Serum IFN-γ and RNAemia temporal profiles as biomarkers of severe COVID-19 in solid organ transplant and immunocompetent patients

Journal of Infection Serum IFN-γ and RNAemia temporal profiles as biomarkers of severe COVID-19 in solid organ transplant and immunocompetent patients --Manuscript Draft-- Manuscript Number: YJINF-D-23-00115 Article Type: COVID-19 Letter to the Editor Section/Category: Letter to the Editor Corresponding Author: Javier Sanchez-Cespedes Virgen del Rocío University Hospital / Institute of Biomedicine of Seville Sevilla, Spain SPAIN First Author: Sonsoles Salto-Alejandre Order of Authors: Sonsoles Salto-Alejandre Marta Carretero-Ledesma Pedro Camacho-Martínez Judith Berastegui-Cabrera Carmen Infante Regino Rodríguez-Álvarez Jorge Alba Patricia Pérez-Palacios Emilio García-Díaz Cristina Roca Julia Praena María José Blanco-Vidal Sonia Santibáñez Rocío Valverde-Ortiz Javier Nieto-Arana Concepción García-García David Gutiérrez-Campos Natalia Maldonado Gabriel Bernal Miguel Ángel Gómez-Bravo José Manuel Sobrino Manuela Aguilar-Guisado Rocío Álvarez-Marín Josune Goikoetxea-Aguirre José Antonio Oteo Zaira R. Palacios-Baena Álvaro Pascual José Antonio Lepe Jesús Rodríguez-Baño Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation José Miguel Cisneros Jerónimo Pachón Javier Sanchez-Cespedes Elisa Cordero Manuscript Region of Origin: SPAIN Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation INFECTIOUS DISEASES GROUP Institute of Biomedicine of Seville (IBiS), lab # 208, 217, 218 Avda. Manuel Siurot s/n 41013 Seville. Spain Phone: +34 955923100 Journal of Infection January 13th, 2023 Prof. Robert Read Editor-In-Chief Dear Editor, We are sending the manuscript “Serum IFN-γ and RNAemia temporal profiles as biomarkers of severe COVID-19 in solid organ transplant and immunocompetent patients” to be considered for publication in the Journal of Infection. We are aware of the high-level scientific and clinical translation value of the articles published in the Journal of Infection. In this context, we are sending our manuscript to be considered by your journal because we believe in the clinical usefulness of our results. We prove that undetectable levels of IFN-γ in serum, at hospital admission, are independently associated with 30-day all-cause mortality in COVID-19, specifically in the no solid organ transplant (SOT) patients. In SOT recipients there is a non-significant trend to higher mortality in the adjusted analysis, and the Kaplan-Meier survival analysis shows an association of undetectable IFN-γ with mortality. However, undetectable IFN-α in serum was not associated with mortality both in no SOT patients and SOT recipients. RNAemia at hospital admission is also a robust predictor of 30-day all-cause mortality in adult COVID-19 inpatients, and it´s predictive ability of unfavourable clinical outcome persists when SOT recipients and no SOT patients are analysed separately. Thus, the main clinical conclusion of our study is that both IFN-γ and RNAemia detection must be included in the first evaluation in patients with COVID-19 when admitted to the hospital, to guide the patient’s management and to assess the antivirals efficacy. We hope you will find this manuscript suitable for publication in Journal of Infection. Thank you for the consideration of the manuscript. Sincerely, Javier Sánchez-Céspedes, B.Sc., Ph.D. Viral Diseases and Infections in Immunodeficiencies Research Group Institute of Biomedicine of Seville (IBiS) Virgen del Rocío University Hospital/CSIC/University of Seville Seville, Spain https://orcid.org/0000-0003-2707-1979 Cover Letter SANCHEZ CESPEDES JAVIER - 34815046S Firmado digitalmente por SANCHEZ CESPEDES JAVIER - 34815046S Fecha: 2023.01.13 14:13:54 +01'00' Serum IFN-γ and RNAemia temporal profiles as biomarkers of severe COVID-19 in solid organ transplant and immunocompetent patients Running Title: IFN-γ and RNAemia profiles impact on COVID-19 outcome Sonsoles Salto-Alejandre1,2,#, Marta Carretero-Ledesma1,2,#, Pedro Camacho-Martínez1,2, Judith Berastegui-Cabrera1,2, Carmen Infante1,2, Regino Rodríguez-Álvarez3, Jorge Alba4, Patricia Pérez-Palacios2,5, Emilio García-Díaz6, Cristina Roca1,2, Julia Praena1,2, María José Blanco-Vidal3, Sonia Santibáñez4, Rocío Valverde-Ortiz7, Javier Nieto- Arana3, Concepción García-García4, María José Blanco-Vida3, David Gutiérrez- Campos2,5, Natalia Maldonado2,5,8, Gabriel Bernal9, Miguel Ángel Gómez-Bravo10, José Manuel Sobrino11, Manuela Aguilar-Guisado1,2,8, Rocío Álvarez-Marín1,2,8, Josune Goikoetxea-Aguirre3, José Antonio Oteo4, Zaira R. Palacios-Baena2,5,8, Álvaro Pascual2,5,8,12, José Antonio Lepe1,2,8,12, Jesús Rodríguez-Baño2,5,8,13, José Miguel Cisneros1,2,8,13, Jerónimo Pachón2,13, Javier Sánchez‑Céspedes1,2,8,*, and Elisa Cordero1,2,8,13, on behalf of The COVIDSOT Working Team 1Division of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain 2Institute of Biomedicine of Seville (IBiS), Virgen del Rocío and Virgen Macarena University Hospitals/CSIC/University of Seville, Seville, Spain. 3Department of Infectious Diseases, Hospital Universitario Cruces, Bizkaia, Spain 4Department of Infectious Diseases, San Pedro-CIBIR University Hospital, Logroño, La Rioja, Spain Title Page 5Unit of Infectious Diseases and Microbiology, Virgen Macarena University Hospital, Seville, Spain 6Medical Surgical Respiratory Unit, Virgen del Rocío University Hospital, Seville, Spain. 7Unit of Nephrology, Virgen Macarena University Hospital, Seville, Spain 8CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain 9Unit of Urology and Nephrology, Virgen del Rocío University Hospital, Seville, Spain. 10General and Digestive Service, Virgen del Rocío University Hospital, Seville, Spain. 11Unit of Cardiology and Cardiovascular Surgery, Virgen del Rocío University Hospital, Seville, Spain. 12Department of Microbiology, University of Seville, Seville, Spain 13Department of Medicine, School of Medicine, University of Seville, Seville, Spain # Both authors contributed equally to this work * Corresponding author: Javier Sánchez-Céspedes, Division of Infectious Diseases, Microbiology and Parasitology. Virgen del Rocío University Hospital. Av. Manuel Siurot s/n, 41013 Seville, Spain. Phone: +34 636 462 616, email: [email protected] Highlights Highlights should be submitted in a separate editable file in the online submission system. Please use 'Highlights' in the file name and include 3 to 5 bullet points (maximum 85 characters, including spaces, per bullet point).  SOT recipients vs. no SOT patients have more undetectable IFN-γ and RNAemia rates.  Undetectable IFN-α rates are similar in SOT recipients and in no SOT patients.  In the no SOT patients, RNAemia and mortality decreased after 10 days of disease.  RNAemia is associated with unfavourable outcome in SOT recipients.  RNAemia and undetectable IFN-γ are associated with mortality in no SOT patients. Highlights (for review) 1 Serum IFN-γ and RNAemia temporal profiles as biomarkers of severe COVID-19 in solid organ transplant and immunocompetent patients Running Title: IFN-γ and RNAemia profiles impact on COVID-19 outcome Sonsoles Salto-Alejandre1,2,#, Marta Carretero-Ledesma1,2,#, Pedro Camacho-Martínez1,2, Judith Berastegui-Cabrera1,2, Carmen Infante1,2, Regino Rodríguez-Álvarez3, Jorge Alba4, Patricia Pérez-Palacios2,5, Emilio García-Díaz6, Cristina Roca1,2, Julia Praena1,2, María José Blanco-Vidal3, Sonia Santibáñez4, Rocío Valverde-Ortiz7, Javier Nieto- Arana3, Concepción García-García4, David Gutiérrez-Campos2,5, Natalia Maldonado2,5,8, Gabriel Bernal9, Miguel Ángel Gómez-Bravo10, José Manuel Sobrino11, Manuela Aguilar-Guisado1,2,8, Rocío Álvarez-Marín1,2,8, Josune Goikoetxea-Aguirre3, José Antonio Oteo4, Zaira R. Palacios-Baena2,5,8, Álvaro Pascual2,5,8,12, José Antonio Lepe1,2,8,12, Jesús Rodríguez-Baño2,5,8,13, José Miguel Cisneros1,2,8,13, Jerónimo Pachón2,13, Javier Sánchez‑Céspedes1,2,8,*, and Elisa Cordero1,2,8,13, on behalf of The COVIDSOT Working Team 1Division of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain 2Institute of Biomedicine of Seville (IBiS), Virgen del Rocío and Virgen Macarena University Hospitals/CSIC/University of Seville, Seville, Spain. 3Department of Infectious Diseases, Hospital Universitario Cruces, Bizkaia, Spain 4Department of Infectious Diseases, San Pedro-CIBIR University Hospital, Logroño, La Rioja, Spain Manuscript Click here to view linked References 2 5Unit of Infectious Diseases and Microbiology, Virgen Macarena University Hospital, Seville, Spain 6Medical Surgical Respiratory Unit, Virgen del Rocío University Hospital, Seville, Spain. 7Unit of Nephrology, Virgen Macarena University Hospital, Seville, Spain 8CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain 9Unit of Urology and Nephrology, Virgen del Rocío University Hospital, Seville, Spain. 10General and Digestive Service, Virgen del Rocío University Hospital, Seville, Spain. 11Unit of Cardiology and Cardiovascular Surgery, Virgen del Rocío University Hospital, Seville, Spain. 12Department of Microbiology, University of Seville, Seville, Spain 13Department of Medicine, School of Medicine, University of Seville, Seville, Spain # Both authors contributed equally to this work * Corresponding author: Javier Sánchez-Céspedes, Division of Infectious Diseases, Microbiology and Parasitology. Virgen del Rocío University Hospital. Av. Manuel Siurot s/n, 41013 Seville, Spain. Phone: +34 636 462 616, email: [email protected] 3 Dear Editor, Currently, the availability of SARS-CoV-2 vaccines, despite the great worldwide differences in vaccination rates1, have focused the impact of the pandemic in immunodepressed patients. Therefore, we read with interest the recent meta-analysis about COVID-19 vaccine in patients with solid malignancies2 which found that 42% and 86% of patients achieved serological response after one and two doses, respectively. Other authors have found that the pooled odds ratio for developing anti-SARS-CoV-2 spike protein IgG was higher in the control group than in solid organ transplant (SOT) recipients3. The infection by SARS-CoV-2 elicits an innate and specific cellular and humoral immune response. Interferons (IFN) are key in the innate immune response during the acute phase of the viral infection, as seen with plasmacytoid dendritic cells expressing high concentrations of types I and III IFNs in COVID-19 patients4,5. In acute COVID-19 and convalescent patients, intracellular cytokine staining after stimulation with SARS-CoV-2 peptide pools, has showed significant IFN-γ increases in CD8 + T- cells, which is associated with viral elimination, and without differences in both phases of the disease6,7. In this context, to gain insight in the innate immune response in SOT recipients with COVID-19, compared with no SOT patients, we have assessed the IFN-α and IFN- ℽ serum levels and RNAemia at hospital admission and by days from the symptom’s onset (DfSO; ≤1 to ≥15 days), as well as their association with unfavourable clinical outcomes (death and/or invasive mechanical ventilation [IMV]). With this aim, we conducted a multicentre prospective observational cohort study, including consecutive adult inpatients with confirmed COVID-19 (RT-PCR in nasopharyngeal swabs) and available samples for IFN-α/IFN-γ serum levels and RNAemia determinations (Methods, Supplementary material), from January 6th 2020 to August 13th 2021, followed until 10 pathogenesis: An update. J Med Virol. 2022;94(11):5128-5148. doi:10.1002/jmv.28000. 8. Brunet-Ratnasingham E, Anand SP, Gantner P, Dyachenko A, Moquin-Beaudry G, Brassard N, et al. Integrated immunovirological profiling validates plasma SARS- CoV-2 RNA as an early predictor of COVID-19 mortality. Sci Adv. 2021;7(48):eabj5629. doi:10.1126/sciadv.abj5629. 9. Bastard P, Rosen LB, Zhang Q, Michailidis E, Hoffmann HH, Zhang Y, et al. Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science. 2020;370(6515):eabd4585. doi:10.1126/science.abd4585. 10. Manry J, Bastard P, Gervais A, Le Voyer T, Rosain J, Philippot Q, et al. The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies. Proc Natl Acad Sci U S A. 2022;119(21):e2200413119. doi:10.1073/pnas.2200413119. 11 Table 1. Comparison of solid organ transplant (SOT) recipients matched (1:2) with no SOT patients according to propensity score a. Variable SOT recipients (n = 33) No SOT patients (n = 66) P value Male sex 20 (60.6) 37 (56.1) 0.666 Age >70 years 4 (12.1) 21 (31.8) 0.033 Dyspnoea 15 (45.5) 36 (54.5) 0.394 SpO2 <95% 17 (51.5) 26 (39.4) 0.251 Neutrophil count >7500/μL 6 (18.2) 6 (9.1) 0.327 Lymphocyte count <1000/µL 18 (54.5) 30 (45.5) 0.394 C-reactive protein >100 mg/L 9 (27.3) 20 (30.3) 0.755 Ferritin >1000 ng/mL 6 (18.2) 10 (15.2) 0.699 D-dimer >600 ng/mL 29 (87.9) 48 (72.7) 0.087 LDH >300 IU/L 14 (42.4) 33 (50.0) 0.477 IFN-α undetectable 3 (9.1) 8 (12.1) 0.747 IFN-α (pg/mL) b 1.43 (0.60–22.01) 11.98 (3.24–23.11) 0.163 IFN-γ undetectable 13 (39.4) 7 (10.6) 0.001 IFN-γ (pg/mL) b 26.14 (0.00–240.96) 145.35 (40.00–330.96) 0.347 RNAemia positive 19 (57.6) 9 (13.6) <0.001 RNAemia (log10 copies/mL) b 2.38 (2.12–3.19) 2.36 (1.92–2.98) 0.921 CCI ≥3 25 (75.8) 37 (56.1) 0.056 CURB-65 ≥2 12 (36.4) 12 (18.8) 0.057 WHO basal score 6–9 c 3 (9.1) 4 (6.1) 0.683 IMV 10 (30.3) 5 (7.6) 0.003 Mortality at day 30 9 (27.3) 3 (4.5) 0.003 WHO final score 7-10 c 13 (39.4) 7 (10.6) 0.001 Data are presented as No. (%). P values are calculated by Cox regression. Abbreviations (in order of appearance): SpO2, peripheral capillary oxygen saturation; LDH, lactate dehydrogenase; IFN, interferon; CCI, Charlson Comorbidity Index (30); CURB-65 (31), Severity Score for Community-Acquired Pneumonia; IMV, invasive mechanical ventilation. a Variables included in the propensity score were sex, dyspnea, SpO2, neutrophil and lymphocyte counts, C-reactive protein, ferritin, D-dimer, and LDH. b Median (IQR). P values are calculated by the Mann-Whitney U test. c Severity rating according to the WHO Clinical Progression Scale (doi: 10.1016/S1473-3099(20)30483-7), ranged from 0 (not infected) to 10 (dead), of which scores 6–9 represent severe disease. 12 Figure 1. SOT recipients (n=47) comparison with no SOT patients (n=408) regarding (A) undetectable IFN-α and IFN-γ serum levels, RNAemia, and mortality, by days from symptoms onset at hospital admission, and (B) Survival Kaplan Meier analysis of patients with and without undetectable IFN-γ serum levels and RNAemia detection. A) IF N - D ays from sym ptom s onset at hospital adm ission % IFN- Undetectable 3 4 to 6 7 to 10 11 TO TA L 0 20 40 60 80 100 R N A em ia D ays from sym ptom s onset at hospital adm ission % R NAem ia detection 3 4 to 6 7 to 10 11 TOTA L 0 20 40 60 80 100 * *** *** *** IF N - D ays from sym ptom s onset at hospital adm ission % IFN- Undetectable 3 4 to 6 7 to 10 11 TO TA L 0 20 40 60 80 100 * * * M o rta lity D ays from sym ptom s onset at hospital adm ission % Mortality 3 4 to 6 7 to 10 11 TOTA L 0 20 40 60 80 100 ** ** *** *** 13 B) Table 1. Comparison of solid organ transplant (SOT) recipients matched (1:2) with no SOT patients according to propensity score a. Variable SOT recipients (n = 33) No SOT patients (n = 66) P value Male sex 20 (60.6) 37 (56.1) 0.666 Age >70 years 4 (12.1) 21 (31.8) 0.033 Dyspnoea 15 (45.5) 36 (54.5) 0.394 SpO2 <95% 17 (51.5) 26 (39.4) 0.251 Neutrophil count >7500/μL 6 (18.2) 6 (9.1) 0.327 Lymphocyte count <1000/µL 18 (54.5) 30 (45.5) 0.394 C-reactive protein >100 mg/L 9 (27.3) 20 (30.3) 0.755 Ferritin >1000 ng/mL 6 (18.2) 10 (15.2) 0.699 D-dimer >600 ng/mL 29 (87.9) 48 (72.7) 0.087 LDH >300 IU/L 14 (42.4) 33 (50.0) 0.477 IFN-α undetectable 3 (9.1) 8 (12.1) 0.747 IFN-α (pg/mL) b 1.43 (0.60–22.01) 11.98 (3.24–23.11) 0.163 IFN-γ undetectable 13 (39.4) 7 (10.6) 0.001 IFN-γ (pg/mL) b 26.14 (0.00–240.96) 145.35 (40.00–330.96) 0.347 RNAemia positive 19 (57.6) 9 (13.6) <0.001 RNAemia (log10 copies/mL) b 2.38 (2.12–3.19) 2.36 (1.92–2.98) 0.921 CCI ≥3 25 (75.8) 37 (56.1) 0.056 CURB-65 ≥2 12 (36.4) 12 (18.8) 0.057 WHO basal score 6–9 c 3 (9.1) 4 (6.1) 0.683 IMV 10 (30.3) 5 (7.6) 0.003 Mortality at day 30 9 (27.3) 3 (4.5) 0.003 WHO final score 7-10 c 13 (39.4) 7 (10.6) 0.001 Data are presented as No. (%). P values are calculated by Cox regression. Abbreviations (in order of appearance): SpO2, peripheral capillary oxygen saturation; LDH, lactate dehydrogenase; IFN, interferon; CCI, Charlson Comorbidity Index (30); CURB-65 (31), Severity Score for Community-Acquired Pneumonia; IMV, invasive mechanical ventilation. a Variables included in the propensity score were sex, dyspnea, SpO2, neutrophil and lymphocyte counts, C-reactive protein, ferritin, D-dimer, and LDH. b Median (IQR). P values are calculated by the Mann-Whitney U test. c Severity rating according to the WHO Clinical Progression Scale (doi: 10.1016/S1473-3099(20)30483-7), ranged from 0 (not infected) to 10 (dead), of which scores 6–9 represent severe disease. Table Click here to access/download;Table;Table 1.docx Figure 1A Click here to access/download;Figure;Figure 1A.tiff Figure 1B Click here to access/download;Figure;Figure 1B.tiff Supplementary file Click here to access/download Supplementary file Viremia-IFN_Supplemental Data_13-1-23.docx