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Lopez-Labrador FX, Huber M, Sidorov IA, Brown JR, Cuypers L, Laenen L, Vanmechelen B, Maes P, Fischer N, Pichler I, Storey N, Atkinson L, Schmutz S, Kufner V, van Boheemen S, Mulders CE, Grundhoff A, Blümke P, Robitaille A, Cinek O, Hubáčková K, Mourik K, Boers SA, Stauber L, Salmona M, Cappy P, Ramette A, Franze' A, LeGoff J, Claas ECJ, Rodriguez C, de Vries JJC. Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics. J Clin Virol 2024; 173:105695. [PMID: 38823290 DOI: 10.1016/j.jcv.2024.105695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/10/2024] [Accepted: 05/18/2024] [Indexed: 06/03/2024]
Abstract
Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 104 copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.
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Affiliation(s)
- F Xavier Lopez-Labrador
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain; Microbiology & Ecology Department, Medical School, University of Valencia, Spain; and CIBERESP, Instituto de Salud Carlos III, Spain
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Igor A Sidorov
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Lize Cuypers
- Department of Laboratory Medicine, University Hospitals Leuven, and Laboratory of Clinical Microbiology, KU, Leuven, Belgium
| | - Lies Laenen
- Department of Laboratory Medicine, University Hospitals Leuven, and Laboratory of Clinical Microbiology, KU, Leuven, Belgium
| | - Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | - Ian Pichler
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Nathaniel Storey
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Laura Atkinson
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Switzerland
| | | | | | | | | | | | - Ondrej Cinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic
| | - Klára Hubáčková
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic
| | - Kees Mourik
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Stefan A Boers
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lea Stauber
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Maud Salmona
- Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | | | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Alessandra Franze'
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain
| | - Jerome LeGoff
- Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jutte J C de Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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2
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Gugulothu P, Bhukya R. Coot-Lion optimized deep learning algorithm for COVID-19 point mutation rate prediction using genome sequences. Comput Methods Biomech Biomed Engin 2024; 27:1410-1429. [PMID: 37668061 DOI: 10.1080/10255842.2023.2244109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 07/08/2023] [Accepted: 07/28/2023] [Indexed: 09/06/2023]
Abstract
In this study, a deep quantum neural network (DQNN) based on the Lion-based Coot algorithm (LBCA-based Deep QNN) is employed to predict COVID-19. Here, the genome sequences are subjected to feature extraction. The fusion of features is performed using the Bray-Curtis distance and the deep belief network (DBN). Lastly, a deep quantum neural network (Deep QNN) is used to predict COVID-19. The LBCA is obtained by integrating Coot algorithm and LOA. The COVID-19 predictions are done with mutation points. The LBCA-based Deep QNN outperformed with testing accuracy of 0.941, true positive rate of 0.931, and false positive rate of 0.869.
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Affiliation(s)
- Praveen Gugulothu
- Department of Computer Science and Engineering, National Institute of Technology Warangal, Hanamkonda, Telangana 506004, India
| | - Raju Bhukya
- Department of Computer Science and Engineering, National Institute of Technology Warangal, Hanamkonda, Telangana 506004, India
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3
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Chen L, Olson LB, Naqvi IA, Sullenger BA, Que LG, Denny TN, Kraft BD. SARS-CoV-2 viremia but not respiratory viral load is associated with respiratory complications in patients with severe COVID-19. BMC Pulm Med 2024; 24:366. [PMID: 39080682 PMCID: PMC11288013 DOI: 10.1186/s12890-024-03183-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Severe COVID-19 carries a high morbidity and mortality. Previous studies have shown an association between COVID-19 severity and SARS-CoV-2 viral load (VL). We sought to measure VL in multiple compartments (urine, plasma, lower respiratory tract) in patients admitted to the intensive care unit (ICU) with severe COVID-19 pneumonia and correlate with clinical outcomes. METHODS Plasma, urine, and endotracheal aspirate (ETA) samples were obtained on days 1, 3, 7, 14, and 21 from subjects admitted to the ICU with severe COVID-19. VL was measured via reverse transcriptase polymerase chain reaction. Clinical data was collected from the electronic health record. Grouped comparisons were performed using Student's t-test or 1-way ANOVA. Linear regression was used to correlate VL from different compartments collected at the same time. Logistic regression was performed to model ventilator-freedom at 28 days as a function of peak plasma VL. RESULTS We enrolled 57 subjects with severe COVID-19 and measured VL in plasma (n = 57), urine (n = 25), and ETA (n = 34). Ventilator-associated pneumonia developed in 63% of subjects. 49% of subjects were viremic on study day 1. VL in plasma and ETA both significantly decreased by day 14 (P < 0.05), and the two were weakly correlated on study day 1 (P = 0.0037, r2 = 0.2343) and on all study days (P < 0.001, r2 = 0.2211). VL were not detected in urine. While no associations were observed with peak ETA VL, subjects with higher peak plasma VL experienced a greater number of respiratory complications, including ventilator-associated pneumonia and fewer ventilator-free and hospital-free days. There was no association between VL in either plasma or ETA and mortality. In viremic patients, plasma VL was significantly lower in subjects that were ICU-free and ventilator-free (P < 0.05), with trends noted for hospital-freedom, ventilator-associated pneumonia, and survival to discharge (P < 0.1). By logistic regression, plasma VL was inversely associated with ventilator-freedom at 28 days (odds ratio 0.14, 95% confidence interval 0.02-0.50). CONCLUSIONS Elevated SARS-CoV-2 VL in the plasma but not in the lower respiratory tract is a novel biomarker in severe COVID-19 for respiratory complications.
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Affiliation(s)
- Lingye Chen
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Lyra B Olson
- Duke Medical Scientist Training Program, Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ibtehaj A Naqvi
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Bruce A Sullenger
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Loretta G Que
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Thomas N Denny
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Bryan D Kraft
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
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Chen Z, Fung E, Wong CK, Ling L, Lui G, Lai CKC, Ng RWY, Sze RKH, Ho WCS, Hui DSC, Chan PKS. Early Metabolomic and Immunologic Biomarkers as Prognostic Indicators for COVID-19. Metabolites 2024; 14:380. [PMID: 39057703 PMCID: PMC11278819 DOI: 10.3390/metabo14070380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
This prospective study in Hong Kong aimed at identifying prognostic metabolomic and immunologic biomarkers for Coronavirus Disease 2019 (COVID-19). We examined 327 patients, mean age 55 (19-89) years, in whom 33.6% were infected with Omicron and 66.4% were infected with earlier variants. The effect size of disease severity on metabolome outweighed others including age, gender, peak C-reactive protein (CRP), vitamin D and peak viral levels. Sixty-five metabolites demonstrated strong associations and the majority (54, 83.1%) were downregulated in severe disease (z score: -3.30 to -8.61). Ten cytokines/chemokines demonstrated strong associations (p < 0.001), and all were upregulated in severe disease. Multiple pairs of metabolomic/immunologic biomarkers showed significant correlations. Fourteen metabolites had the area under the receiver operating characteristic curve (AUC) > 0.8, suggesting a high predictive value. Three metabolites carried high sensitivity for severe disease: triglycerides in medium high-density lipoprotein (MHDL) (sensitivity: 0.94), free cholesterol-to-total lipids ratio in very small very-low-density lipoprotein (VLDL) (0.93), cholesteryl esters-to-total lipids ratio in chylomicrons and extremely large VLDL (0.92);whereas metabolites with the highest specificity were creatinine (specificity: 0.94), phospholipids in large VLDL (0.94) and triglycerides-to-total lipids ratio in large VLDL (0.93). Five cytokines/chemokines, namely, interleukin (IL)-6, IL-18, IL-10, macrophage inflammatory protein (MIP)-1b and tumour necrosis factor (TNF)-a, had AUC > 0.8. In conclusion, we demonstrated a tight interaction and prognostic potential of metabolomic and immunologic biomarkers enabling an outcome-based patient stratification.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; (Z.C.); (C.K.C.L.); (R.W.Y.N.); (R.K.H.S.); (W.C.S.H.)
| | - Erik Fung
- Cardiovascular Science Center and Division of Cardiology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China;
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, White City, London SW7 2AZ, UK
| | - Chun-Kwok Wong
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China;
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China;
| | - Grace Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; (G.L.); (D.S.C.H.)
| | - Christopher K. C. Lai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; (Z.C.); (C.K.C.L.); (R.W.Y.N.); (R.K.H.S.); (W.C.S.H.)
| | - Rita W. Y. Ng
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; (Z.C.); (C.K.C.L.); (R.W.Y.N.); (R.K.H.S.); (W.C.S.H.)
| | - Ryan K. H. Sze
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; (Z.C.); (C.K.C.L.); (R.W.Y.N.); (R.K.H.S.); (W.C.S.H.)
| | - Wendy C. S. Ho
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; (Z.C.); (C.K.C.L.); (R.W.Y.N.); (R.K.H.S.); (W.C.S.H.)
| | - David S. C. Hui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; (G.L.); (D.S.C.H.)
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; (Z.C.); (C.K.C.L.); (R.W.Y.N.); (R.K.H.S.); (W.C.S.H.)
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5
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Kwizera A, Kabatoro D, Owachi D, Kansiime J, Kateregga G, Nanyunja D, Sendagire C, Nyakato D, Olaro C, Audureau E, Mekontso Dessap A. Respiratory support with standard low-flow oxygen therapy, high-flow oxygen therapy or continuous positive airway pressure in adults with acute hypoxaemic respiratory failure in a resource-limited setting: protocol for a randomised, open-label, clinical trial - the Acute Respiratory Intervention StudiEs in Africa (ARISE-AFRICA) study. BMJ Open 2024; 14:e082223. [PMID: 38951007 PMCID: PMC11218023 DOI: 10.1136/bmjopen-2023-082223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/19/2024] [Indexed: 07/03/2024] Open
Abstract
RATIONALE Acute hypoxaemic respiratory failure (AHRF) is associated with high mortality in sub-Saharan Africa. This is at least in part due to critical care-related resource constraints including limited access to invasive mechanical ventilation and/or highly skilled acute care workers. Continuous positive airway pressure (CPAP) and high-flow oxygen by nasal cannula (HFNC) may prove useful to reduce intubation, and therefore, improve survival outcomes among critically ill patients, particularly in resource-limited settings, but data in such settings are lacking. The aim of this study is to determine whether CPAP or HFNC as compared with standard oxygen therapy, could reduce mortality among adults presenting with AHRF in a resource-limited setting. METHODS This is a prospective, multicentre, randomised, controlled, stepped wedge trial, in which patients presenting with AHRF in Uganda will be randomly assigned to standard oxygen therapy delivered through a face mask, HFNC oxygen or CPAP. The primary outcome is all-cause mortality at 28 days. Secondary outcomes include the number of patients with criteria for intubation at day 7, the number of patients intubated at day 28, ventilator-free days at day 28 and tolerance of each respiratory support. ETHICS AND DISSEMINATION The study has obtained ethical approval from the Research and Ethics Committee, School of Biomedical Sciences, College of Health Sciences, Makerere University as well as the Uganda National Council for Science and Technology. Patients will be included after informed consent. The results will be submitted for publication in peer-reviewed journals. TRIAL REGISTRATION NUMBER NCT04693403. PROTOCOL VERSION 8 September 2023; version 5.
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Affiliation(s)
- Arthur Kwizera
- Department of Anaesthesia and Critical Care, Makerere University College of Health Sciences, Kampala, Uganda
| | - Daphne Kabatoro
- Department of Anaesthesia and Critical Care, Makerere University College of Health Sciences, Kampala, Uganda
| | - Darius Owachi
- Department of Emergency Medicine, Kiruddu National Referral Hospital, Kampala, Uganda
| | - Jackson Kansiime
- Department of Internal Medicine, St Mary's Hospital, Gulu, Uganda
| | - George Kateregga
- Department of Anaesthesia and Intensive Care, Mbarara Regional Referral Hospital, Mbarara, Uganda
| | - Doreen Nanyunja
- Department of Internal Medicine, China-Uganda Friendship Hospital Naguru, Kampala, Uganda
| | | | | | | | - Etienne Audureau
- CEPIA EA7376, Universite Paris-Est Creteil Val de Marne, Creteil, France
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Gutierrez-Chavez C, Aperrigue-Lira S, Ortiz-Saavedra B, Paz I. Chemokine receptors in COVID-19 infection. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 388:53-94. [PMID: 39260938 DOI: 10.1016/bs.ircmb.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Chemokine receptors play diverse roles in the immune response against pathogens by recruiting innate and adaptive immune cells to sites of infection. However, their involvement could also be detrimental, causing tissue damage and exacerbating respiratory diseases by triggering histological alterations such as fibrosis and remodeling. This chapter reviews the role of chemokine receptors in the immune defense against SARS-CoV-2 infection. In COVID-19, CXCR3 is expressed mainly in T cells, and its upregulation is related to an increase in SARS-CoV-2-specific antibodies but also to COVID-19 severity. CCR5 is a key player in T-cell recruitment, and its suppression leads to reduced inflammation and viremia levels. Conversely, CXCR6 is implicated in the aberrant migration of memory T cells within airways. On the other hand, increased CCR4+ cells in the blood and decreased CCR4+ cells in lung cells are associated with severe COVID-19. Additionally, CCR2 is associated with an increase in macrophage recruitment to lung tissues. Elevated levels of CXCR1 and CXCR2, which are predominantly expressed in neutrophils, are associated with the severity of the disease, and finally, the expression of CX3CR1 in cytotoxic T lymphocytes affects the retention of these cells in lung tissues, thereby impacting the severity of COVID-19. Despite the efforts of many clinical trials to find effective therapies for COVID-19 using chemokine receptor inhibitors, no conclusive results have been found due to the small number of patients, redundancy, and co-expression of chemokine receptors by immune cells, which explains the difficulty in finding a single therapeutic target or effective treatment.
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Affiliation(s)
| | - Shalom Aperrigue-Lira
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru; Grupo de Investigación en Inmunología-GII, UNSA, Arequipa, Peru
| | - Brando Ortiz-Saavedra
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru; Grupo de Investigación en Inmunología-GII, UNSA, Arequipa, Peru
| | - Irmia Paz
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru.
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Oliveira TT, Freitas JF, de Medeiros VPB, Xavier TJDS, Agnez-Lima LF. Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity. Life Sci Alliance 2024; 7:e202302358. [PMID: 38262689 PMCID: PMC10806258 DOI: 10.26508/lsa.202302358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024] Open
Abstract
During the COVID-19 pandemic, RNA-seq datasets were produced to investigate the virus-host relationship. However, much of these data remains underexplored. To improve the search for molecular targets and biomarkers, we performed an integrated analysis of multiple RNA-seq datasets, expanding the cohort and including patients from different countries, encompassing severe and mild COVID-19 patients. Our analysis revealed that severe COVID-19 patients exhibit overexpression of genes coding for proteins of extracellular exosomes, endomembrane system, and neutrophil granules (e.g., S100A9, LY96, and RAB1B), which may play an essential role in the cellular response to infection. Concurrently, these patients exhibit down-regulation of genes encoding components of the T cell receptor complex and nucleolus, including TP53, IL2RB, and NCL Finally, SPI1 may emerge as a central transcriptional factor associated with the up-regulated genes, whereas TP53, MYC, and MAX were associated with the down-regulated genes during COVID-19. This study identified targets and transcriptional factors, lighting on the molecular pathophysiology of syndrome coronavirus 2 infection.
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Affiliation(s)
- Thais Teixeira Oliveira
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Júlia Firme Freitas
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | | | - Thiago Jesus da Silva Xavier
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Lucymara Fassarella Agnez-Lima
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
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8
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Bay P, Loegel C, Ly A, Soulier A, N'Debi M, Seng S, Kassasseya C, Rodriguez C, Pawlotsky JM, de Prost N, Fourati S. Clinical Phenotypes and Molecular Characteristics of Respiratory Syncytial Virus in Adults: A Monocentric Prospective Study Between 2019 and 2022. J Infect Dis 2024; 229:728-732. [PMID: 37926099 DOI: 10.1093/infdis/jiad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) infection is a major cause of pneumonia in adults. Little is known on the viral genetic diversity and the associated clinical phenotypes in this population. This single-center prospective cohort study included RSV-infected patients hospitalized between January 2019 and December 2022. Of 100 patients, including 41 with severe infection, 72 were infected with RSV-B. RSV genome sequencing showed no clustering according to severity. Patients infected with RSV-B with risk factors for severe pneumonia had significantly higher fusion protein diversity scores. No amino acid substitutions conferring resistance to nirsevimab were detected.
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Affiliation(s)
- Pierre Bay
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil, Créteil, France
- Équipe "Virus, Hépatologie, Cancer," INSERM U955, Université Paris-Est-Créteil, Créteil, France
| | - Cloé Loegel
- Équipe "Virus, Hépatologie, Cancer," INSERM U955, Université Paris-Est-Créteil, Créteil, France
| | - Arnaud Ly
- Équipe "Virus, Hépatologie, Cancer," INSERM U955, Université Paris-Est-Créteil, Créteil, France
| | - Alexandre Soulier
- Équipe "Virus, Hépatologie, Cancer," INSERM U955, Université Paris-Est-Créteil, Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Mélissa N'Debi
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Sarah Seng
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Christian Kassasseya
- Service d'Accueil des Urgences, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Christophe Rodriguez
- Équipe "Virus, Hépatologie, Cancer," INSERM U955, Université Paris-Est-Créteil, Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Jean-Michel Pawlotsky
- Équipe "Virus, Hépatologie, Cancer," INSERM U955, Université Paris-Est-Créteil, Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Nicolas de Prost
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil, Créteil, France
| | - Slim Fourati
- Équipe "Virus, Hépatologie, Cancer," INSERM U955, Université Paris-Est-Créteil, Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
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Marchand S, Rodriguez C, Woerther PL. [High-throughput sequencing for infectious disease diagnoses: Example of shotgun metagenomics in central nervous system infections]. Rev Med Interne 2024; 45:166-173. [PMID: 37230923 DOI: 10.1016/j.revmed.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The advent of high-throughput sequencing in clinical microbiology is opening the way to new diagnostic and prognostic approaches in infectious diseases. Detection, identification and characterisation of pathogenic microorganisms are essential steps in diagnosis and implementation of appropriate antimicrobial therapy. However, standard methods of microbiological diagnosis are failing in some cases. In addition, the emergence of new infections, facilitated by international travel and global warming, requires the implementation of innovative diagnostic methods. Among the different strategies used in clinical microbiology and reviewed in this article, shotgun metagenomics is the only technique that allows today a panpathogenic and unbiased detection of all microorganisms potentially responsible for an infectious disease, including those still unknown. The aims of this article are to present the different possible strategies of high-throughput sequencing used in the microbiological diagnosis of infectious diseases and to highlight the diagnostic contribution of shotgun metagenomics in the field of central nervous system infections.
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Affiliation(s)
- S Marchand
- Département de microbiologie, hôpital Henri Mondor, AP-HP, Créteil, France; Plateforme de génomique, hôpital Henri Mondor, AP-HP, Créteil, France.
| | - C Rodriguez
- Département de microbiologie, hôpital Henri Mondor, AP-HP, Créteil, France; Plateforme de génomique, hôpital Henri Mondor, AP-HP, Créteil, France; Inserm U955, université Paris-Est Créteil, Créteil, France
| | - P-L Woerther
- Département de microbiologie, hôpital Henri Mondor, AP-HP, Créteil, France; Plateforme de génomique, hôpital Henri Mondor, AP-HP, Créteil, France; EA 7380 Dynamyc, université Paris-Est Créteil, Créteil, France
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10
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Chernov AS, Rodionov MV, Kazakov VA, Ivanova KA, Meshcheryakov FA, Kudriaeva AA, Gabibov AG, Telegin GB, Belogurov AA. CCR5/CXCR3 antagonist TAK-779 prevents diffuse alveolar damage of the lung in the murine model of the acute respiratory distress syndrome. Front Pharmacol 2024; 15:1351655. [PMID: 38449806 PMCID: PMC10915062 DOI: 10.3389/fphar.2024.1351655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Introduction: The acute respiratory distress syndrome (ARDS), secondary to viral pneumonitis, is one of the main causes of high mortality in patients with COVID-19 (novel coronavirus disease 2019)-ongoing SARS-CoV-2 infection- reached more than 0.7 billion registered cases. Methods: Recently, we elaborated a non-surgical and reproducible method of the unilateral total diffuse alveolar damage (DAD) of the left lung in ICR mice-a publicly available imitation of the ARDS caused by SARS-CoV-2. Our data read that two C-C chemokine receptor 5 (CCR5) ligands, macrophage inflammatory proteins (MIPs) MIP-1α/CCL3 and MIP-1β/CCL4, are upregulated in this DAD model up to three orders of magnitude compared to the background level. Results: Here, we showed that a nonpeptide compound TAK-779, an antagonist of CCR5/CXCR3, readily prevents DAD in the lung with a single injection of 2.5 mg/kg. Histological analysis revealed reduced peribronchial and perivascular mononuclear infiltration in the lung and mononuclear infiltration of the wall and lumen of the alveoli in the TAK-779-treated animals. Administration of TAK-779 decreased the 3-5-fold level of serum cytokines and chemokines in animals with DAD, including CCR5 ligands MIP-1α/β, MCP-1, and CCL5. Computed tomography revealed rapid recovery of the density and volume of the affected lung in TAK-779-treated animals. Discussion: Our pre-clinical data suggest that TAK-779 is more effective than the administration of dexamethasone or the anti-IL6R therapeutic antibody tocilizumab, which brings novel therapeutic modality to TAK-779 and other CCR5 inhibitors for the treatment of virus-induced hyperinflammation syndromes, including COVID-19.
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Affiliation(s)
- Aleksandr S. Chernov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maksim V. Rodionov
- Medical Radiological Research Center (MRRC), A.F. Tsyb-Branch of the National Medical Radiological Research Center of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vitaly A. Kazakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Karina A. Ivanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Fedor A. Meshcheryakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna A. Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander G. Gabibov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Life Sciences, Higher School of Economics, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Georgii B. Telegin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Biological Chemistry, Ministry of Health of Russian Federation, Russian University of Medicine, Moscow, Russia
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11
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Okoh GR, Ariel E, Whitmore D, Horwood PF. Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies. ECOHEALTH 2023; 20:427-440. [PMID: 38091182 DOI: 10.1007/s10393-023-01659-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/26/2023] [Indexed: 02/21/2024]
Abstract
The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1-2, agile wallaby polyomavirus 1-2, agile wallaby associated picobirnavirus 1-9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.
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Affiliation(s)
- God'spower Richard Okoh
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - David Whitmore
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
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12
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Bay P, Rodriguez C, Caruso S, Demontant V, Boizeau L, Soulier A, Woerther PL, Mekontso-Dessap A, Pawlotsky JM, de Prost N, Fourati S. Omicron induced distinct immune respiratory transcriptomics signatures compared to pre-existing variants in critically ill COVID-19 patients. J Med Virol 2023; 95:e29268. [PMID: 38050838 DOI: 10.1002/jmv.29268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]
Abstract
Severe coronavirus disease 2019 (COVID-19) is related to dysregulated immune responses. We aimed to explore the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on the immune response by nasopharyngeal transcriptomic in critically-ill patients. This prospective monocentric study included COVID-19 patients requiring intensive care unit (ICU) admission between March 2020 and 2022. Patients were classified according to VOC (ancestral, Alpha, Delta, and Omicron). Eighty-eight patients with severe COVID-19 were included after matching (on prespecified clinical criteria). Profiling of gene expression markers of innate and adaptive immune responses were investigated by respiratory transcriptomics at ICU admission. Eighty-eight patients were included in the study after matching (ancestral [n = 24], Alpha [n = 24], Delta [n = 22], and Omicron [n = 18] variants). Respiratory transcriptomic analysis revealed distinct innate and adaptive immune profiling between variants. In comparison with the ancestral variant, there was a reduced expression of neutrophil degranulation, T cell activation, cytokines signalling pathways in patients infected with Alpha and Delta variants. In contrast, there was a higher expression of neutrophil degranulation, T and B cells activation, and inflammatory interleukins pathways in patients infected with Omicron. To conclude, Omicron induced distinct immune respiratory transcriptomics signatures compared to pre-existing variants in patients with severe COVID-19, pointing to an evolving pathophysiology of severe COVID-19 in the Omicron era.
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Affiliation(s)
- Pierre Bay
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Christophe Rodriguez
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Stefano Caruso
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Pathologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Vanessa Demontant
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Laure Boizeau
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Alexandre Soulier
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Paul L Woerther
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- EA 7380 Dynamic, Université Paris-Est-Créteil (UPEC), École Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Armand Mekontso-Dessap
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Jean-Michel Pawlotsky
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Nicolas de Prost
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Slim Fourati
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
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13
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Lema NK, Gemeda MT, Woldesemayat AA. Recent Advances in Metagenomic Approaches, Applications, and Challenge. Curr Microbiol 2023; 80:347. [PMID: 37733134 DOI: 10.1007/s00284-023-03451-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/20/2023] [Indexed: 09/22/2023]
Abstract
Advances in metagenomics analysis with the advent of next-generation sequencing have extended our knowledge of microbial communities as compared to conventional techniques providing advanced approach to identify novel and uncultivable microorganisms based on their genetic information derived from a particular environment. Shotgun metagenomics involves investigating the DNA of the entire community without the requirement of PCR amplification. It provides access to study all genes present in the sample. On the other hand, amplicon sequencing targets taxonomically important marker genes, the analysis of which is restricted to previously known DNA sequences. While sequence-based metagenomics is used to analyze DNA sequences directly from the environment without the requirement of library construction and with limited identification of novel genes and products that can be complemented by functional genomics, function-based metagenomics requires fragmentation and cloning of extracted metagenome DNA in a suitable host with subsequent functional screening and sequencing clone for detection of a novel gene. Although advances were made in metagenomics, different challenges arise. This review provides insight into advances in the metagenomic approaches combined with next-generation sequencing, their recent applications highlighting the emerging ones, such as in astrobiology, forensic sciences, and SARS-CoV-2 infection diagnosis, and the challenges associated. This review further discusses the different types of metagenomics and outlines advancements in bioinformatics tools and their significance in the analysis of metagenomic datasets.
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Affiliation(s)
- Niguse K Lema
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Department of Biotechnology, Arba Minch University, Arba Minch, Ethiopia
| | - Mesfin T Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Adugna A Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
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14
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Pita-Martínez C, Pérez-García F, Virseda Berdices A, Martin-Vicente M, Castilla-García L, Hervás Fernández I, González Ventosa V, Muñoz-Gómez MJ, Cuadros-González J, Bermejo-Martin JF, Resino S, Martínez I. A deficient immune response to SARS-CoV-2 in the nasopharynx is associated with severe COVID-19 pneumonia. Int J Infect Dis 2023; 134:126-132. [PMID: 37290572 PMCID: PMC10245280 DOI: 10.1016/j.ijid.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVES We analyzed the expression of inflammatory and antiviral genes in the nasopharynx of SARS-CoV-2 infected patients and their association with the severity of COVID-19 pneumonia. METHODS We conducted a cross-sectional study on 223 SARS-CoV-2 infected patients. Clinical data were collected from medical records, and nasopharyngeal samples were collected in the first 24 hours after admission to the emergency room. The gene expression of eight proinflammatory/antiviral genes (plasminogen activator urokinase receptor [PLAUR], interleukin [IL]-6, IL-8, interferon [IFN]-β, IFN-stimulated gene 15 [ISG15], retinoic acid-inducible gene I [RIG-I], C-C motif ligand 5 [CCL5], and chemokine C-X-C motif ligand 10 [CXCL10]) were quantified by real-time polymerase chain reaction. Outcome variables were: (i) pneumonia; (ii) severe pneumonia or acute respiratory distress syndrome. Statistical analysis was performed using multivariate logistic regression analyses. RESULTS We enrolled 84 mild, 88 moderate, and 51 severe/critical cases. High expression of PLAUR (adjusted odds ratio [aOR] = 1.25; P = 0.032, risk factor) and low expression of CXCL10 (aOR = 0.89; P = 0.048, protective factor) were associated with pneumonia. Furthermore, lower values of ISG15 (aOR = 0.88, P = 0.021), RIG-I (aOR = 0.87, P = 0.034), CCL5 (aOR = 0.73, P <0.001), and CXCL10 (aOR = 0.84, P = 0.002) were risk factors for severe pneumonia/acute respiratory distress syndrome. CONCLUSION An unbalanced early innate immune response to SARS-CoV-2 in the nasopharynx, characterized by high expression of PLAUR and low expression of antiviral genes (ISG15 and RIG-I), and chemokines (CCL5 and CXCL10), was associated with COVID-19 severity.
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Affiliation(s)
- Carlos Pita-Martínez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Felipe Pérez-García
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain; Universidad de Alcalá, Facultad de Medicina, Departamento de Biomedicina y Biotecnología, Madrid, Spain
| | - Ana Virseda Berdices
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Martin-Vicente
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Lucía Castilla-García
- Servicio de Hematología y Hemoterapia, Hospital Universitario Príncipe de Asturias, Madrid, Spain
| | - Irene Hervás Fernández
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain
| | | | - María José Muñoz-Gómez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Cuadros-González
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain; Universidad de Alcalá, Facultad de Medicina, Departamento de Biomedicina y Biotecnología, Madrid, Spain
| | - Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Isidoro Martínez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
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15
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Chan AP, Siddique A, Desplat Y, Choi Y, Ranganathan S, Choudhary KS, Khalid MF, Diaz J, Bezney J, DeAscanis D, George Z, Wong S, Selleck W, Bowers J, Zismann V, Reining L, Highlander S, Brown K, Armstrong JR, Hakak Y, Schork NJ. A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness. CELL REPORTS METHODS 2023; 3:100463. [PMID: 37323571 PMCID: PMC10110940 DOI: 10.1016/j.crmeth.2023.100463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/22/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
The lack of preparedness for detecting and responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen (i.e., COVID-19) has caused enormous harm to public health and the economy. Testing strategies deployed on a population scale at day zero, i.e., the time of the first reported case, would be of significant value. Next-generation sequencing (NGS) has such capabilities; however, it has limited detection sensitivity for low-copy-number pathogens. Here, we leverage the CRISPR-Cas9 system to effectively remove abundant sequences not contributing to pathogen detection and show that NGS detection sensitivity of SARS-CoV-2 approaches that of RT-qPCR. The resulting sequence data can also be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single molecular and analysis workflow. This NGS work flow is pathogen agnostic and, therefore, has the potential to transform how large-scale pandemic response and focused clinical infectious disease testing are pursued in the future.
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Affiliation(s)
- Agnes P. Chan
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | | | | | - Yongwook Choi
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | | | | | | | - Josh Diaz
- Jumpcode Genomics, San Diego, CA 92121, USA
| | - Jon Bezney
- Jumpcode Genomics, San Diego, CA 92121, USA
| | | | | | - Shukmei Wong
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - William Selleck
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - Jolene Bowers
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - Victoria Zismann
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - Lauren Reining
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - Sarah Highlander
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | | | | | | | - Nicholas J. Schork
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
- The University of California, San Diego, San Diego, CA 92093, USA
- The Scripps Research Institute, San Diego, CA 92037, USA
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16
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Rodriguez C, Boizeau L, Soulier A, N'Debi M, Demontant V, Trawinski E, Seng S, Fontaine H, Woerther PL, Marchand S, Fourati S, Chevaliez S, Cappy P, Pol S, Pawlotsky JM. Unknown Circovirus in Immunosuppressed Patient with Hepatitis, France, 2022. Emerg Infect Dis 2023; 29:1051-1054. [PMID: 37081594 PMCID: PMC10124635 DOI: 10.3201/eid2905.221485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Hepatitis of undetermined origin can be caused by a wide variety of pathogens, sometimes emerging pathogens. We report the discovery, by means of routine shotgun metagenomics, of a new virus belonging to the family Circoviridae, genus Circovirus, in a patient in France who had acute hepatitis of unknown origin.
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17
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Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
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18
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Altintop SE, Unalan-Altintop T, Cihangiroglu M, Onarer P, Milletli-Sezgin F, Gozukara M, Gozukara B, Zengin E. COVID-19 in elderly: Correlations of viral load, clinical course, laboratory parameters, among patients vaccinated with CoronaVac. Acta Microbiol Immunol Hung 2022; 69:277-282. [PMID: 36370367 DOI: 10.1556/030.2022.01849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022]
Abstract
SARS-CoV-2 virus was initially identified in Wuhan, China, in December 2019 and a global pandemic was declared in March 2020 by World Health Organization. COVID-19 disease is characterized with severe pneumonia and hypoxemia, especially in the elderly population. The elderly population was primarily vaccinated with CoronaVac, which is a whole virion inactivated vaccine (Sinovac Biotech, China) in Turkey. This study aimed to investigate the association of viral load and laboratory parameters with the severity of the disease and vaccination status in elderly (older than 60 years old) COVID-19 patients. The age range of the patients was 61-97 years old with a mean of 71.80. Vaccinated patients had a lower viral load (P = 0.253) in nasopharyngeal swabs during breakthrough COVID-19 infection compared to unvaccinated ones and were hospitalized for a shorter period of time in hospital wards (P = 0.035). A lower number of patients were vaccinated in both moderate (n = 33, 29.20%) and severe/critical group (n = 46, 34.07%) (P = 0.412). Only 17 (32.08%) vaccinated patients were hospitalized in an intensive care unit (ICU), whereas 36 (67.92%) of the ICU patients were unvaccinated (P = 0.931). Severe/critical patients had higher c-reactive protein (CRP), platelet-to-lymphocyte ratio (PLR), fibrinogen, ferritin, and lactate dehydrogenase (LDH) levels compared to the moderate group on the admission day (P < 0.05). Our study suggested that elderly patients vaccinated with CoronaVac had a shorter stay in hospitals and according to our results CRP, PLR, fibrinogen, ferritin, and LDH levels could be used to determine the severity of the infections.
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Affiliation(s)
| | - Tugce Unalan-Altintop
- 2Department of Medical Microbiology, Amasya University Sabuncuoglu Serefeddin Research and Training Hospital, Amasya, Turkey
| | - Mustafa Cihangiroglu
- 3Department of Infectious Disease and Clinical Microbiology, Faculty of Medicine, Amasya University, Amasya, Turkey
| | - Pelin Onarer
- 2Department of Medical Microbiology, Amasya University Sabuncuoglu Serefeddin Research and Training Hospital, Amasya, Turkey
| | | | - Melih Gozukara
- 5Amasya Provincial Directorate of Health, Amasya, Turkey
| | - Bilge Gozukara
- 1Suluova State Hospital, Department of Internal Medicine, Amasya, Turkey
| | - Erman Zengin
- 5Amasya Provincial Directorate of Health, Amasya, Turkey
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19
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More TH, Mozafari B, Märtens A, Herr C, Lepper PM, Danziger G, Volk T, Hoersch S, Krawczyk M, Guenther K, Hiller K, Bals R. Plasma Metabolome Alterations Discriminate between COVID-19 and Non-COVID-19 Pneumonia. Metabolites 2022; 12:1058. [PMID: 36355140 PMCID: PMC9693035 DOI: 10.3390/metabo12111058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 03/10/2024] Open
Abstract
Pneumonia is a common cause of morbidity and mortality and is most often caused by bacterial pathogens. COVID-19 is characterized by lung infection with potential progressive organ failure. The systemic consequences of both disease on the systemic blood metabolome are not fully understood. The aim of this study was to compare the blood metabolome of both diseases and we hypothesize that plasma metabolomics may help to identify the systemic effects of these diseases. Therefore, we profiled the plasma metabolome of 43 cases of COVID-19 pneumonia, 23 cases of non-COVID-19 pneumonia, and 26 controls using a non-targeted approach. Metabolic alterations differentiating the three groups were detected, with specific metabolic changes distinguishing the two types of pneumonia groups. A comparison of venous and arterial blood plasma samples from the same subjects revealed the distinct metabolic effects of pulmonary pneumonia. In addition, a machine learning signature of four metabolites was predictive of the disease outcome of COVID-19 subjects with an area under the curve (AUC) of 86 ± 10 %. Overall, the results of this study uncover systemic metabolic changes that could be linked to the etiology of COVID-19 pneumonia and non-COVID-19 pneumonia.
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Affiliation(s)
- Tushar H. More
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Bahareh Mozafari
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Andre Märtens
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Christian Herr
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Philipp M. Lepper
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Guy Danziger
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Thomas Volk
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Saarland University, 66421 Homburg, Germany
| | - Sabrina Hoersch
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Saarland University, 66421 Homburg, Germany
| | - Marcin Krawczyk
- Department of Internal Medicine II-Gastroenterology, Saarland University, 66421 Homburg, Germany
| | - Katharina Guenther
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Robert Bals
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
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20
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Uruma Y, Manabe T, Fujikura Y, Iikura M, Hojo M, Kudo K. Effect of asthma, COPD, and ACO on COVID-19: A systematic review and meta-analysis. PLoS One 2022; 17:e0276774. [PMID: 36318528 PMCID: PMC9624422 DOI: 10.1371/journal.pone.0276774] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION The prevalence of asthma, chronic obstructive pulmonary disease (COPD), and asthma-COPD overlap (ACO) in patients with COVID-19 varies, as well as their risks of mortality. The present study aimed to assess the prevalence of asthma, COPD, and ACO as comorbidities, and to determine their risks of mortality in patients with COVID-19 using a systematic review and meta-analysis. METHODS We systematically reviewed clinical studies that reported the comorbidities of asthma, COPD, and ACO in patients with COVID-19. We searched various databases including PubMed (from inception to 27 September 2021) for eligible studies written in English. A meta-analysis was performed using the random-effect model for measuring the prevalence of asthma, COPD, and ACO as comorbidities, and the mortality risk of asthma, COPD, and ACO in patients with COVID-19 was estimated. A stratified analysis was conducted according to country. RESULTS One hundred one studies were eligible, and 1,229,434 patients with COVID-19 were identified. Among them, the estimated prevalence of asthma, COPD, and ACO using a meta-analysis was 10.04% (95% confidence interval [CI], 8.79-11.30), 8.18% (95% CI, 7.01-9.35), and 3.70% (95% CI, 2.40-5.00), respectively. The odds ratio for mortality of pre-existing asthma in COVID-19 patients was 0.89 (95% CI, 0.55-1.4; p = 0.630), while that in pre-existing COPD in COVID-19 patients was 3.79 (95% CI, 2.74-5.24; p<0.001). France showed the highest prevalence of asthma followed by the UK, while that of COPD was highest in the Netherlands followed by India. CONCLUSION Pre-existing asthma and COPD are associated with the incidence of COVID-19. Having COPD significantly increases the risk of mortality in patients with COVID-19. These differences appear to be influenced by the difference of locations of disease pathophysiology and by the daily diagnosis and treatment policy of each country.
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Affiliation(s)
- Yuka Uruma
- Nagoya City University Medical School, Aichi, Japan
| | - Toshie Manabe
- Nagoya City University Graduate School of Medical Sciences, Aichi, Japan
- Nagoya City University West Medical Center, Aichi, Japan
| | - Yuji Fujikura
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan
- Department of Medical Risk Management and Infection Control, National Defense Medical College Hospital, Tokorozawa, Japan
| | - Motoyasu Iikura
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Koichiro Kudo
- Yurin Hospital, Tokyo, Japan
- Waseda University, Institute for Asia Human Community, Tokyo, Japan
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21
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Pius-Sadowska E, Niedźwiedź A, Kulig P, Baumert B, Sobuś A, Rogińska D, Łuczkowska K, Ulańczyk Z, Wnęk S, Karolak I, Paczkowska E, Kotfis K, Kawa M, Stecewicz I, Zawodny P, Machaliński B. CXCL8, CCL2, and CMV Seropositivity as New Prognostic Factors for a Severe COVID-19 Course. Int J Mol Sci 2022; 23:ijms231911338. [PMID: 36232655 PMCID: PMC9570115 DOI: 10.3390/ijms231911338] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
The exact pathophysiology of severe COVID-19 is not entirely elucidated, but it has been established that hyperinflammatory responses and cytokine storms play important roles. The aim of this study was to examine CMV status, select chemokines, and complement components in COVID-19, and how concentrations of given molecules differ over time at both molecular and proteomic levels. A total of 210 COVID-19 patients (50 ICU and 160 non-ICU patients) and 80 healthy controls were enrolled in this study. Concentrations of select chemokines (CXCL8, CXCL10, CCL2, CCL3, CCR1) and complement factors (C2, C9, CFD, C4BPA, C5AR1, CR1) were examined at mRNA and protein levels with regard to a COVID-19 course (ICU vs. non-ICU group) and CMV status at different time intervals. We detected several significant differences in chemokines and complement profiles between ICU and non-ICU groups. Pro-inflammatory chemokines and the complement system appeared to greatly contribute to the pathogenesis and development of severe COVID-19. Higher concentrations of CXCL8 and CCL2 in the plasma, with reduced mRNA expression presumably through negative feedback mechanisms, as well as CMV-positive status, correlated with more severe courses of COVID-19. Therefore, CXCL8, CCL2, and CMV seropositivity should be considered as new prognostic factors for severe COVID-19 courses. However, more in-depth research is needed.
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Affiliation(s)
- Ewa Pius-Sadowska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Anna Niedźwiedź
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Piotr Kulig
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Bartłomiej Baumert
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Anna Sobuś
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Dorota Rogińska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Karolina Łuczkowska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Zofia Ulańczyk
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Szymon Wnęk
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Igor Karolak
- Department of Anesthesiology, Intensive Therapy and Acute Intoxications, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Edyta Paczkowska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Katarzyna Kotfis
- Department of Anesthesiology, Intensive Therapy and Acute Intoxications, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Miłosz Kawa
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Iwona Stecewicz
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Piotr Zawodny
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
- Correspondence: ; Tel.: +48-91-4661-546
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22
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da Silva SJR. Comparing studies of SARS-CoV-2 viral loads requires caution. J Med Virol 2022; 94:1811-1812. [PMID: 35092062 PMCID: PMC9015287 DOI: 10.1002/jmv.27631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Department of Pharmaceutical SciencesLeslie Dan Faculty of Pharmacy, University of TorontoTorontoONCanada
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of VirologyAggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz)RecifePernambucoBrazil
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23
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Budhraja A, Basu A, Gheware A, Abhilash D, Rajagopala S, Pakala S, Sumit M, Ray A, Subramaniam A, Mathur P, Nambirajan A, Kumar S, Gupta R, Wig N, Trikha A, Guleria R, Sarkar C, Gupta I, Jain D. Molecular signature of postmortem lung tissue from COVID-19 patients suggests distinct trajectories driving mortality. Dis Model Mech 2022; 15:dmm049572. [PMID: 35438176 PMCID: PMC9194484 DOI: 10.1242/dmm.049572] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/07/2022] [Indexed: 12/19/2022] Open
Abstract
To elucidate the molecular mechanisms that manifest lung abnormalities during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, we performed whole-transcriptome sequencing of lung autopsies from 31 patients with severe COVID-19 and ten uninfected controls. Using metatranscriptomics, we identified the existence of two distinct molecular signatures of lethal COVID-19. The dominant 'classical' signature (n=23) showed upregulation of the unfolded protein response, steroid biosynthesis and complement activation, supported by massive metabolic reprogramming leading to characteristic lung damage. The rarer signature (n=8) that potentially represents 'cytokine release syndrome' (CRS) showed upregulation of cytokines such as IL1 and CCL19, but absence of complement activation. We found that a majority of patients cleared SARS-CoV-2 infection, but they suffered from acute dysbiosis with characteristic enrichment of opportunistic pathogens such as Staphylococcus cohnii in 'classical' patients and Pasteurella multocida in CRS patients. Our results suggest two distinct models of lung pathology in severe COVID-19 patients, which can be identified through complement activation, presence of specific cytokines and characteristic microbiome. These findings can be used to design personalized therapy using in silico identified drug molecules or in mitigating specific secondary infections.
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Affiliation(s)
- Anshul Budhraja
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Anubhav Basu
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Atish Gheware
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Dasari Abhilash
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Seesandra Rajagopala
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman Pakala
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madhuresh Sumit
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Animesh Ray
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Arulselvi Subramaniam
- Department of Laboratory Medicine, JPNATC, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Purva Mathur
- Department of Laboratory Medicine, JPNATC, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sachin Kumar
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ritu Gupta
- Laboratory Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital (IRCH), All India Institute of Medical Sciences, New Delhi 110029, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Anjan Trikha
- Department of Anaesthesiology, Critical Care and Pain Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Randeep Guleria
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
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24
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Rahaman MM, Sarkar MMH, Rahman MS, Islam MR, Islam I, Saha O, Akter S, Banu TA, Jahan I, Habib MA, Goswami B, Bari L, Malek MA, Khan MS. Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach. J Med Virol 2021; 94:1670-1688. [PMID: 34939673 DOI: 10.1002/jmv.27537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
Bangladesh experiences a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approach. Screening for SARS-CoV-2 by RT-PCR and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated=10, non-vaccinated=7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the co-infected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta,V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthy, the RBD region of S protein of all the isolates harbored similar substitutions including K417N, E484K and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS=0.621). Furthermore, we found different bacterial co-infection like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoni and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and non-vaccinated patients in Bangladesh. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Md Murshed Hasan Sarkar
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science Technology, Jashore, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Shahina Akter
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Tanjian Akhtar Banu
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Iffat Jahan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Md Ahasan Habib
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Barna Goswami
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Latiful Bari
- Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Abdul Malek
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Salim Khan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
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25
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Pérez-García F, Martin-Vicente M, Rojas-García RL, Castilla-García L, Muñoz-Gomez MJ, Hervás Fernández I, González Ventosa V, Vidal-Alcántara EJ, Cuadros-González J, Bermejo-Martin JF, Resino S, Martínez I. High SARS-CoV-2 viral load and low CCL5 expression levels in the upper respiratory tract are associated with COVID-19 severity. J Infect Dis 2021; 225:977-982. [PMID: 34910814 PMCID: PMC8754799 DOI: 10.1093/infdis/jiab604] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/01/2023] Open
Abstract
Mucosal immune response in the upper respiratory tract is crucial for the initial control of viral replication, the clearance of SARS-CoV-2, and the progression of the coronavirus disease 2019 (COVID-19). We analyzed the SARS-CoV-2 RNA load and the expression of selected immune genes in the upper respiratory tract (nasopharynx) of 255 SARS-CoV-2 infected patients and evaluated their association with severe COVID-19. SARS-CoV-2 replication in the nasopharyngeal mucosa induces the expression of several innate immune genes. High SARS-CoV-2 viral load and low CCL5 expression levels were associated with ICU admission or death, although CCL5 was the best predictor of COVID-19 severity.
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Affiliation(s)
- Felipe Pérez-García
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain.,Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain.,Departamento de Biomedicina y Biotecnología, Facultad de Medicina. Universidad de Alcalá de Henares, Madrid, Spain
| | - María Martin-Vicente
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Lía Rojas-García
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Lucia Castilla-García
- Servicio de Hematología y Hemoterapia, Hospital Universitario Príncipe de Asturias, Madrid, Spain
| | - María José Muñoz-Gomez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Irene Hervás Fernández
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain
| | | | - Erick Joan Vidal-Alcántara
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Juan Cuadros-González
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain.,Departamento de Biomedicina y Biotecnología, Facultad de Medicina. Universidad de Alcalá de Henares, Madrid, Spain
| | - Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Salamanca, Spain.,Hospital Universitario Río Hortega, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Isidoro Martínez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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26
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Carbo EC, Blankenspoor I, Goeman JJ, Kroes ACM, Claas ECJ, De Vries JJC. Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield. Expert Rev Mol Diagn 2021; 21:1139-1146. [PMID: 34607520 DOI: 10.1080/14737159.2021.1985467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. AREAS COVERED This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. EXPERT OPINION The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ivar Blankenspoor
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloys C M Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C De Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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