blood immunity to SARS-CoV-2 associated with high seroprevalence before Delta wave in Africa, Springer Science and Business Media LLC.
Hall JN, Bah SY, Khalid H, Brailey A, Coleman S, Kirk T, Hussain N, Tovey M, Chaudhuri RR, Davies S , Tilley L et al (2024) Molecular characterisation ofStreptococcus pyogenes(StrepA) non-invasive isolates during the 2022-23 UK upsurge, Cold Spring Harbor Laboratory.
Hall JN, Armitage EP, Senghore E, Darboe S, Barry M, Camara J, Bah S, Keeley AJ, McCarthy JS, Smeesters P , Turner CE et al (2024) Molecular methods enhance the detection of pyoderma-related Streptococcus pyogenes and emm-type distribution in children, Cold Spring Harbor Laboratory.
Brudenell EL, Pohare MB, Zafred D, Phipps J, Hornsby HR, Darby J, Dai J, Liggett E, Cain K, Barran PE , de Silva TI et al (2024) Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in Escherichia coli, Cold Spring Harbor Laboratory.
Openshaw P, Liew F, Efstathiou C, Fontanella S, Richardson M, Saunders R, Swieboda D, Sidhu J, Ascough S, Moore S , Mohamed N et al (2023) Large scale phenotyping of long COVID inflammation reveals mechanistic subtypes of disease after COVID-19 hospitalisation, Research Square Platform LLC.
Ali M, Longet S, Neale I, Rongkard P, Chowdhury FUH, Hill J, Brown A, Laidlaw S, Tipton T, Hoque A , Hassan N et al (2023) Obesity Differs from Diabetes Mellitus in Antibody and T Cell Responses Post COVID-19 Recovery, Cold Spring Harbor Laboratory.
Liew F, Efstathiou C, Fontanella S, Richardson M, Saunders R, Swieboda D, Sidhu JK, Ascough S, Moore SC, Mohamed N , Nunag J et al (2023) Large scale phenotyping of long COVID inflammation reveals mechanistic subtypes of disease, Cold Spring Harbor Laboratory.
Neale I, Ali M, Kronsteiner B, Longet S, Abraham P, Deeks AS, Brown A, Moore SC, Stafford L, Dobson SL , Plowright M et al (2023) CD4+ and CD8+ T cell and antibody correlates of protection against Delta vaccine breakthrough infection: A nested case-control study within the PITCH study, Cold Spring Harbor Laboratory.
Hornsby H, Nicols AR, Longet S, Liu C, Tomic A, Angyal A, Kronsteiner B, Tyerman JK, Tipton T, Zhang P , Gallis Ramalho M et al (2023) Omicron BA.1/BA.2 infections in triple-vaccinated individuals enhance a diverse repertoire of mucosal and blood immune responses, Cold Spring Harbor Laboratory.
Bah SY, Kujabi MA, Darboe S, Kebbeh N, Kebbeh BFK, Kanteh A, Bojang R, Lawn JE, Kampmann B, Abdul Karim S , de Silva TI et al (2022) EARLY ACQUISITION AND CARRIAGE OF GENETICALLY DIVERSE MULTI-DRUG RESISTANT GRAM-NEGATIVE BACILLI IN HOSPITALISED SMALL VULNERABLE NEWBORNS IN THE GAMBIA, Cold Spring Harbor Laboratory.
Liew F, Talwar S, Cross A, Willett BJ, Scott S, Logan N, Siggins MK, Swieboda D, Sidhu JK, Efstathiou C , Moore SC et al (2022) Nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination, Cold Spring Harbor Laboratory.
Kanteh A, Jallow HS, Manneh J, Sanyang B, Kujabi MA, Ndure SL, Jarju S, Sey AP, Damilare DK, Bah Y , Sambou S et al (2022) Genomic epidemiology of SARS-CoV-2 infections in The Gambia, March 2020 to Jan 2022, Cold Spring Harbor Laboratory.
Peto L, Rodger G, Carter DP, Osman KL, Yavuz M, Johnson K, Raza M, Parker MD, Wyles MD, Andersson M , Justice A et al (2020) Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing, Cold Spring Harbor Laboratory.
Leary S, Gaudieri S, Parker MD, Chopra A, James I, Pakala S, Alves E, John M, Lindsey BB, Keeley AJ , Rowland-Jones SL et al (2020) Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level, Cold Spring Harbor Laboratory.
Armitage EP, Senghore E, Darboe S, Barry M, Camara J, Bah S, Marks M, Cerami C, Roca A, Antonio M , Turner CE et al (2019) High burden and seasonal variation of paediatric scabies and pyoderma prevalence in The Gambia: a cross-sectional study, Cold Spring Harbor Laboratory.
Jarju S, Senghore E, Brotherton H, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang M , Saidy B et al () Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia, Cold Spring Harbor Laboratory.
Turtle L, Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A , de Silva TI et al () Outcome of COVID-19 in hospitalised immunocompromised patients: an analysis of the WHO ISARIC CCP-UK prospective cohort study, Cold Spring Harbor Laboratory.
Flowers P, McLeod J, Mapp F, Stirrup O, Blackstone J, Snell LB, Peters C, Thomson E, Holmes A, Price J , Partridge D et al () How acceptable is rapid whole genome sequencing for infectious disease management in hospitals? Perspectives of those involved in managing nosocomial SARS-CoV-2, Cold Spring Harbor Laboratory.
Moore SC, Kronsteiner B, Longet S, Adele S, Deeks AS, Liu C, Dejnirattisai W, Silva Reyes L, Meardon N, Faustini S , Al-Taei S et al () Evolution of long-term hybrid immunity in healthcare workers after different COVID-19 vaccination regimens: a longitudinal observational cohort study, Cold Spring Harbor Laboratory.
Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K , Saluja T et al () Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study, Cold Spring Harbor Laboratory.
Phillips E, Adele S, Malone T, Deeks A, Stafford L, Dobson SL, Amini A, Skelly D, Eyre D, Jeffery K , Conlon CP et al () Comparison of two T cell assays to evaluate T cell responses to SARS-CoV-2 following vaccination in naïve and convalescent healthcare workers, Cold Spring Harbor Laboratory.
Smallman-Raynor MR & Cliff AD () Spatial Growth Rate of Emerging SARS-CoV-2 Lineages in England, September 2020–December 2021, Cold Spring Harbor Laboratory.
Asante I, Nienyun Hsu S, Boatemaa L, Kwash L, Aduesi-Poku M, Odom JK, Awuku-Larbi Y, Foulkes BH, Oliver-Commey J, Asiedu E , Parker M et al () Genomic Surveillance of SARS-CoV-2 in Ghana: Leveraging an Integrated National Influenza and SARS-CoV-2 Platform.
Moore S, Kronsteiner B, Longet S, Adele S, Deeks A, Liu C, Dejnirattisai W, Silva Reyes L, Meardon N, Faustini S , Al-Taei S et al () Evolution of Long-Term Hybrid Immunity in Healthcare Workers after Different Covid-19 Vaccination Regimens: A Longitudinal Observational Cohort Study.
Williams DM, Hornsby H, Shehata OM, Brown R, Zafred D, Shun-Shion ASM, Hodder AJ, Bliss D, Metcalfe A, Edgar JR , Gordon DE et al () A high content microscopy-based platform for detecting antibodies to the nucleocapsid, spike and membrane proteins of SARS-CoV-2, Cold Spring Harbor Laboratory.
Kartsonaki C () Characteristics and outcomes of an international cohort of 400,000 hospitalised patients with Covid-19, Cold Spring Harbor Laboratory.
Bah SY, Keeley AJ, Armitage EP, Khalid H, Chaudhuri RR, Senghore E, Manneh J, Tilley L, Marks M, Darboe S , Sesay AK et al () Comparative genomic analysis of skin and soft tissue Streptococcus pyogenes isolates from low- and high-income settings, Cold Spring Harbor Laboratory.
Hodgson D, Colton H, Hornsby H, Brown R, Mckenzie J, Bradley KL, James C, Lindsey BB, Birch S, Marsh L , Wood S et al () Risk factors for SARS-CoV-2 seroprevalence following the first pandemic wave in UK healthcare workers in a large NHS Foundation Trust.
Stirrup OT, Boshier FAT, Venturini C, Guerra-Assunção JA, Alcolea-Medina A, Becket AH, Charalampous T, da Silva Filipe A, Glaysher S, Khan T , Kulasegara-Shylini R et al () SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men, Cold Spring Harbor Laboratory.
Tomic* A, Skelly* DT, Ogbe* A, O'Connor* D, Pace M, Adland E, Alexander F, Ali M, Allott K, Ansari MA , Sandra Belij-Rammerstorfer et al () Divergent trajectories of antiviral memory after SARS-Cov-2 infection, Research Square Platform LLC.
de Silva TI, Liu G, Lindsey BB, Dong D, Shah D, Mentzer AJ, Angyal A, Brown R, Parker MD, Yin Z , Yao X et al () The Impact of Viral Mutations on Recognition by SARS-CoV-2 Specific T-Cells.
Jeewandara C, Jayathilaka D, Ranasinghe D, Hsu NS, Ariyaratne D, Jayadas TT, Madushanka D, Lindsey BB, Gomes L, Parker MD , Wijewickrama A et al () Genomic and epidemiological analysis of SARS-CoV-2 viruses in Sri Lanka, Cold Spring Harbor Laboratory.
Blackstone J, Stirrup O, Mapp F, Panca M, Copas A, Flowers P, Hockey L, Price J, Partridge D, Peters C , de Silva T et al () Protocol for the COG-UK hospital onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in United Kingdom NHS hospitals, Cold Spring Harbor Laboratory.
Angyal A, Longet S, Moore S, Payne RP, Harding A, Tipton T, Rongkard P, Hering LM, Meardon N, Skelly D , Gillson N et al () T-Cell and Antibody Responses to First BNT162b2 Vaccine Dose in Previously SARS-CoV-2-Infected and Infection-Naive UK Healthcare Workers: A Multicentre, Prospective, Observational Cohort Study.
Parker MD, Lindsey BB, Shah DR, Hsu S, Keeley AJ, Partridge DG, Leary S, Cope A, State A, Johnson K , Ali N et al () Altered Subgenomic RNA Expression in SARS-CoV-2 B.1.1.7 Infections.
Golubchik T, Lythgoe KA, Hall M, Ferretti L, Fryer HR, MacIntyre-Cockett G, de Cesare M, Trebes A, Piazza P, Buck D , Todd JA et al () Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein, Cold Spring Harbor Laboratory.
Leclerc QJ, Fuller NM, Keogh RH, Diaz-Ordaz K, Sekula R, Semple MG, Atkins KE, Procter SR & Knight GM () Importance of patient bed pathways and length of stay differences in predicting COVID-19 bed occupancy in England, Cold Spring Harbor Laboratory.
Mashe T, Takawira FT, Martins LDO, Gudza-Mugabe M, Chirenda J, Munyanyi M, Chaibva BV, Tarupiwa A, Gumbo H, Juru A , Nyagupe C et al () Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread, Cold Spring Harbor Laboratory.
Payne RP, Longet S, Austin JA, Skelly D, Dejnirattisai W, Adele S, Meardon N, Faustini S, Al-Taei S, Moore S , Tipton T et al () Sustained T Cell Immunity, Protection and Boosting Using Extended Dosing Intervals of BNT162b2 mRNA Vaccine.
Peno C, Armitage E, Clerc M, Balcazar CL, Jagne YJ, Drammeh S, Jarju S, Sallah H, Senghore E, Lindsey BB , Camara J et al () The Effect of Live Attenuated Influenza Vaccine on Pneumococcal Colonisation Densities Among Children Aged 24-59 Months in the Gambia - A Phase IV, Open Label, Randomised Controlled Trial.
Tettamanti FAT, Venturini C, Stirrup OT, Guerra-Assuncao JA, Alcolea-Medina A, Becket AH, Byott M, Charalampous T, da Silva Filipe A, Frampton D , Glaysher S et al () The Alpha Variant B.1.1.7 Was Not Associated With Excess Healthcare Acquired COVID-19 Infection in a Multi-Centre UK Hospital Study.
Costa-Martins AG, Mane K, Lindsey BB, Ogava RLT, Castro Í, Jagne YJ, Sallah H, Armitage E, Ahadzie B, Ellis-Watson R , Tregoning JS et al () Pre-Existing Upregulation of Interferon Pathways in the Nasopharynx Impacts Viral Shedding Following Live Attenuated Influenza Vaccine Challenge in Children.
Russell CD, Fairfield CJ, Drake TM, Turtle L, Seaton RA, Wootton DG, Sigfrid L, Harrison EM, Docherty A, de Silva TI , Egan C et al () Co-Infections, Secondary Infections, and Antimicrobial Usage in Hospitalised Patients with COVID-19 from the ISARIC WHO CCP-UK Study: A Prospective, Multicentre Cohort Study.
Kearns P, Siebert S, willicombe M, Gaskell C, Kirkham A, Pirrie S, Bowden S, Magwaro S, Hughes A, Lim Z , Dimitriadis S et al () Examining the Immunological Effects of COVID-19 Vaccination in Patients with Conditions Potentially Leading to Diminished Immune Response Capacity – The OCTAVE Trial.
Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CAB, Russell TW, Tully DC, Washburne AD , Wenseleers T et al () Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England, Cold Spring Harbor Laboratory.
Roca A () Intense and Mild Wave of COVID-19 in the Gambia: A Cohort Analysis.
Roca A () Intense and Mild Wave of COVID-19 in The Gambia: a Cohort Analysis, Cold Spring Harbor Laboratory.
Jagne I, Keeley AJ, Bojang A, Camara B, Jallow E, Senghore E, Oluwalana C, Bah SY, Turner CE, Sesay AK , D’Alessandro U et al () Impact of intra-partum Azithromycin on carriage of group A streptococcus in The Gambia: a posthoc analysis of a double-blind randomized placebo-controlled trial, Cold Spring Harbor Laboratory.
Stirrup OT, Hughes J, Parker M, Partridge DG, Shepherd JG, Blackstone J, Coll F, Keeley AJ, Lindsey BB, Marek A , Peters C et al () Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.
Ogbe A, Kronsteiner B, Skelly DT, Pace M, Brown A, Adland E, Adair K, Akhter HD, Ali M, Ali S-E , Angyal A et al () T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses.
ten-Caten F, Gonzalez-Dias P, Castro Í, Ogava RLT, Giddaluru J, Silva JCS, Martins F, Gonçalves ANA, Costa-Martins AG, Araujo JD , Viegas AC et al () In-depth Analysis of Laboratory Parameters Reveals the Interplay Between Sex, Age and Systemic Inflammation in Individuals with COVID-19.
Weissman D, Alameh M-G, de Silva T, Collini P, Hornsby H, Brown R, LaBranche CC, Edwards RJ, Sutherland L, Santra S , Mansouri K et al () D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization, Cold Spring Harbor Laboratory.
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Foley B, Giorgi EE, Bhattacharya T, Parker MD , Partridge DG et al () Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2, Cold Spring Harbor Laboratory.
Adams ER, Ainsworth M, Anand R, Andersson MI, Auckland K, Baillie JK, Barnes E, Beer S, Bell J, Berry T , Bibi S et al () Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel, Cold Spring Harbor Laboratory.
Lindsey BB, Jagne YJ, Armitage EP, Singanayagam A, Sallah HJ, Drammeh S, Senghore E, Mohammed NI, Jeffries D, Höschler K , Tregoning JS et al () Use of a pandemic H1N1 strain with updated haemagglutinin and neuraminidase results in increased nasopharyngeal shedding and improved immunogenicity to Russian-backbone live attenuated influenza vaccine among children aged 2 – 4 years old: an open-label, prospective, observational, phase 4 study in The Gambia, Cold Spring Harbor Laboratory.
McTavish SM, Snow SJ, Cook EC, Pichon B, Coleman S, Coombs GW, Pang S, Arias CA, Díaz L, Boldock E , Davies S et al () Genomic and epidemiological evidence of a dominant Panton-Valentine leucocidin-positive Methicillin Resistant Staphylococcus aureus lineage in Sri Lanka with spread to the United Kingdom and Australia, Cold Spring Harbor Laboratory.
Tettamanti FAT, Venturini C, Stirrup OT, Guerra-Assuncao JA, Alcolea-Medina A, Becket AH, Byott M, Charalampous T, da Silva Filipe A, Frampton D , Glaysher S et al () The Alpha Variant B.1.1.7 Was Not Associated With Excess Healthcare Acquired COVID-19 Infection in a Multi-Centre UK Hospital Study.
Boswell MT, Nazziwa J, Kuroki K, Palm A, Karlson S, Månsson F, Biague A, da Silva ZJ, Onyango CO, de Silva TI , Jaye A et al () Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS, Cold Spring Harbor Laboratory.

Teaching interests: I am involved in delivering the undergraduate (MBChB) Infectious Diseases, Tropical Medicine and Microbiology curriculum at the University of Sheffield. I also lecture on the MSc in Antimicrobial Resistance (MED404), Molecular Medicine MSc (MED6006) and Pharmacology of Respiratory Disease (CDL302, Biomedical Science).

Professional activities and memberships

National and International

British Infection Association Scientific and Research Secretary (2023 - )
Wellcome Trust Early Career Award Interview Committee, Infection and Immunobiology (2022 - )
Africa Research Excellence Fund (https://www.africaresearchexcellencefund.org.uk/) College of Experts (2022 - )
Chair, Vaccines Subcommittee, British Society of Blood and Marrow Transplantation and cellular therapy (BSBMTCt), vaccination subcommittee (2023 - )
Associate Editor, Journal of Infection (2019 - )

Local

Co-Director, Florey Institute of Infection (2023 - )
Director of CL3 suite, Medical School, University of Sheffield (2022 - )
UREC Ethics reviewer for Medical School (2022 -)
University of Sheffield Biosafety Committee (2019 -)

Research themes and key projects

Mucosal and systemic immunity to respiratory viruses

Hybrid immunity to SARS-CoV-2 in Zimbabwean adults with HIV and other chronic diseases (Bill and Melinda Gates Foundation, 2023 – 2026). Key collaborators: Professor Sarah Rowland-Jones, Professor Katharina Kranzer, Professor Andrew Prendergast.
Study of SARS-CoV-2 systemic and mucosal immunity within a household transmission study in The Gambia (UKRI). Key collaborators: Prof. Beate Kampmann, Professor Adam Kucharski.
Study of SARS-CoV-2 T-cell and antibody responses as part of the PITCH study, OCTAVE study and IMMPROVE consortium (2024 – 2028).
Part of a consortium to establish a Global Paediatric Cell Atlas of Nasal and Oral Mucosa (Chan Zuckerberg Initiative, 2021 – 2025).
Supervisor for Dr. Ben Lindsey, Wellcome Trust 4ward North Clinical PhD fellowship on inflammatory memory in the upper respiratory tract following respiratory viral infections (2023 – 2026).

Epidemiology of respiratory viruses

Surveillance for SARS-CoV-2 and other respiratory viruses by establishment of a sentinel surveillance platform for influenza-like illness in The Gambia, along with a household transmission cohort (TransVir) with Prof. Beate Kampmann, Professor Adam Kucharski, Dr. Abdul Karim Sesay.
University of Sheffield lead for the COVID-19 Genomics Consortium UK (COG-UK), using Oxford Nanopore Technology (ONT) to sequence SARS-CoV-2 isolates in South Yorkshire. Building on our group’s sequencing expertise gained during this project, we are now focusing on optimising ONT-based assays with direct utility in NHS diagnostic microbiology and virology laboratories. This aligns work with key deliverables our group are leading within the Infection and Immunity Theme of NIHR Sheffield Biomedical Research Centre (BRC).

The epidemiology and immune responses to Streptococcus pyogenes

Several clinical and molecular epidemiology studies forming part of the MRC Unit The Gambia Strep A research portfolio, with Dr. Claire Turner (School of Biosciences), Prof. Michael Marks (LSHTM) and Prof Ed Clarke (MRC Gambia).

Co-supervisor for three Wellcome Trust Clinical PhD Training Fellows in Global Health (Dr. Edwin Armitage, Dr. Alex Keeley, Dr Ed Monk) who are using the platform of a household and school transmission studies to explore transmission and natural immunity to S. pyogenes.
Co-lead at the MRC Gambia in a global network of scientists seeking to define correlates of immune protection in natural infection with Streptococcus pyogenes (iSpy Network, 2023 - 2027).
Lead for immunology studies across UoS and MRC Gambia in a Wellcome Trust funded S. pyogenes human challenge study to establish correlates of protection (2025 – 2027).