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Mehta R, Chekmeneva E, Jackson H, Sands C, Mills E, Arancon D, Li HK, Arkell P, Rawson TM, Hammond R, Amran M, Haber A, Cooke GS, Noursadeghi M, Kaforou M, Lewis MR, Takats Z, Sriskandan S. Antiviral metabolite 3'-deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19. Med 2022; 3:204-215.e6. [PMID: 35128501 PMCID: PMC8801973 DOI: 10.1016/j.medj.2022.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/14/2021] [Accepted: 01/21/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND There is a critical need for rapid viral infection diagnostics to enable prompt case identification in pandemic settings and support targeted antimicrobial prescribing. METHODS Using untargeted high-resolution liquid chromatography coupled with mass spectrometry, we compared the admission serum metabolome of emergency department patients with viral infections (including COVID-19), bacterial infections, inflammatory conditions, and healthy controls. Sera from an independent cohort of emergency department patients admitted with viral or bacterial infections underwent profiling to validate findings. Associations between whole-blood gene expression and the identified metabolite of interest were examined. FINDINGS 3'-Deoxy-3',4'-didehydro-cytidine (ddhC), a free base of the only known human antiviral small molecule ddhC-triphosphate (ddhCTP), was detected for the first time in serum. When comparing 60 viral with 101 non-viral cases in the discovery cohort, ddhC was the most significantly differentially abundant metabolite, generating an area under the receiver operating characteristic curve (AUC) of 0.954 (95% CI: 0.923-0.986). In the validation cohort, ddhC was again the most significantly differentially abundant metabolite when comparing 40 viral with 40 bacterial cases, generating an AUC of 0.81 (95% CI 0.708-0.915). Transcripts of viperin and CMPK2, enzymes responsible for ddhCTP synthesis, were among the five genes most highly correlated with ddhC abundance. CONCLUSIONS The antiviral precursor molecule ddhC is detectable in serum and an accurate marker for acute viral infection. Interferon-inducible genes viperin and CMPK2 are implicated in ddhC production in vivo. These findings highlight a future diagnostic role for ddhC in viral diagnosis, pandemic preparedness, and acute infection management. FUNDING NIHR Imperial BRC; UKRI.
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Affiliation(s)
- Ravi Mehta
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Elena Chekmeneva
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Heather Jackson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Caroline Sands
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Ewurabena Mills
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | | | - Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London SW7 2AZ, UK
| | - Paul Arkell
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Timothy M. Rawson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
- Division of Infection & Immunity, University College London, London WC1 E6BT, UK
| | - Robert Hammond
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Maisarah Amran
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Anna Haber
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Graham S. Cooke
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Mahdad Noursadeghi
- Division of Infection & Immunity, University College London, London WC1 E6BT, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Matthew R. Lewis
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Zoltan Takats
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London SW7 2AZ, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London W12 0NN, UK
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Li HK, Kaforou M, Rodriguez-Manzano J, Channon-Wells S, Moniri A, Habgood-Coote D, Gupta RK, Mills EA, Arancon D, Lin J, Chiu YH, Pennisi I, Miglietta L, Mehta R, Obaray N, Herberg JA, Wright VJ, Georgiou P, Shallcross LJ, Mentzer AJ, Levin M, Cooke GS, Noursadeghi M, Sriskandan S. Discovery and validation of a three-gene signature to distinguish COVID-19 and other viral infections in emergency infectious disease presentations: a case-control and observational cohort study. Lancet Microbe 2021; 2:e594-e603. [PMID: 34423323 PMCID: PMC8367196 DOI: 10.1016/s2666-5247(21)00145-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Emergency admissions for infection often lack initial diagnostic certainty. COVID-19 has highlighted a need for novel diagnostic approaches to indicate likelihood of viral infection in a pandemic setting. We aimed to derive and validate a blood transcriptional signature to detect viral infections, including COVID-19, among adults with suspected infection who presented to the emergency department. Methods Individuals (aged ≥18 years) presenting with suspected infection to an emergency department at a major teaching hospital in the UK were prospectively recruited as part of the Bioresource in Adult Infectious Diseases (BioAID) discovery cohort. Whole-blood RNA sequencing was done on samples from participants with subsequently confirmed viral, bacterial, or no infection diagnoses. Differentially expressed host genes that met additional filtering criteria were subjected to feature selection to derive the most parsimonious discriminating signature. We validated the signature via RT-qPCR in a prospective validation cohort of participants who presented to an emergency department with undifferentiated fever, and a second case-control validation cohort of emergency department participants with PCR-positive COVID-19 or bacterial infection. We assessed signature performance by calculating the area under receiver operating characteristic curves (AUROCs), sensitivities, and specificities. Findings A three-gene transcript signature, comprising HERC6, IGF1R, and NAGK, was derived from the discovery cohort of 56 participants with bacterial infections and 27 with viral infections. In the validation cohort of 200 participants, the signature differentiated bacterial from viral infections with an AUROC of 0·976 (95% CI 0·919−1·000), sensitivity of 97·3% (85·8−99·9), and specificity of 100% (63·1−100). The AUROC for C-reactive protein (CRP) was 0·833 (0·694−0·944) and for leukocyte count was 0·938 (0·840−0·986). The signature achieved higher net benefit in decision curve analysis than either CRP or leukocyte count for discriminating viral infections from all other infections. In the second validation analysis, which included SARS-CoV-2-positive participants, the signature discriminated 35 bacterial infections from 34 SARS-CoV-2-positive COVID-19 infections with AUROC of 0·953 (0·893−0·992), sensitivity 88·6%, and specificity of 94·1%. Interpretation This novel three-gene signature discriminates viral infections, including COVID-19, from other emergency infection presentations in adults, outperforming both leukocyte count and CRP, thus potentially providing substantial clinical utility in managing acute presentations with infection. Funding National Institute for Health Research, Medical Research Council, Wellcome Trust, and EU-FP7.
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Affiliation(s)
- Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Imperial College London, London, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London, UK
| | | | - Ahmad Moniri
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
| | | | - Rishi K Gupta
- Institute of Global Health, University College London, London, UK
| | - Ewurabena A Mills
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Jessica Lin
- Department of Infectious Disease, Imperial College London, London, UK
| | - Yueh-Ho Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ivana Pennisi
- Department of Infectious Disease, Imperial College London, London, UK
| | - Luca Miglietta
- Department of Infectious Disease, Imperial College London, London, UK
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
| | - Ravi Mehta
- Department of Infectious Disease, Imperial College London, London, UK
| | - Nelofar Obaray
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jethro A Herberg
- Department of Infectious Disease, Imperial College London, London, UK
| | - Victoria J Wright
- Department of Infectious Disease, Imperial College London, London, UK
| | - Pantelis Georgiou
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
- Centre for Bio-Inspired Technology, Imperial College London, London, UK
| | | | | | - Michael Levin
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham S Cooke
- Department of Infectious Disease, Imperial College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London, UK
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