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Geng LN, Bonilla H, Hedlin H, Jacobson KB, Tian L, Jagannathan P, Yang PC, Subramanian AK, Liang JW, Shen S, Deng Y, Shaw BJ, Botzheim B, Desai M, Pathak D, Jazayeri Y, Thai D, O’Donnell A, Mohaptra S, Leang Z, Reynolds GZM, Brooks EF, Bhatt AS, Shafer RW, Miglis MG, Quach T, Tiwari A, Banerjee A, Lopez RN, De Jesus M, Charnas LR, Utz PJ, Singh U. Nirmatrelvir-Ritonavir and Symptoms in Adults With Postacute Sequelae of SARS-CoV-2 Infection: The STOP-PASC Randomized Clinical Trial. JAMA Intern Med 2024; 184:1024-1034. [PMID: 38848477 PMCID: PMC11161857 DOI: 10.1001/jamainternmed.2024.2007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/30/2024] [Indexed: 06/09/2024]
Abstract
Importance There is an urgent need to identify treatments for postacute sequelae of SARS-CoV-2 infection (PASC). Objective To assess the efficacy of a 15-day course of nirmatrelvir-ritonavir in reducing the severity of select PASC symptoms. Design, Setting, and Participants This was a 15-week blinded, placebo-controlled, randomized clinical trial conducted from November 2022 to September 2023 at Stanford University (California). The participants were adults with moderate to severe PASC symptoms of 3 months or longer duration. Interventions Participants were randomized 2:1 to treatment with oral nirmatrelvir-ritonavir (NMV/r, 300 mg and 100 mg) or with placebo-ritonavir (PBO/r) twice daily for 15 days. Main Outcomes and Measures Primary outcome was a pooled severity of 6 PASC symptoms (fatigue, brain fog, shortness of breath, body aches, gastrointestinal symptoms, and cardiovascular symptoms) based on a Likert scale score at 10 weeks. Secondary outcomes included symptom severity at different time points, symptom burden and relief, patient global measures, Patient-Reported Outcomes Measurement Information System (PROMIS) measures, orthostatic vital signs, and sit-to-stand test change from baseline. Results Of the 155 participants (median [IQR] age, 43 [34-54] years; 92 [59%] females), 102 were randomized to the NMV/r group and 53 to the PBO/r group. Nearly all participants (n = 153) had received the primary series for COVID-19 vaccination. Mean (SD) time between index SARS-CoV-2 infection and randomization was 17.5 (9.1) months. There was no statistically significant difference in the model-derived severity outcome pooled across the 6 core symptoms at 10 weeks between the NMV/r and PBO/r groups. No statistically significant between-group differences were found at 10 weeks in the Patient Global Impression of Severity or Patient Global Impression of Change scores, summative symptom scores, and change from baseline to 10 weeks in PROMIS fatigue, dyspnea, cognitive function, and physical function measures. Adverse event rates were similar in NMV/r and PBO/r groups and mostly of low grade. Conclusions and Relevance The results of this randomized clinical trial showed that a 15-day course of NMV/r in a population of patients with PASC was generally safe but did not demonstrate a significant benefit for improving select PASC symptoms in a mostly vaccinated cohort with protracted symptom duration. Further studies are needed to determine the role of antivirals in the treatment of PASC. Trial Registration ClinicalTrials.gov Identifier: NCT05576662.
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Affiliation(s)
- Linda N. Geng
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Hector Bonilla
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Haley Hedlin
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Karen B. Jacobson
- Department of Medicine, Stanford University School of Medicine, Stanford, California
- Kaiser Permanente Northern California Division of Research, Oakland
| | - Lu Tian
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford, California
| | - Prasanna Jagannathan
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Phillip C. Yang
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Aruna K. Subramanian
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Jane W. Liang
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Sa Shen
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Yaowei Deng
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Blake J. Shaw
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Bren Botzheim
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Manisha Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Divya Pathak
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Yasmin Jazayeri
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Daniel Thai
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Andrew O’Donnell
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Sukanya Mohaptra
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Zenita Leang
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Erin F. Brooks
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Ami S. Bhatt
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Robert W. Shafer
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Mitchell G. Miglis
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California
| | - Tom Quach
- Stanford University, Stanford, California
| | | | - Anindita Banerjee
- Pfizer Research and Development, Pfizer Inc, Cambridge, Massachusetts
| | - Rene N. Lopez
- Clinical Research Collaborations COE, Worldwide Medical and Safety, Pfizer Inc, Groton, Connecticut
| | - Magdia De Jesus
- Strategic Planning, Worldwide Medical and Safety, Pfizer Inc, New York, New York
| | - Lawrence R. Charnas
- Clinical Research Collaborations COE, Worldwide Medical and Safety, Pfizer Inc, Groton, Connecticut
| | - Paul J. Utz
- Department of Medicine, Stanford University School of Medicine, Stanford, California
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California
| | - Upinder Singh
- Department of Medicine, Stanford University School of Medicine, Stanford, California
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
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2
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Palmer CS, Perdios C, Abdel-Mohsen M, Mudd J, Datta PK, Maness NJ, Lehmicke G, Golden N, Hellmers L, Coyne C, Moore Green K, Midkiff C, Williams K, Tiburcio R, Fahlberg M, Boykin K, Kenway C, Russell-Lodrigue K, Birnbaum A, Bohm R, Blair R, Dufour JP, Fischer T, Saied AA, Rappaport J. Non-human primate model of long-COVID identifies immune associates of hyperglycemia. Nat Commun 2024; 15:6664. [PMID: 39164284 PMCID: PMC11335872 DOI: 10.1038/s41467-024-50339-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 07/08/2024] [Indexed: 08/22/2024] Open
Abstract
Hyperglycemia, and exacerbation of pre-existing deficits in glucose metabolism, are manifestations of the post-acute sequelae of SARS-CoV-2. Our understanding of metabolic decline after acute COVID-19 remains unclear due to the lack of animal models. Here, we report a non-human primate model of metabolic post-acute sequelae of SARS-CoV-2 using SARS-CoV-2 infected African green monkeys. Using this model, we identify a dysregulated blood chemokine signature during acute COVID-19 that correlates with elevated and persistent hyperglycemia four months post-infection. Hyperglycemia also correlates with liver glycogen levels, but there is no evidence of substantial long-term SARS-CoV-2 replication in the liver and pancreas. Finally, we report a favorable glycemic effect of the SARS-CoV-2 mRNA vaccine, administered on day 4 post-infection. Together, these data suggest that the African green monkey model exhibits important similarities to humans and can be utilized to assess therapeutic candidates to combat COVID-related metabolic defects.
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Affiliation(s)
- Clovis S Palmer
- Tulane National Primate Research Center, Covington, LA, USA.
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA.
| | - Chrysostomos Perdios
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Joseph Mudd
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasun K Datta
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Nicholas J Maness
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Nadia Golden
- Tulane National Primate Research Center, Covington, LA, USA
| | - Linh Hellmers
- Tulane National Primate Research Center, Covington, LA, USA
| | - Carol Coyne
- Tulane National Primate Research Center, Covington, LA, USA
| | | | - Cecily Midkiff
- Tulane National Primate Research Center, Covington, LA, USA
| | | | - Rafael Tiburcio
- Division of Experimental Medicine, Department of Medicine, University of San Francisco, CA, USA
| | | | - Kyndal Boykin
- Tulane National Primate Research Center, Covington, LA, USA
| | - Carys Kenway
- Tulane National Primate Research Center, Covington, LA, USA
| | - Kasi Russell-Lodrigue
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Rudolf Bohm
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Robert Blair
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jason P Dufour
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Tracy Fischer
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Ahmad A Saied
- Tulane National Primate Research Center, Covington, LA, USA
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jay Rappaport
- Tulane National Primate Research Center, Covington, LA, USA.
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA.
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3
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Ribeiro AVC, Mannarino CF, Novo SPC, Prado T, Lermontov A, de Paula BB, Fumian TM, Miagostovich MP. Assessment of crAssphage as a biological variable for SARS-CoV-2 data normalization in wastewater surveillance. J Appl Microbiol 2024; 135:lxae177. [PMID: 39013607 DOI: 10.1093/jambio/lxae177] [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: 03/20/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/18/2024]
Abstract
AIMS This study aimed to assess the use of cross-assembled phage (crAssphage) as an endogenous control employing a multivariate normalization analysis and its application as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) data normalizer. METHODS AND RESULTS A total of 188 twelve-hour composite raw sewage samples were obtained from eight wastewater treatment plants (WWTP) during a 1-year monitoring period. Employing the N1 and N2 target regions, SARS-CoV-2 RNA was detected in 94% (177) and 90% (170) of the samples, respectively, with a global median of 5 log10 genomic copies per liter (GC l-1). CrAssphage was detected in 100% of the samples, ranging from 8.29 to 10.43 log10 GC l-1, with a median of 9.46 ± 0.40 log10 GC l-1, presenting both spatial and temporal variabilities. CONCLUSIONS Although SARS-CoV-2 data normalization employing crAssphage revealed a correlation with clinical cases occurring during the study period, crAssphage normalization by the flow per capita per day of each WWTP increased this correlation, corroborating the importance of normalizing wastewater surveillance data in disease trend monitoring.
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Affiliation(s)
- André Vinicius Costa Ribeiro
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - Camille Ferreira Mannarino
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - Shênia Patrícia Corrêa Novo
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - Tatiana Prado
- Laboratory of Respiratory, Exanthematic, Enteroviruses and Viral Emergencies, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - André Lermontov
- Chemical and Biochemical Process Technology, School of Chemistry/Federal University of Rio de Janeiro - EQ/UFRJ, Rio de Janeiro 21941-909, Brazil
| | - Bruna Barbosa de Paula
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
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4
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Greenwald MA, Namin S, Zajdowicz J, Jones AL, Fritts L, Kuehnert MJ, Miller CJ, Ray G. Testing of tissue specimens obtained from SARS-CoV-2 nasopharyngeal swab-positive donors. Cell Tissue Bank 2024; 25:583-604. [PMID: 37995051 PMCID: PMC11143015 DOI: 10.1007/s10561-023-10119-8] [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: 03/14/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Risk for transmission of SARS-CoV-2 through allogeneic human tissue transplantation is unknown. To further evaluate the risk of virus transmission, tissues were obtained from deceased donors who had tested positive for SARS-CoV-2 RNA via nasopharyngeal swab. This study evaluated an array of human tissues recovered for transplantation, including bone, tendon, skin, fascia lata, vascular tissues, and heart valves. Tissue samples and plasma or serum samples, if available, were tested for viral RNA (vRNA) using a real time PCR system for the presence of virus RNA. All samples were tested in quadruplicate for both subgenomic (sgRNA) and genomic (gRNA) RNA encoding the SARS-CoV-2 nucleocapsid gene. Amplification of a cellular housekeeping gene served as the positive control for every sample. A total of 47 tissue samples from 17 donors were tested for SARS-CoV-2 RNA. Four donors had plasma or serum available for paired testing. SARS-CoV-2 RNA was not detected from any tissue or plasma/serum sample tested. Based on these findings, risk of transmission through the transplantation of tissue types studied from SARS-CoV-2 infected donors is likely to be low.
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Affiliation(s)
- Melissa A Greenwald
- Donor Alliance, Denver, CO, USA.
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
| | | | | | | | | | - Matthew J Kuehnert
- MTF Biologics, Edison, NJ, USA
- Hackensack Meridian School of Medicine, Hackensack, NJ, USA
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5
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Wulandari S, Nuryastuti T, Oktoviani FN, Daniwijaya MEW, Supriyati E, Arguni E, Hartono, Wibawa T. The association between high mobility group box 1 (HMGB1) and Interleukin-18 (IL-18) serum concentrations in COVID-19 inpatients. Heliyon 2024; 10:e26619. [PMID: 38434314 PMCID: PMC10907672 DOI: 10.1016/j.heliyon.2024.e26619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
Background High mobility group box 1 (HMGB1) and interleukin-18 (IL-18) are involved in various non-coronavirus disease pathogenesis and are reported as potential biomarkers for coronavirus disease (COVID-19). However, their association with COVID-19 pathogenesis has not yet been explored. Aim This study aimed to investigate the association between HMGB1 and IL-18 concentrations in the sera of COVID-19 patients versus non-COVID-19 patients. Material and methods We used stored serum samples obtained from 30 COVID-19 patients and 30 non-COVID-19 patients. We collected data on age, gender, treatment status, principal diagnosis, and comorbidity from patient medical records. HMGB1 and IL-18 concentrations were analyzed in the serum by enzyme-linked immunosorbent assay (ELISA). The swab samples' RT-PCR cycle threshold (CT) values were obtained from the laboratory database. Results HMGB1 concentrations were increased in the COVID-19 inpatients and non-COVID-19 inpatients compared to non-COVID-19 outpatients (COVID-19 inpatients vs. non-COVID-19 outpatients: 151.33 (90.27-192.38) vs. 80.75 (54.16-128.72) ng/ml; p = 0.0316; non-COVID-19 inpatients vs. non-COVID-19 outpatients: 152.66 (104.04-288.51) vs. 80.75 (54.16-128.72) ng/ml; p = 0.0199). IL-18 concentrations were also higher in the COVID-19 inpatients and non-COVID-19 inpatients compared to non-COVID-19 outpatients (COVID-19 inpatients vs. non-COVID-19 outpatients: 620.00 (461.50-849.6) vs. 403.10 (372.70-556.90) pg/ml; p = 0.0376; non-COVID-19 inpatients vs. non-COVID-19 outpatients: 835.70 (558.30-1602.00) vs. 403.10 (372.70-556.90) pg/ml; p = 0.0026). Moreover, HMGB1 was associated with IL-18 concentrations in the sera of COVID-19 inpatients (p = 0.0337; r = 0.5500). Conclusion The association of HMGB1 and IL-18 in COVID-19 might indicate the potential for a dangerous cycle leading to a cytokine storm to occur.
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Affiliation(s)
- Sri Wulandari
- Doctorate Program of Medicine and Health Science, Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Physiology, Faculty of Medicine, Universitas Sebelas Maret, Surakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Farida Nur Oktoviani
- Department of Microbiology, Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hartono
- Department of Physiology, Faculty of Medicine, Universitas Sebelas Maret, Surakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada, Yogyakarta, Indonesia
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6
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Martínez-González B, Soria ME, Mínguez P, Lorenzo-Redondo R, Salar-Vidal L, López-García A, Esteban-Muñoz M, Durán-Pastor A, Somovilla P, García-Crespo C, de Ávila AI, Gómez J, Esteban J, Fernández-Roblas R, Gadea I, Domingo E, Perales C. SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? Front Microbiol 2024; 15:1358258. [PMID: 38559344 PMCID: PMC10979541 DOI: 10.3389/fmicb.2024.1358258] [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: 12/19/2023] [Accepted: 02/21/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade. Methods Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra. Results In 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon. Discussion We evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spread─in particular Omicron lineages─that does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hosts.
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Affiliation(s)
- Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - María Eugenia Soria
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ramón Lorenzo-Redondo
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Alberto López-García
- Health Research Institute IIS-FJD, Fundación Jiménez Diaz University Hospital, Madrid, Spain
| | - Mario Esteban-Muñoz
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Jordi Gómez
- Instituto de Parasitología y Biomedicina “López-Neyra” (CSIC), Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Ricardo Fernández-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
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7
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Röltgen K, Boyd SD. Antibody and B Cell Responses to SARS-CoV-2 Infection and Vaccination: The End of the Beginning. ANNUAL REVIEW OF PATHOLOGY 2024; 19:69-97. [PMID: 37738512 DOI: 10.1146/annurev-pathmechdis-031521-042754] [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: 09/24/2023]
Abstract
As the COVID-19 pandemic has evolved during the past years, interactions between human immune systems, rapidly mutating and selected SARS-CoV-2 viral variants, and effective vaccines have complicated the landscape of individual immunological histories. Here, we review some key findings for antibody and B cell-mediated immunity, including responses to the highly mutated omicron variants; immunological imprinting and other impacts of successive viral antigenic variant exposures on antibody and B cell memory; responses in secondary lymphoid and mucosal tissues and non-neutralizing antibody-mediated immunity; responses in populations vulnerable to severe disease such as those with cancer, immunodeficiencies, and other comorbidities, as well as populations showing apparent resistance to severe disease such as many African populations; and evidence of antibody involvement in postacute sequelae of infection or long COVID. Despite the initial phase of the pandemic ending, human populations will continue to face challenges presented by this unpredictable virus.
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Affiliation(s)
- Katharina Röltgen
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA;
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
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8
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Lamb KD, Luka MM, Saathoff M, Orton RJ, Phan MVT, Cotten M, Yuan K, Robertson DL. Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Comput Biol 2024; 20:e1011795. [PMID: 38271457 PMCID: PMC10868779 DOI: 10.1371/journal.pcbi.1011795] [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: 07/12/2023] [Revised: 02/15/2024] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped by viral, individual human and population factors. SARS-CoV-2 variants are defined by their unique combinations of mutations and there has been a clear adaptation to more efficient human infection since the emergence of this new human coronavirus in late 2019. Here, we use machine learning models to identify shared signatures, i.e., common underlying mutational processes and link these to the subset of mutations that define the variants of concern (VOCs). First, we examined the global SARS-CoV-2 genomes and associated metadata to determine how viral properties and public health measures have influenced the magnitude of waves, as measured by the number of infection cases, in different geographic locations using regression models. This analysis showed that, as expected, both public health measures and virus properties were associated with the waves of regional SARS-CoV-2 reported infection numbers and this impact varies geographically. We attribute this to intrinsic differences such as vaccine coverage, testing and sequencing capacity and the effectiveness of government stringency. To assess underlying evolutionary change, we used non-negative matrix factorisation and observed three distinct mutational signatures, unique in their substitution patterns and exposures from the SARS-CoV-2 genomes. Signatures 1, 2 and 3 were biased to C→T, T→C/A→G and G→T point mutations. We hypothesise assignments of these mutational signatures to the host antiviral molecules APOBEC, ADAR and ROS respectively. We observe a shift amidst the pandemic in relative mutational signature activity from predominantly Signature 1 changes to an increasingly high proportion of changes consistent with Signature 2. This could represent changes in how the virus and the host immune response interact and indicates how SARS-CoV-2 may continue to generate variation in the future. Linkage of the detected mutational signatures to the VOC-defining amino acids substitutions indicates the majority of SARS-CoV-2's evolutionary capacity is likely to be associated with the action of host antiviral molecules rather than virus replication errors.
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Affiliation(s)
- Kieran D. Lamb
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Martha M. Luka
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Megan Saathoff
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| | - Richard J. Orton
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| | - My V. T. Phan
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- College of Health Solutions, Arizona State University, Phoenix, Arizona, United States of America
| | - Matthew Cotten
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- College of Health Solutions, Arizona State University, Phoenix, Arizona, United States of America
- Complex Adaptive Systems Initiative, Arizona State University, Scottsdale, Arizona, United States of America
| | - Ke Yuan
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Cancer Research UK Scotland Institute, Glasgow, Scotland, United Kingdom
| | - David L. Robertson
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
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9
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Yakti FAZ, Abusalah L, Ganji V. Sarcopenia and Mortality in Critically Ill COVID-19 Patients. Life (Basel) 2023; 14:24. [PMID: 38255640 PMCID: PMC10820280 DOI: 10.3390/life14010024] [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: 05/22/2023] [Revised: 11/10/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
COVID-19 can manifest as either asymptomatic or progressing to a severe phase in some patients, which may require hospitalization. These patients may experience dyspnea and hypoxia, leading to the development of acute respiratory distress syndrome. Studies have reported an increased risk of severe sarcopenia in COVID-19 patients during and after recovery. This narrative review aimed to summarize and synthesize available studies on the association between sarcopenia and mortality in critically ill COVID-19 patients. A total of 22 studies conducted on hospitalized COVID-19 patients were included in this review. Of those, 17 studies reported a direct association, while 5 studies showed no association between sarcopenia and mortality in severe COVID-19 patients. It is important to maintain muscle quality and quantity in defense against COVID-19. The measurement of lean muscle mass should be included in the risk assessment of severely ill COVID-19 patients as part of the therapy plan.
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Affiliation(s)
- Fatima Al Zahra Yakti
- Human Nutrition Department, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (F.A.Z.Y.); (L.A.)
| | - Lana Abusalah
- Human Nutrition Department, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (F.A.Z.Y.); (L.A.)
| | - Vijay Ganji
- Department of Nutrition and Dietetics, School of Health and Human Sciences, Indiana University Indianapolis, 1050 Wishard Blvd., Indianapolis, IN 46202, USA
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10
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Lombardo D, Musolino C, Chines V, Caminiti G, Palermo C, Cacciola I, Raffa G, Pollicino T. Assessing Genomic Mutations in SARS-CoV-2: Potential Resistance to Antiviral Drugs in Viral Populations from Untreated COVID-19 Patients. Microorganisms 2023; 12:2. [PMID: 38276171 PMCID: PMC10821222 DOI: 10.3390/microorganisms12010002] [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: 10/30/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Naturally occurring SARS-CoV-2 variants mutated in genomic regions targeted by antiviral drugs have not been extensively studied. This study investigated the potential of the RNA-dependent RNA polymerase (RdRp) complex subunits and non-structural protein (Nsp)5 of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to accumulate natural mutations that could affect the efficacy of antiviral drugs. To this aim, SARS-CoV-2 genomic sequences isolated from 4155 drug-naive individuals from southern Italy were analyzed using the Illumina MiSeq platform. Sequencing of the 4155 samples showed the following viral variant distribution: 71.2% Delta, 22.2% Omicron, and 6.4% Alpha. In the Nsp12 sequences, we found 84 amino acid substitutions. The most common one was P323L, detected in 3777/4155 (91%) samples, with 2906/3777 (69.9%) also showing the G671S substitution in combination. Additionally, we identified 28, 14, and 24 different amino acid substitutions in the Nsp5, Nsp7, and Nsp8 genomic regions, respectively. Of note, the V186F and A191V substitutions, affecting residues adjacent to the active site of Nsp5 (the target of the antiviral drug Paxlovid), were found in 157/4155 (3.8%) and 3/4155 (0.07%) samples, respectively. In conclusion, the RdRp complex subunits and the Nsp5 genomic region exhibit susceptibility to accumulating natural mutations. This susceptibility poses a potential risk to the efficacy of antiviral drugs, as these mutations may compromise the drug ability to inhibit viral replication.
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Affiliation(s)
- Daniele Lombardo
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Cristina Musolino
- Department of Human Pathology, University Hospital of Messina, 98124 Messina, Italy;
| | - Valeria Chines
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Giuseppe Caminiti
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Claudia Palermo
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Irene Cacciola
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Giuseppina Raffa
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Teresa Pollicino
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
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11
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Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N. Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience 2023; 26:108449. [PMID: 38213785 PMCID: PMC10783605 DOI: 10.1016/j.isci.2023.108449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.
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Affiliation(s)
- Anvita Bhargava
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Ugo Szachnowski
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Dominika Foretek
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Vincent Caval
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Sophie-Marie Aicher
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | | | - Patricia Jeannin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Guillaume Beauclair
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Marc Monot
- Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France
| | - Antonin Morillon
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
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12
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Saturday T, van Doremalen N. Pathogenesis of severe acute respiratory syndrome coronavirus-2 in nonhuman primates. Curr Opin Virol 2023; 63:101375. [PMID: 37826865 DOI: 10.1016/j.coviro.2023.101375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
The continued pressure of COVID-19 on public health worldwide underlines the need for a better understanding of the mechanisms of disease caused by severe acute respiratory syndrome coronavirus-2. Though many animal models are readily available for use, the nonhuman primate (NHP) models are considered the gold standard in recapitulating disease progression in humans. In this review, we highlight the relevant research since the beginning of the pandemic to critically evaluate the importance of this model. We characterize the disease's clinical manifestations, aspects of viral replication and shedding, induction of the host's immune response, and pathological findings that broaden our understanding of the importance of NHPs in research to strengthen our public health approach to the pandemic.
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Affiliation(s)
- Taylor Saturday
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
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13
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Heinrich F, Mertz KD, Glatzel M, Beer M, Krasemann S. Using autopsies to dissect COVID-19 pathogenesis. Nat Microbiol 2023; 8:1986-1994. [PMID: 37798476 DOI: 10.1038/s41564-023-01488-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 09/04/2023] [Indexed: 10/07/2023]
Abstract
The emergence of SARS-CoV-2 has resulted in millions of deaths as a result of COVID-19. Suitable models were missing at the beginning of the pandemic, and studies investigating disease pathogenesis relied on patients who had succumbed to COVID-19. Since then, autopsies of patients have substantially contributed to our understanding of the pathogenesis of COVID-19 and associated major organ complications. Here we summarize how autopsies have complemented experimental studies, mainly in animal models, and how they have facilitated critical knowledge of COVID-19 to improve daily clinical practice and develop therapeutic interventions. Employing advanced histopathologic and molecular genetic methods in post-mortem tissues, the COVID-19 pandemic has highlighted the importance of autopsies for virology research and clinical practice in current and emerging infectious diseases.
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Affiliation(s)
- Fabian Heinrich
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten D Mertz
- Institute of Pathology, Kantonsspital Baselland, Liestal, Switzerland
- University of Basel, Basel, Switzerland
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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14
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He YF, Liu JQ, Hu XD, Li HM, Wu N, Wang J, Jiang ZG. Breastfeeding vs. breast milk transmission during COVID-19 pandemic, which is more important? Front Pediatr 2023; 11:1253333. [PMID: 37744448 PMCID: PMC10511770 DOI: 10.3389/fped.2023.1253333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
The catastrophic coronavirus disease 2019 (COVID-19) pandemic has raised many health questions, and whether breast milk from SARS-CoV-2 infected mothers may be a vector for SARS-CoV-2 transmission has become a hot topic of concern worldwide. Currently, there are extremely limited and conflicting data on the risk of infection in infants through breastfeeding. For this reason, we investigated almost all current clinical studies and systematically analyzed the presence of SARS-CoV-2 and antibodies in the breast milk of mothers infected with SARS-CoV-2, their effects on newborns, and the mechanisms involved. A total of 82 studies were included in this review, of which 66 examined the presence of SARS-CoV-2 in breast milk samples from mothers diagnosed with COVID-19, 29 reported results of antibody detection of SARS-CoV-2 in breast milk, and 13 reported both nucleic acid and antibody test results. Seventeen studies indicated the presence of detectable SARS-CoV-2 nucleic acid in breast milk samples, and only two studies monitored viral activity, both of which reported that infectious viruses could not be cultured from RNA-positive breast milk samples. All 29 studies indicated the presence of at least one of the three antibodies, IgA, IgG and IgM, in breast milk. Five studies indicated the presence of at least one antibody in the serum of breastfed newborns. No COVID-19-related deaths were reported in all 1,346 newborns. Our study suggests that direct breastfeeding does not pose an additional risk of infection to newborns and that breast milk is a beneficial source of anti-SARS-CoV-2 antibodies that provide passive immune protection to infants. In addition, direct breastfeeding would provide maternal benefits. Our review supports the recommendation to encourage direct breastfeeding under appropriate infection control guidelines. Systematic Review Registration: https://www.crd.york.ac.uk/PROSPERO/#myprospero, identifier: 458043.
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Affiliation(s)
- Yan-fei He
- Health Management Center, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jun-qiang Liu
- Department of Thoracic Surgery, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiao-dong Hu
- Department of Endocrinology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hu-ming Li
- Department of Respiratory Medicine, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Ni Wu
- Health Management Center, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jie Wang
- Health Management Center, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhi-gang Jiang
- Department of Statistics, Zunyi Medical University, Zunyi, China
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15
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Greenwald MA, Grebe E, Green V, Jones AL, Linnen JM, Williamson P, Busch MP, Kuehnert MJ. Low rate of detection of SARS-CoV-2 RNA in deceased tissue donors. Cell Tissue Bank 2023; 24:585-596. [PMID: 36484950 PMCID: PMC9734833 DOI: 10.1007/s10561-022-10054-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022]
Abstract
Given the possibility for disease transmission, this study was performed to determine whether there is detectable SARS-CoV-2 viral RNA in the blood of deceased tissue donors. A retrospective analysis of blood samples from eligible deceased tissue donors from Oct 2019 through June 2020 was performed. Plasma aliquots were initially tested with a SARS-CoV-2 NAT Assay; positive samples were further tested using an alternate NAT and an antibody assay. The proportion of donors with confirmed RNAemia and 95% confidence intervals were computed. Of donor samples collected in 2019, 894 yielded valid results, with 6 initially positive, none of which confirmed positive by alternate NAT. Of donor samples collected in 2020, 2562 yielded valid initial NAT results, with 21 (0.8%) initially positive. Among those, 3 were confirmed by alternate NAT, 17 were not confirmed, and 1 had an invalid alternate NAT result. The rate of SARS-CoV-2 RNAemia in deceased tissue donors is approximately 1 per 1000, and it is unknown whether this RNAemia reflects the presence of infectious virus. Given these results, the risk of transmission through tissue is thought likely to be low.
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Affiliation(s)
- Melissa A. Greenwald
- Donor Alliance, Denver, CO USA
- Uniformed Services University of the Health Sciences, Bethesda, MD USA
- MA Greenwald Consulting, Chicago, IL USA
| | - Eduard Grebe
- Vitalant Research Institute, San Francisco, CA USA
- University of California San Francisco, San Francisco, CA USA
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
| | | | | | | | | | - Michael P. Busch
- Vitalant Research Institute, San Francisco, CA USA
- University of California San Francisco, San Francisco, CA USA
| | - Matthew J. Kuehnert
- Musculoskeletal Transplant Foundation, Edison, NJ USA
- Hackensack Meridian School of Medicine, Hackensack, NJ USA
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16
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Fryer HR, Golubchik T, Hall M, Fraser C, Hinch R, Ferretti L, Thomson L, Nurtay A, Pellis L, House T, MacIntyre-Cockett G, Trebes A, Buck D, Piazza P, Green A, Lonie LJ, Smith D, Bashton M, Crown M, Nelson A, McCann CM, Adnan Tariq M, Elstob CJ, Nunes Dos Santos R, Richards Z, Xhang X, Hawley J, Lee MR, Carrillo-Barragan P, Chapman I, Harthern-Flint S, Bonsall D, Lythgoe KA. Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias. PLoS Pathog 2023; 19:e1011461. [PMID: 37578971 PMCID: PMC10449197 DOI: 10.1371/journal.ppat.1011461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 08/24/2023] [Accepted: 06/05/2023] [Indexed: 08/16/2023] Open
Abstract
In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. By analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior exposure, viral burden was 44% lower among Alpha variant infections, compared to those with the predecessor strain, B.1.177. Vaccination reduced viral burden by 67%, and among vaccinated individuals, viral burden was 286% higher among Delta variant, compared to Alpha variant, infections. In addition, viral burden increased by 17% for every 10-year age increment of the infected individual. In summary, within-host viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant.
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Affiliation(s)
- Helen R. Fryer
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Robert Hinch
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Laura Thomson
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Lorenzo Pellis
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
| | | | - Amy Trebes
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - David Buck
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Angie Green
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Lorne J Lonie
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Darren Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Matthew Crown
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Clare M. McCann
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Mohammed Adnan Tariq
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Claire J. Elstob
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Rui Nunes Dos Santos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Zack Richards
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Xin Xhang
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Joseph Hawley
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Mark R. Lee
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Priscilla Carrillo-Barragan
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Isobel Chapman
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Sarah Harthern-Flint
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | | | - David Bonsall
- Pandemic Sciences Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Katrina A. Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Department of Biology, University of Oxford, Oxford, United Kingdom
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17
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Pavan M, Fanti CD, Lucia AD, Canato E, Acquasaliente L, Sonvico F, Delgado J, Hicks A, Torrelles JB, Kulkarni V, Dwivedi V, Zanellato AM, Galesso D, Pasut G, Buttini F, Martinez-Sobrido L, Guarise C. AEROSOLIZED SULFATED HYALURONAN DERIVATIVES PROLONG THE SURVIVAL OF K18 ACE2 MICE INFECTED WITH A LETHAL DOSE OF SARS-COV-2. Eur J Pharm Sci 2023:106489. [PMID: 37311533 DOI: 10.1016/j.ejps.2023.106489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/19/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Despite several vaccines that are currently approved for human use to control the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent medical need for therapeutic and prophylactic options. SARS-CoV-2 binding and entry in human cells involves interactions of its spike (S) protein with several host cell surface factors, including heparan sulfate proteoglycans (HSPGs), transmembrane protease serine 2 (TMPRSS2), and angiotensin-converting enzyme 2 (ACE2). In this paper we investigated the potential of sulphated Hyaluronic Acid (sHA), a HSPG mimicking polymer, to inhibit the binding of SARS-CoV-2 S protein to human ACE2 receptor. After the assessment of different sulfation degree of sHA backbone, a series of sHA functionalized with different hydrophobic side chains were synthesized and screened. The compound showing the highest binding affinity to the viral S protein was further characterized by surface plasmon resonance (SPR) towards ACE2 and viral S protein binding domain. Selected compounds were formulated as solutions for nebulization and, after being characterized in terms of aerosolization performance and droplet size distribution, their efficacy was assessed in vivo using the K18 human (h)ACE2 transgenic mouse model of SARS-CoV-2 infection.
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Affiliation(s)
- Mauro Pavan
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy.
| | - Chiara D Fanti
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
| | - Alba Di Lucia
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
| | - Elena Canato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Fabio Sonvico
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27a, 43124 Parma, Italy
| | - Jennifer Delgado
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Amberlee Hicks
- Population Health and Host-Pathogens Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Jordi B Torrelles
- Population Health and Host-Pathogens Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Varun Dwivedi
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Anna M Zanellato
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
| | - Devis Galesso
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
| | - Gianfranco Pasut
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Francesca Buttini
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27a, 43124 Parma, Italy
| | - Luis Martinez-Sobrido
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Cristian Guarise
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
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18
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Liu Y, Qin Z, Zhou J, Jia X, Li H, Wang X, Chen Y, Sun Z, He X, Li H, Wang G, Chang H. Nano-biosensor for SARS-CoV-2/COVID-19 detection: methods, mechanism and interface design. RSC Adv 2023; 13:17883-17906. [PMID: 37323463 PMCID: PMC10262965 DOI: 10.1039/d3ra02560h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
The epidemic of coronavirus disease 2019 (COVID-19) was a huge disaster to human society. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to COVID-19, has resulted in a large number of deaths. Even though the reverse transcription-polymerase chain reaction (RT-PCR) is the most efficient method for the detection of SARS-CoV-2, the disadvantages (such as long detection time, professional operators, expensive instruments, and laboratory equipment) limit its application. In this review, the different kinds of nano-biosensors based on surface-enhanced Raman scattering (SERS), surface plasmon resonance (SPR), field-effect transistor (FET), fluorescence methods, and electrochemical methods are summarized, starting with a concise description of their sensing mechanism. The different bioprobes (such as ACE2, S protein-antibody, IgG antibody, IgM antibody, and SARS-CoV-2 DNA probes) with different bio-principles are introduced. The key structural components of the biosensors are briefly introduced to give readers an understanding of the principles behind the testing methods. In particular, SARS-CoV-2-related RNA mutation detection and its challenges are also briefly described. We hope that this review will encourage readers with different research backgrounds to design SARS-CoV-2 nano-biosensors with high selectivity and sensitivity.
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Affiliation(s)
- Yansheng Liu
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
- Quantum-Nano Matter and Device Lab, State Key Laboratory of Material Processing and Die and Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology Wuhan 430074 Hubei China
| | - Zhenle Qin
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Jin Zhou
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Xiaobo Jia
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Hongli Li
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Xiaohong Wang
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Yating Chen
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Zijun Sun
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Xiong He
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Hongda Li
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
- Quantum-Nano Matter and Device Lab, State Key Laboratory of Material Processing and Die and Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology Wuhan 430074 Hubei China
| | - Guofu Wang
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Haixin Chang
- Quantum-Nano Matter and Device Lab, State Key Laboratory of Material Processing and Die and Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology Wuhan 430074 Hubei China
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19
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Stasenko SV, Kovalchuk AV, Eremin EV, Drugova OV, Zarechnova NV, Tsirkova MM, Permyakov SA, Parin SB, Polevaya SA. Using Machine Learning Algorithms to Determine the Post-COVID State of a Person by Their Rhythmogram. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23115272. [PMID: 37299999 DOI: 10.3390/s23115272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
This study introduces a novel method for detecting the post-COVID state using ECG data. By leveraging a convolutional neural network, we identify "cardiospikes" present in the ECG data of individuals who have experienced a COVID-19 infection. With a test sample, we achieve an 87 percent accuracy in detecting these cardiospikes. Importantly, our research demonstrates that these observed cardiospikes are not artifacts of hardware-software signal distortions, but rather possess an inherent nature, indicating their potential as markers for COVID-specific modes of heart rhythm regulation. Additionally, we conduct blood parameter measurements on recovered COVID-19 patients and construct corresponding profiles. These findings contribute to the field of remote screening using mobile devices and heart rate telemetry for diagnosing and monitoring COVID-19.
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Affiliation(s)
- Sergey V Stasenko
- Neurotechnology Department, Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Andrey V Kovalchuk
- Laboratory of Autowave Processes, Institute of Applied Physics, Russian Academy of Sciences, 603950 Nizhny Novgorod, Russia
| | - Evgeny V Eremin
- Faculty of Social Sciences, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Olga V Drugova
- Department of Medical Biophysics, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
| | - Natalya V Zarechnova
- GBUZ NO "Nizhny Novgorod Regional Clinical Oncological Dispensary", 603126 Nizhny Novgorod, Russia
| | - Maria M Tsirkova
- Clinical Hospital No. 2, Privolzhsky District Medical Center, 603032 Nizhny Novgorod, Russia
| | - Sergey A Permyakov
- Faculty of Social Sciences, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Sergey B Parin
- Faculty of Social Sciences, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Sofia A Polevaya
- Faculty of Social Sciences, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
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20
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Low Z, Lani R, Tiong V, Poh C, AbuBakar S, Hassandarvish P. COVID-19 Therapeutic Potential of Natural Products. Int J Mol Sci 2023; 24:ijms24119589. [PMID: 37298539 DOI: 10.3390/ijms24119589] [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: 05/06/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Despite the fact that coronavirus disease 2019 (COVID-19) treatment and management are now considerably regulated, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still one of the leading causes of death in 2022. The availability of COVID-19 vaccines, FDA-approved antivirals, and monoclonal antibodies in low-income countries still poses an issue to be addressed. Natural products, particularly traditional Chinese medicines (TCMs) and medicinal plant extracts (or their active component), have challenged the dominance of drug repurposing and synthetic compound libraries in COVID-19 therapeutics. Their abundant resources and excellent antiviral performance make natural products a relatively cheap and readily available alternative for COVID-19 therapeutics. Here, we deliberately review the anti-SARS-CoV-2 mechanisms of the natural products, their potency (pharmacological profiles), and application strategies for COVID-19 intervention. In light of their advantages, this review is intended to acknowledge the potential of natural products as COVID-19 therapeutic candidates.
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Affiliation(s)
- Zhaoxuan Low
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Rafidah Lani
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Vunjia Tiong
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chitlaa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Petaling Jaya 47500, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Pouya Hassandarvish
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
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21
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Maffia-Bizzozero S, Cevallos C, Lenicov FR, Freiberger RN, Lopez CAM, Guano Toaquiza A, Sviercz F, Jarmoluk P, Bustos C, D’Addario AC, Quarleri J, Delpino MV. Viable SARS-CoV-2 Omicron sub-variants isolated from autopsy tissues. Front Microbiol 2023; 14:1192832. [PMID: 37283920 PMCID: PMC10240073 DOI: 10.3389/fmicb.2023.1192832] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction Pulmonary and extrapulmonary manifestations have been described after infection with SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). The virus is known to persist in multiple organs due to its tropism for several tissues. However, previous reports were unable to provide definitive information about whether the virus is viable and transmissible. It has been hypothesized that the persisting reservoirs of SARS-CoV-2 in tissues could be one of the multiple potentially overlapping causes of long COVID. Methods In the present study, we investigated autopsy materials obtained from 21 cadaveric donors with documented first infection or reinfection at the time of death. The cases studied included recipients of different formulations of COVID-19 vaccines. The aim was to find the presence of SARS-CoV-2 in the lungs, heart, liver, kidneys, and intestines. We used two technical approaches: the detection and quantification of viral genomic RNA using RT-qPCR, and virus infectivity using permissive in vitro Vero E6 culture. Results All tissues analyzed showed the presence of SARS-CoV-2 genomic RNA but at dissimilar levels ranging from 1.01 × 102 copies/mL to 1.14 × 108 copies/mL, even among those cases who had been COVID-19 vaccinated. Importantly, different amounts of replication-competent virus were detected in the culture media from the studied tissues. The highest viral load were measured in the lung (≈1.4 × 106 copies/mL) and heart (≈1.9 × 106 copies/mL) samples. Additionally, based on partial Spike gene sequences, SARS-CoV-2 characterization revealed the presence of multiple Omicron sub-variants exhibiting a high level of nucleotide and amino acid identity among them. Discussion These findings highlight that SARS-CoV-2 can spread to multiple tissue locations such as the lungs, heart, liver, kidneys, and intestines, both after primary infection and after reinfections with the Omicron variant, contributing to extending knowledge about the pathogenesis of acute infection and understanding the sequelae of clinical manifestations that are observed during post-acute COVID-19.
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Affiliation(s)
| | - Cintia Cevallos
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Federico Remes Lenicov
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rosa Nicole Freiberger
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Cinthya Alicia Marcela Lopez
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alex Guano Toaquiza
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Franco Sviercz
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Patricio Jarmoluk
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | | | - Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M. Victoria Delpino
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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22
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Simpson J, Ray A, Marcon C, dos Santos Natividade R, Dorrazehi GM, Durlet K, Koehler M, Alsteens D. Single-Molecule Analysis of SARS-CoV-2 Binding to C-Type Lectin Receptors. NANO LETTERS 2023; 23:1496-1504. [PMID: 36758952 PMCID: PMC9924085 DOI: 10.1021/acs.nanolett.2c04931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Despite intense scrutiny throughout the pandemic, development of efficacious drugs against SARS-CoV-2 spread remains hindered. Understanding the underlying mechanisms of viral infection is fundamental for developing novel treatments. While angiotensin converting enzyme 2 (ACE2) is accepted as the key entry receptor of the virus, other infection mechanisms exist. Dendritic cell-specific intercellular adhesion molecule-3 grabbing non-integrin (DC-SIGN) and its counterpart DC-SIGN-related (DC-SIGNR, also known as L-SIGN) have been recognized as possessing functional roles in COVID-19 disease and binding to SARS-CoV-2 has been demonstrated previously with ensemble and qualitative techniques. Here we examine the thermodynamic and kinetic parameters of the ligand-receptor interaction between these C-type lectins and the SARS-CoV-2 S1 protein using force-distance curve-based AFM and biolayer interferometry. We evidence that the S1 receptor binding domain is likely involved in this bond formation. Further, we employed deglycosidases and examined a nonglycosylated S1 variant to confirm the significance of glycosylation in this interaction. We demonstrate that the high affinity interactions observed occur through a mechanism distinct from that of ACE2.
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Affiliation(s)
- Joshua
D. Simpson
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Ankita Ray
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Claire Marcon
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Rita dos Santos Natividade
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Gol Mohammad Dorrazehi
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Kimberly Durlet
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
- Walloon
Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
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23
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Aryal B, Tillotson J, Ok K, Stoltzfus AT, Michel SLJ, Rao VA. Metal-induced oxidative stress and human plasma protein oxidation after SARS-CoV-2 infection. Sci Rep 2023; 13:2441. [PMID: 36765106 PMCID: PMC9916496 DOI: 10.1038/s41598-023-29119-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Pathogenesis of COVID-19 by SARS-CoV-2 resulted in a global pandemic and public health emergency in 2020. Viral infection can induce oxidative stress through reactive oxygen species (ROS). Inflammation and environmental stress are major sources of oxidative stress after infection. Micronutrients such as iron, copper, zinc, and manganese play various roles in human tissues and their imbalance in blood can impact immune responses against pathogens including SARS CoV-2. We hypothesized that alteration of free metal ions during infection and metal-catalyzed oxidation plays a critical role towards pathogenesis after infection. We analyzed convalescent and hospitalized COVID-19 patient plasma using orthogonal analytical techniques to determine redox active metal concentrations, overall protein oxidation, oxidative modifications, and protein levels via proteomics to understand the consequences of metal-induced oxidative stress in COVID-19 plasma proteins. Metal analysis using ICP-MS showed significantly greater concentrations of copper in COVID-19 plasma compared to healthy controls. We demonstrate significantly greater total protein carbonylation, other oxidative modifications, and deamidation of plasma proteins in COVID-19 plasma compared to healthy controls. Proteomics analysis showed that levels of redox active proteins including hemoglobulin were elevated in COVID-19 plasma. Molecular modeling concurred with potential interactions between iron binding proteins and SARS CoV-2 surface proteins. Overall, increased levels of redox active metals and protein oxidation indicate that oxidative stress-induced protein oxidation in COVID-19 may be a consequence of the interactions of SARS-CoV-2 proteins with host cell metal binding proteins resulting in altered cellular homeostasis.
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Affiliation(s)
- Baikuntha Aryal
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administrations, Silver Spring, MD, 20993, USA
| | - Joseph Tillotson
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administrations, Silver Spring, MD, 20993, USA
- Pfizer Inc., Cambridge, MA, USA
| | - Kiwon Ok
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Andrew T Stoltzfus
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - V Ashutosh Rao
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administrations, Silver Spring, MD, 20993, USA.
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24
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Hoque MN, Rahman MS, Sarkar MMH, Habib MA, Akter S, Banu TA, Goswami B, Jahan I, Hossain MA, Khan MS, Islam T. Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients. PLoS One 2023; 18:e0278134. [PMID: 36656835 PMCID: PMC9851516 DOI: 10.1371/journal.pone.0278134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/09/2022] [Indexed: 01/20/2023] Open
Abstract
We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.
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Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Md Ahashan Habib
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - M. Anwar Hossain
- Jashore Unive rsity of Science and Technology, Jashore, Bangladesh
| | - M. Salim Khan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, Bangladesh
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25
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Wulandari S, Hartono, Wibawa T. The role of HMGB1 in COVID-19-induced cytokine storm and its potential therapeutic targets: A review. Immunology 2023; 169:117-131. [PMID: 36571562 PMCID: PMC9880760 DOI: 10.1111/imm.13623] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/22/2022] [Indexed: 12/27/2022] Open
Abstract
Hyperinflammation characterized by elevated proinflammatory cytokines known as 'cytokine storms' is the major cause of high severity and mortality seen in COVID-19 patients. The pathology behind the cytokine storms is currently unknown. Increased HMGB1 levels in serum/plasma of COVID-19 patients were reported by many studies, which positively correlated with the level of proinflammatory cytokines. Dead cells following SARS-CoV-2 infection might release a large amount of HMGB1 and RNA of SARS-CoV-2 into extracellular space. HMGB1 is a well-known inflammatory mediator. Additionally, extracellular HMGB1 might interact with SARS-CoV-2 RNA because of its high capability to bind with a wide variety of molecules including nucleic acids and could trigger massive proinflammatory immune responses. This review aimed to critically explore the many possible pathways by which HMGB1-SARS-CoV-2 RNA complexes mediate proinflammatory responses in COVID-19. The contribution of these pathways to impair host immune responses against SARS-CoV-2 infection leading to a cytokine storm was also evaluated. Moreover, since blocking the HMGB1-SARS-CoV-2 RNA interaction might have therapeutic value, some of the HMGB1 antagonists have been reviewed. The HMGB1- SARS-CoV-2 RNA complexes might trigger endocytosis via RAGE which is linked to lysosomal rupture, PRRs activation, and pyroptotic death. High levels of the proinflammatory cytokines produced might suppress many immune cells leading to uncontrolled viral infection and cell damage with more HMGB1 released. Altogether these mechanisms might initiate a proinflammatory cycle leading to a cytokine storm. HMGB1 antagonists could be considered to give benefit in alleviating cytokine storms and serve as a potential candidate for COVID-19 therapy.
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Affiliation(s)
- Sri Wulandari
- Doctorate Program of Medicine and Health Science, Faculty of MedicinePublic Health and Nursing Universitas Gadjah MadaYogyakartaIndonesia,Department of Physiology, Faculty of MedicineUniversitas Sebelas MaretSurakartaIndonesia
| | - Hartono
- Department of Physiology, Faculty of MedicineUniversitas Sebelas MaretSurakartaIndonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of MedicinePublic Health and Nursing Universitas Gadjah MadaYogyakartaIndonesia
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Lawry LL, Lugo-Robles R, McIver V. Overlooked sex and gender aspects of emerging infectious disease outbreaks: Lessons learned from COVID-19 to move towards health equity in pandemic response. Front Glob Womens Health 2023; 4:1141064. [PMID: 36891170 PMCID: PMC9986530 DOI: 10.3389/fgwh.2023.1141064] [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: 01/09/2023] [Accepted: 02/01/2023] [Indexed: 02/22/2023] Open
Abstract
Sex and gender issues are especially important in emerging infectious diseases (EIDs) but are routinely overlooked despite data and practice. Each of these have an effect either directly, via the effects on vulnerability to infectious diseases, exposures to infectious pathogens, and responses to illness, and indirectly through effects on disease prevention and control programs. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the viral agent of coronavirus disease 2019 (COVID-19) has underscored the importance of understanding the sex and gender impacts on pandemics. This review takes a broader looks at how sex and gender impact vulnerability, exposure risk, and treatment and response that affect incidence, duration, severity, morbidity, mortality, and disability of EIDs. And although EID epidemic and pandemic plans need to be "pro-women", they need to be broader and include all sex and gender factors. Incorporation of these factors are a priority at the local, national, and global policy levels to fulfil the gaps in scientific research, public health intervention programs and pharmaceutical service strengthening to reduce emerging disease inequities in the population during pandemics and epidemics. A failure to do so creates acceptance of the inequities and infringes on fairness and human rights norms.
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Affiliation(s)
- Lynn Lieberman Lawry
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, MD, United States
| | - Roberta Lugo-Robles
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, MD, United States.,Department of Preventive Medicine and Biostatistics, Henry M. Jackson Foundation, Bethesda, MD, United States
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27
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Kong W, Montano M, Corley MJ, Helmy E, Kobayashi H, Kinisu M, Suryawanshi R, Luo X, Royer LA, Roan NR, Ott M, Ndhlovu LC, Greene WC. Neuropilin-1 Mediates SARS-CoV-2 Infection of Astrocytes in Brain Organoids, Inducing Inflammation Leading to Dysfunction and Death of Neurons. mBio 2022; 13:e0230822. [PMID: 36314791 PMCID: PMC9765283 DOI: 10.1128/mbio.02308-22] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is frequently associated with neurological deficits, but how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces these effects remains unclear. Here, we show that astrocytes are readily infected by SARS-CoV-2, but surprisingly, neuropilin-1, not angiotensin-converting enzyme 2 (ACE2), serves as the principal receptor mediating cell entry. Infection is further positively modulated by the two-pore segment channel 2 (TPC2) protein that regulates membrane trafficking and endocytosis. Astrocyte infection produces a pathological response closely resembling reactive astrogliosis characterized by elevated type I interferon (IFN) production, increased inflammation, and the decreased expression of transporters of water, ions, choline, and neurotransmitters. These combined events initiated within astrocytes produce a hostile microenvironment that promotes the dysfunction and death of uninfected bystander neurons. IMPORTANCE SARS-CoV-2 infection primarily targets the lung but may also damage other organs, including the brain, heart, kidney, and intestine. Central nervous system (CNS) pathologies include loss of smell and taste, headache, delirium, acute psychosis, seizures, and stroke. Pathological loss of gray matter occurs in SARS-CoV-2 infection, but it is unclear whether this is due to direct viral infection, indirect effects associated with systemic inflammation, or both. Here, we used induced pluripotent stem cell (iPSC)-derived brain organoids and primary human astrocytes from the cerebral cortex to study direct SARS-CoV-2 infection. Our findings support a model where SARS-CoV-2 infection of astrocytes produces a panoply of changes in the expression of genes regulating innate immune signaling and inflammatory responses. The deregulation of these genes in astrocytes produces a microenvironment within the CNS that ultimately disrupts normal neuron function, promoting neuronal cell death and CNS deficits.
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Affiliation(s)
- Weili Kong
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Mauricio Montano
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Ekram Helmy
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | | | - Martin Kinisu
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | | | - Xiaoyu Luo
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | | | - Nadia R. Roan
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
| | - Melanie Ott
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Warner C. Greene
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
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28
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Nwabufo CK, Bendayan R. Pharmacokinetic considerations to optimize clinical outcomes for COVID-19 drugs. Trends Pharmacol Sci 2022; 43:1041-1054. [PMID: 36374805 PMCID: PMC9510059 DOI: 10.1016/j.tips.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
The development of clinically effective drugs that could complement existing vaccines is urgently needed to reduce the morbidity and mortality associated with COVID-19. Drug-metabolizing enzymes, membrane-associated drug transporters, and inflammatory responses can partly determine the safety and efficacy of COVID-19 drugs by controlling their concentrations in both the systemic circulation and in peripheral tissues. It is still unknown how these factors affect how well COVID-19 drugs work in the clinic. We explore how drug metabolism and transport, as well as SARS-CoV-2-associated inflammatory response at disease target sites, may affect the clinical outcomes of COVID-19 drugs. In addition, we provide expert opinion on potential strategies for overcoming the clinical pharmacology and pathophysiological obstacles to improve COVID-19 drug effectiveness.
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Affiliation(s)
- Chukwunonso K Nwabufo
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Reina Bendayan
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.
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Koval CE, Eltemamy M, Poggio ED, Schold JD, Wee AC. Comparative outcomes for over 100 deceased donor kidney transplants from SARS-CoV-2 positive donors: A single-center experience. Am J Transplant 2022; 22:2903-2911. [PMID: 36176236 PMCID: PMC9538585 DOI: 10.1111/ajt.17203] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/03/2022] [Accepted: 09/16/2022] [Indexed: 01/25/2023]
Abstract
Emerging data support the safety of transplantation of extra-pulmonary organs from donors with SARS-CoV-2-detection. Our center offered kidney transplantation (KT) from deceased donors (DD) with SARS-CoV-2 with and without COVID-19 as a cause of death (CoV + COD and CoV+) to consenting candidates. No pre-emptive antiviral therapies were given. We retrospectively compared outcomes to contemporaneous DDKTs with negative SARS-CoV-2 testing (CoVneg). From February 1, 2021 to January 31, 2022, there were 220 adult KTs, including 115 (52%) from 35 CoV+ and 33 CoV + COD donors. Compared to CoVneg and CoV+, CoV + COD were more often DCD (100% vs. 40% and 46%, p < .01) with longer cold ischemia times (25.2 h vs. 22.9 h and 22.2 h, p = .02). At median follow-up of 5.7 months, recipients of CoV+, CoV + COD and CoVneg kidneys had similar rates of delayed graft function (10.3%, 21.8% and 21.9%, p = .16), rejection (5.1%, 0% and 8.5%, p = .07), graft failure (1.7%, 0% and 0%, p = .35), mortality (0.9%, 0% and 3.7%; p = .29), and COVID-19 diagnoses (13.6%, 7.1%, and 15.2%, p = .33). Though follow-up was shorter, CoV + COD was associated with lower but acceptable eGFR on multivariable analysis. KT from DDs at various stages of SARS-CoV-2 infection appears safe and successful. Extended follow-up is required to assess the impact of CoV + COD donors on longer term graft function.
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Affiliation(s)
- Christine E. Koval
- Department of Infectious Diseases, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA,Correspondence Christine E. Koval, Department of Infectious Diseases, Cleveland Clinic Foundation, 500 Euclid Avenue, G-21, Cleveland, Ohio 44195, USA.
| | - Mohamed Eltemamy
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Emilio D. Poggio
- Department of Kidney Medicine, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jesse D. Schold
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Alvin C. Wee
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio, USA
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30
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Cuicchi D, Gabrielli L, Tardio ML, Rossini G, D’Errico A, Viale P, Lazzarotto T, Poggioli G. Virological and histological evaluation of intestinal samples in COVID-19 patients. World J Gastroenterol 2022; 28:6282-6293. [PMID: 36504555 PMCID: PMC9730443 DOI: 10.3748/wjg.v28.i44.6282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/30/2022] [Accepted: 11/17/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the pathogen responsible for pandemic coronavirus disease 2019 (COVID-19). It is a highly contagious virus which primarily affects the respiratory tract, nevertheless, the lungs are not the only target organs of the virus. The intestinal tract could represent an additional tropism site for SARS-CoV-2. Several observations have collectively suggested that enteric infections can occur in COVID-19 patients. However, the detection of viral RNA in gastrointestinal (GI) tissue samples has not been adequately investigated and results are conflicting.
AIM To detect the presence of SARS-CoV-2 RNA in intestinal mucosa samples and to evaluate histological features.
METHODS The COVID-19 patients hospitalized at an Italian tertiary hospital from April 2020 to March 2021 were evaluated for enrollment in an observational, monocentric trial. The study population was composed of two groups of adult patients. In the first group (biopsy group, 30 patients), patients were eligible for inclusion if they had mild to moderate disease and if they agreed to have a rectal biopsy; in the second group (surgical specimen group, 6 patients), patients were eligible for inclusion if they underwent intestinal resection during index hospitalization. Fifty-nine intestinal mucosal samples were analyzed.
RESULTS Viral RNA was not detectable in any of the rectal biopsies performed (0/53). Histological examination showed no enterocyte damage, but slight edema of the lamina propria with mild inflammatory lymphoplasmacytic infiltration. There was no difference in inflammatory infiltrates in patients with and without GI symptoms. SARS-CoV-2 RNA was detected in fecal samples in 6 cases out of 14 cases examined (42.9%). In the surgical specimen group, all patients underwent emergency intestinal resection. Viral RNA was detected in 2 surgical specimens of the 6 examined, both of which were from patients with active neoplastic disease. Histological examination also pointed out abundant macrophages, granulocytes and plasma cells infiltrating the muscular layer and adipose tissue, and focal vasculitis.
CONCLUSION Mild-moderate COVID-19 may not be associated with rectal infection by the virus. More comprehensive autopsies or surgical specimens are needed to provide histological evidence of intestinal infection.
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Affiliation(s)
- Dajana Cuicchi
- Department of Medical and Surgical Sciences, Surgery of the Alimentary Tract, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Liliana Gabrielli
- Department of Experimental, Diagnostic and Specialty Medicine, Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Maria Lucia Tardio
- Department of Experimental, Diagnostic and Specialty Medicine, Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Giada Rossini
- Department of Experimental, Diagnostic and Specialty Medicine, Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Antonietta D’Errico
- Department of Experimental, Diagnostic and Specialty Medicine, Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Pierluigi Viale
- Department for Integrated Infectious Risk Management, Infectious Diseases Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
- Infectious Diseases Unit, Department for Integrated Infectious Risk Management, University of Bologna, Bologna 40138, Italy
| | - Tiziana Lazzarotto
- Department of Experimental, Diagnostic and Specialty Medicine, Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
- Section of Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna 40138, Italy
| | - Gilberto Poggioli
- Department of Medical and Surgical Sciences, Surgery of the Alimentary Tract, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
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31
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Xie L, Li J, Ai Y, He H, Chen X, Yin M, Li W, Huang W, Luo MY, He J. Current strategies for SARS-CoV-2 molecular detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4625-4642. [PMID: 36349688 DOI: 10.1039/d2ay01313d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.
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Affiliation(s)
- Lei Xie
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Junlin Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Ying Ai
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510080, China
| | - Haolan He
- Guangzhou Eighth People's Hospital, Guangzhou 510080, China
| | - Xiuyun Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Mingyu Yin
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wanxi Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wenguan Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Min-Yi Luo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Jinyang He
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
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De Vlieger L, Vandenbroucke RE, Van Hoecke L. Recent insights into viral infections as a trigger and accelerator in alzheimer's disease. Drug Discov Today 2022; 27:103340. [PMID: 35987492 PMCID: PMC9385395 DOI: 10.1016/j.drudis.2022.103340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder for which only symptomatic medication is available, except for the recently FDA-approved aducanumab. This lack of effective treatment urges us to investigate alternative paths that might contribute to disease development. In light of the recent SARS-CoV-2 pandemic and the disturbing neurological complications seen in some patients, it is desirable to (re)investigate the viability of the viral infection theory claiming that a microbe could affect AD initiation and/or progression. Here, we review the most important evidence for this theory with a special focus on two viruses, namely HSV-1 and SARS-CoV-2. Moreover, we discuss the possible involvement of extracellular vesicles (EVs). This overview will contribute to a more rational approach of potential treatment strategies for AD patients.
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Affiliation(s)
- Lize De Vlieger
- Barriers in Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Roosmarijn E Vandenbroucke
- Barriers in Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Lien Van Hoecke
- Barriers in Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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Guérin-Rechdaoui S, Bize A, Levesque-Ninio C, Janvier A, Lacroix C, Le Brizoual F, Barbier J, Amsaleg CR, Azimi S, Rocher V. Fate of SARS-CoV-2 coronavirus in wastewater treatment sludge during storage and thermophilic anaerobic digestion. ENVIRONMENTAL RESEARCH 2022; 214:114057. [PMID: 35995225 PMCID: PMC9391084 DOI: 10.1016/j.envres.2022.114057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Since the COVID-19 outbreak has started in late 2019, SARS-CoV-2 has been widely detected in human stools and in urban wastewater. No infectious SARS-CoV-2 particles have been detected in raw wastewater until now, but it has been reported occasionally in human stools. This has raised questions on the fate of SARS-CoV-2 during wastewater treatment and notably in its end-product, wastewater treatment sludge, which is classically valorized by land spreading for agricultural amendment. In the present work, we focused on SARS-CoV-2 stability in wastewater treatment sludge, either during storage (4 °C, room temperature) or thermophilic anaerobic digestion (50 °C). Anaerobic digestion is one of the possible processes for sludge valorization. Experiments were conducted in laboratory pilots; SARS-CoV-2 detection was based on RT-quantitative PCR or RT-digital droplet PCR. In addition to SARS-CoV-2, Bovine Coronavirus (BCoV) particles were used as surrogate virus. The RNA from SARS-CoV-2 particles, inactivated or not, was close to the detection limit but stable in wastewater treatment sludge, over the whole duration of the assays at 4 °C (55 days) and at ambient temperature (∼20 °C, 25 days). By contrast, the RNA levels of BCoV and inactivated SARS-CoV-2 particles decreased rapidly during the thermophilic anaerobic digestion of wastewater treatment sludge lasting for 5 days, with final levels that were close to the detection limit. Although the particles' infectivity was not assessed, these results suggest that thermophilic anaerobic digestion is a suitable process for sludge sanitation, consistent with previous knowledge on other coronaviruses.
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Affiliation(s)
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PROSE, Antony, 92160, France
| | - Camille Levesque-Ninio
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Alice Janvier
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Carlyne Lacroix
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
| | - Florence Le Brizoual
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Jérôme Barbier
- ID Solutions, Development Department, Grabels, 34790, France
| | | | - Sam Azimi
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
| | - Vincent Rocher
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
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Chen J, Song J, Dai L, Post SR, Qin Z. SARS-CoV-2 infection and lytic reactivation of herpesviruses: A potential threat in the postpandemic era? J Med Virol 2022; 94:5103-5111. [PMID: 35819034 PMCID: PMC9350099 DOI: 10.1002/jmv.27994] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 02/06/2023]
Abstract
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative pathogen for the coronavirus disease 2019 (COVID-19) pandemic, has greatly stressed our healthcare system. In addition to severe respiratory and systematic symptoms, several comorbidities increase the risk of fatal disease outcomes, including chronic viral infections. Increasing cases of lytic reactivation of human herpesviruses in COVID-19 patients and vaccinated people have been reported recently. SARS-CoV2 coinfection, COVID-19 treatments, and vaccination may aggravate those herpesvirus-associated diseases by reactivating the viruses in latently infected host cells. In this review, we summarize recent clinical findings and limited mechanistic studies regarding the relationship between SARS-CoV-2 and different human herpesviruses that suggest an ongoing potential threat to human health in the postpandemic era.
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Affiliation(s)
- Jungang Chen
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Jiao Song
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Lu Dai
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Steven R. Post
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Zhiqiang Qin
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
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Leal D, Ferreira J, Mansilha A. Thromboembolic risk in pregnant women with SARS-CoV-2 infection - A systematic review. Taiwan J Obstet Gynecol 2022; 61:941-950. [PMID: 36427996 PMCID: PMC9500082 DOI: 10.1016/j.tjog.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2022] [Indexed: 12/15/2022] Open
Abstract
The infection by SARS-CoV-2 is associated with a thromboembolic complications risk theoretically increased. Pregnancy, isolated, is considered a pro-thrombotic state. This systematic review has the main goal to evaluate the thromboembolic risk in pregnant women with COVID-19 disease, namely for pulmonary embolism (PE) and deep vein thrombosis (DVT). The secondary goal is the evaluation of the need for thromboprophylaxis in these cases. Three databases - PubMed, Scopus and Web of Science - were searched on October 2021, using the following Mesh terms and keywords: "(covid-19 OR SARS-CoV-2 OR Covid) AND (pregnancy) AND (coagulopathy OR blood coagulation disorders OR thrombotic complications OR thromboembolic risk OR venous thromboembolism OR venous thrombosis)". Information about thrombotic complications in pregnancy and thromboprophylaxis was collected, by two independent reviewers. In total, 12 articles were analyzed, corresponding to 18205 pregnant women with SARS- CoV-2 infection. A total of 85 cases of thromboembolic events were diagnosed (0.46%, 95% CI 0.37-0.58%), of which only 17 reported the use of thromboprophylaxis (20.00%, 95% CI 12.10-30.08%). There were 3 deaths due to thromboembolic complications (3.53%, 95% CI 0.73-9.97%). In conclusion, in pregnant women, the SARS-CoV-2 infection increases the risk of thromboembolic complications. However, the risk is not greater than in the general population. It is recommended thromboprophylaxis with low molecular weight heparin for hospitalized pregnant women, and in groups with moderate to high thromboembolic risk at home self-isolation.
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Affiliation(s)
- Diana Leal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal.
| | - Joana Ferreira
- Department of Vascular Surgery, Centro Hospitalar de Trás-os-Montes e Alto Douro, Vila Real, Portugal; Centro Académico Hospital da Senhora da Oliveira, Guimarães, Portugal; Department of Angiology and Vascular Surgery, Hospital CUF, Porto, Portugal
| | - Armando Mansilha
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal; Head of the Department of Angiology and Vascular Surgery, Centro Hospitalar Universitário de São João, Porto, Portugal; Head of the Department of Angiology and Vascular Surgery, Hospital CUF, Porto, Portugal
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Immunological and Pathological Peculiarity of Severe Acute Respiratory Syndrome Coronavirus 2 Beta Variant. Microbiol Spectr 2022; 10:e0237122. [PMID: 36005818 PMCID: PMC9602775 DOI: 10.1128/spectrum.02371-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Diverse severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged since the beginning of the COVID-19 pandemic. We investigated the immunological and pathological peculiarity of the SARS-CoV-2 beta variant of concern (VoC) compared to the ancestral strain. Comparative analysis of phenotype and pathology revealed that the beta VoC induces slower disease progression and a prolonged presymptomatic period in the early stages of SARS-CoV-2 infection but ultimately causes sudden death in the late stages of infection in the K18-hACE2 mouse model. The beta VoC induced enhanced activation of CXCL1/2-CXCR2-NLRP3-IL-1β signal cascade accelerating neutrophil recruitment and lung pathology in beta variant-infected mice, as evidenced by multiple analyses of SARS-CoV-2-induced inflammatory cytokines and transcriptomes. CCL2 was one of the most highly secreted cytokines in the early stages of infection. Its blockade reduced virus-induced weight loss and delayed mortality. Our study provides a better understanding of the variant characteristics and need for treatment. IMPORTANCE Since the outbreak of COVID-19, diverse SARS-CoV-2 variants have been identified. These variants have different infectivity and transmissibility from the ancestral strains. However, underlying molecular mechanisms have not yet been fully elucidated. In our study, the beta variant showed distinct pathological conditions and cytokine release kinetics from an ancestral strain in a mouse model. It was associated with higher neutrophil recruitment by increased levels of CXCL1/2, CXCR2, and interleukin 1β (IL-1β) at a later stage of viral infection. Our study will provide a better understanding of SARS-CoV-2 pathogenesis.
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D’Alessandro E, Kawasaki A, Eandi CM. Pathogenesis of Vascular Retinal Manifestations in COVID-19 Patients: A Review. Biomedicines 2022; 10:2710. [PMID: 36359227 PMCID: PMC9687698 DOI: 10.3390/biomedicines10112710] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 07/29/2023] Open
Abstract
Pandemic infection secondary to coronavirus disease 2019 (COVID-19) had an important impact on the general population affecting not only respiratory tract but also many other organs. Ocular manifestations are quite common at the level of the anterior segment (conjunctivitis, dry eye), while posterior segment and, in particular, retinal findings are less frequent. In the retina, COVID-19 is associated with vascular events. Since retinal arteries and veins represent an accessible window to the microvasculature of the rest of the body, a better understanding of the profile of retinal vascular occlusive events may help elucidate mechanisms of thrombo-occlusive complications in other organs in patients affected by COVID-19. In this review, we conducted a systematic literature search focused on retinal arterial and/or retinal venous manifestations. Twenty-one studies were included, describing a wide range of manifestations from mild signs like cotton wool spots, focal and flame-shaped hemorrhages, and vein dilation to more severe retinal artery and vein occlusions. Two principal pathogenetic mechanisms are considered responsible for these complications: a hypercoagulative state and a massive inflammatory response leading to a disseminated intravascular coagulation-like syndrome.
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Affiliation(s)
- Elisa D’Alessandro
- Fondation Asile des Aveugles, Hôpital Ophtalmique Jules Gonin, University of Lausanne, 1004 Lausanne, Switzerland
| | - Aki Kawasaki
- Fondation Asile des Aveugles, Hôpital Ophtalmique Jules Gonin, University of Lausanne, 1004 Lausanne, Switzerland
| | - Chiara M. Eandi
- Fondation Asile des Aveugles, Hôpital Ophtalmique Jules Gonin, University of Lausanne, 1004 Lausanne, Switzerland
- Department of Surgical Sciences, University of Torino, 10126 Torino, Italy
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Barberá-Riera M, Porru S, Barneo-Muñoz M, Villasante Ferrer A, Carrasco P, de Llanos R, Llueca A, Delgado-Saborit JM. Genetic Load of SARS-CoV-2 in Aerosols Collected in Operating Theaters. Appl Environ Microbiol 2022; 88:e0129722. [PMID: 36102660 PMCID: PMC9552596 DOI: 10.1128/aem.01297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
After the outbreak of COVID-19, additional protocols have been established to prevent the transmission of the SARS-CoV-2 from the patient to the health personnel and vice versa in health care settings. However, in the case of emergency surgeries, it is not always possible to ensure that the patient is not infected with SARS-CoV-2, assuming a potential source of transmission of the virus to health personnel. This work aimed to evaluate the presence of the SARS-CoV-2 and quantify the viral load in indoor air samples collected inside operating rooms, where emergency and scheduled operations take place. Samples were collected for 3 weeks inside two operating rooms for 24 h at 38 L/min in quartz filters. RNA was extracted from the filters and analyzed using RT-qPCR targeting SARS-CoV-2 genes E, N1 and N2 regions. SARS-CoV-2 RNA was detected in 11.3% of aerosol samples collected in operating rooms, despite with low concentrations (not detected at 13.5 cg/m3 and 10.5 cg/m3 in the scheduled and emergency operating rooms, respectively). Potential sources of airborne SARS-CoV-2 could be aerosolization of the virus during aerosol-generating procedures and in open surgery from patients that might have been recently infected with the virus, despite presenting a negative COVID-19 test. Another source could be related to health care workers unknowingly infected with the virus and exhaling SARS-CoV-2 virions into the air. These results highlight the importance of reinforcing preventive measures against COVID-19 in operating rooms, such as the correct use of protective equipment, screening programs for health care workers, and information campaigns. IMPORTANCE Operating rooms are critical environments in which asepsis must be ensured. The COVID-19 pandemic entailed the implementation of additional preventative measures in health care settings, including operating theaters. Although one of the measures is to operate only COVID-19 free patients, this measure cannot be always implemented, especially in emergency interventions. Therefore, a surveillance campaign was conducted during 3 weeks in two operating rooms to assess the level of SARS-CoV-2 genetic material detected in operating theaters with the aim to assess the risk of COVID-19 transmission during operating procedures. SARS-CoV-2 genetic material was detected in 11% of aerosol samples collected in operating rooms, despite with low concentrations. Plausible SARS-CoV-2 sources have been discussed, including patients and health care personnel infected with the virus. These results highlight the importance of reinforcing preventive measures against COVID-19 in operating rooms, such as the correct use of protective equipment, screening programs for health care workers and information campaigns.
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Affiliation(s)
- María Barberá-Riera
- Department of Medicine, School of Health Sciences, Universitat Jaume I, Castellón de la Plana, Spain
| | - Simona Porru
- Department of Medicine, School of Health Sciences, Universitat Jaume I, Castellón de la Plana, Spain
| | - Manuela Barneo-Muñoz
- Department of Medicine, School of Health Sciences, Universitat Jaume I, Castellón de la Plana, Spain
| | - Andrea Villasante Ferrer
- Department of Medicine, School of Health Sciences, Universitat Jaume I, Castellón de la Plana, Spain
| | - Paula Carrasco
- Department of Medicine, School of Health Sciences, Universitat Jaume I, Castellón de la Plana, Spain
- Epidemiology and Environmental Health Joint Research Unit, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, FISABIO–Universitat Jaume I–Universitat de València, Valencia, Spain
| | - Rosa de Llanos
- Department of Medicine, School of Health Sciences, Universitat Jaume I, Castellón de la Plana, Spain
| | - Antoni Llueca
- Department of Medicine, School of Health Sciences, Universitat Jaume I, Castellón de la Plana, Spain
- Multidisciplinary Unit of Abdominal Pelvic Oncology Surgery (MUAPOS), University General Hospital of Castellon, Castellón, Spain
| | - Juana María Delgado-Saborit
- Department of Medicine, School of Health Sciences, Universitat Jaume I, Castellón de la Plana, Spain
- Epidemiology and Environmental Health Joint Research Unit, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, FISABIO–Universitat Jaume I–Universitat de València, Valencia, Spain
- Environmental Research Group, MRC Centre for Environment and Health, Imperial College London, United Kingdom
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Aramini B, Masciale V, Samarelli AV, Tonelli R, Cerri S, Clini E, Stella F, Dominici M. Biological effects of COVID-19 on lung cancer: Can we drive our decisions. Front Oncol 2022; 12:1029830. [PMID: 36300087 PMCID: PMC9589049 DOI: 10.3389/fonc.2022.1029830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
COVID-19 infection caused by SARS-CoV-2 is considered catastrophic because it affects multiple organs, particularly those of the respiratory tract. Although the consequences of this infection are not fully clear, it causes damage to the lungs, the cardiovascular and nervous systems, and other organs, subsequently inducing organ failure. In particular, the effects of SARS-CoV-2-induced inflammation on cancer cells and the tumor microenvironment need to be investigated. COVID-19 may alter the tumor microenvironment, promoting cancer cell proliferation and dormant cancer cell (DCC) reawakening. DCCs reawakened upon infection with SARS-CoV-2 can populate the premetastatic niche in the lungs and other organs, leading to tumor dissemination. DCC reawakening and consequent neutrophil and monocyte/macrophage activation with an uncontrolled cascade of pro-inflammatory cytokines are the most severe clinical effects of COVID-19. Moreover, neutrophil extracellular traps have been demonstrated to activate the dissemination of premetastatic cells into the lungs. Further studies are warranted to better define the roles of COVID-19 in inflammation as well as in tumor development and tumor cell metastasis; the results of these studies will aid in the development of further targeted therapies, both for cancer prevention and the treatment of patients with COVID-19.
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Affiliation(s)
- Beatrice Aramini
- Division of Thoracic Surgery, Department of Experimental, Diagnostic and Specialty Medicine—DIMES of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni—L. Pierantoni Hospital, Forlì, Italy
- *Correspondence: Beatrice Aramini,
| | - Valentina Masciale
- Division of Oncology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Laboratory of Cell Therapy, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Anna Valeria Samarelli
- Laboratory of Cell Therapy, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberto Tonelli
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefania Cerri
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Enrico Clini
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Franco Stella
- Division of Thoracic Surgery, Department of Experimental, Diagnostic and Specialty Medicine—DIMES of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni—L. Pierantoni Hospital, Forlì, Italy
| | - Massimo Dominici
- Division of Oncology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Laboratory of Cell Therapy, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
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Muacevic A, Adler JR. Breastfeeding Practices During COVID-19: A Narrative Article. Cureus 2022; 14:e30588. [PMID: 36420243 PMCID: PMC9678492 DOI: 10.7759/cureus.30588] [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: 07/27/2022] [Accepted: 10/22/2022] [Indexed: 01/25/2023] Open
Abstract
COVID-19 was declared a pandemic because of the rapid rise in cases worldwide. Since then, it has altered the ordinary lives of people around the globe. The surge in the pandemic also questioned breastfeeding practices. As breastfeeding is one of the most critical steps toward the wellness of the newborn and maternal health, whether to follow this practice with a child born COVID-19 positive or in the case of suspected infection in the mother was also questioned. There was little information and awareness on the influence of COVID-19 on breastfeeding and postnatal care of newborns; as a result, this situation created havoc and confusion about which processes were to be carried out and how. Thus, this article examines the supporting data and correct procedures to carry out while breastfeeding newborns born during the pandemic. For the collection of evidence, searches were conducted using PubMed and Web of Science along with multiple data published on the websites of the World Health Organization (WHO) and Ministry of Health and Family Welfare, Government of India (MoHFW) between the period March 2020 to March 2022. Articles suggested significant changes in the hospital policies, such as disallowing visits to the mother or baby and changes in the mentality of mothers where a few mothers breastfed their newborn with all the septic care, like masks and frequent handwashing practices and others discontinued breastfeeding and used artificial feeds for the newborn. Even the WHO guidelines state that the mother should breastfeed the infant with good septic care. However, due to the havoc of the pandemic and miscommunication of the various policies, there was a gap in implementing the correct measures. This article provides insight into the breastfeeding scenario in COVID-19-positive or suspected mothers with COVID-19.
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Martins M, do Nascimento GM, Nooruzzaman M, Yuan F, Chen C, Caserta LC, Miller AD, Whittaker GR, Fang Y, Diel DG. The Omicron Variant BA.1.1 Presents a Lower Pathogenicity than B.1 D614G and Delta Variants in a Feline Model of SARS-CoV-2 Infection. J Virol 2022; 96:e0096122. [PMID: 36000850 PMCID: PMC9472624 DOI: 10.1128/jvi.00961-22] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/29/2022] [Indexed: 11/20/2022] Open
Abstract
Omicron (B.1.1.529) is the most recent SARS-CoV-2 variant of concern, which emerged in late 2021 and rapidly achieved global predominance by early 2022. In this study, we compared the infection dynamics, tissue tropism, and pathogenesis and pathogenicity of SARS-CoV-2 D614G (B.1), Delta (B.1.617.2), and Omicron BA.1.1 (B.1.1.529) variants in a highly susceptible feline model of infection. Although D614G- and Delta-inoculated cats became lethargic and showed increased body temperatures between days 1 and 3 postinfection (pi), Omicron-inoculated cats remained subclinical and, similar to control animals, gained weight throughout the 14-day experimental period. Intranasal inoculation of cats with D614G- and the Delta variants resulted in high infectious virus shedding in nasal secretions (up to 6.3 log10 TCID50.Ml-1), whereas strikingly lower level of viruses shedding (<3.1 log10 TCID50.Ml-1) was observed in Omicron-inoculated animals. In addition, tissue distribution of the Omicron variant was markedly reduced in comparison to the D614G and Delta variants, as evidenced by lower in situ viral RNA detection, in situ viral immunofluorescence staining, and viral loads in tissues on days 3, 5, and 14 pi. Nasal turbinate, trachea, and lung were the main-but not the only-sites of replication for all three viral variants. However, only scarce virus staining and lower viral titers suggest lower levels of viral replication in tissues from Omicron-infected animals. Notably, while D614G- and Delta-inoculated cats presented pneumonia, histologic examination of the lungs from Omicron-infected cats revealed mild to modest inflammation. Together, these results demonstrate that the Omicron variant BA.1.1 is less pathogenic than D614G and Delta variants in a highly susceptible feline model. IMPORTANCE The SARS-CoV-2 Omicron (B.1.1.529) variant of concern emerged in South Africa late in 2021 and rapidly spread across the world causing a significant increase in the number of infections. Importantly, this variant was also associated with an increased risk of reinfections. However, the number of hospitalizations and deaths due to COVID-19 did not follow the same trends. These early observations suggested effective protection conferred by immunizations and/or overall lower virulence of the highly mutated variant virus. In this study we present novel evidence demonstrating that the Omicron BA.1.1 variant of concern presents a lower pathogenicity when compared to D614G- or Delta variants in cats. Clinical, virological, and pathological evaluations revealed lower disease severity, viral replication, and lung pathology in Omicron-infected cats when compared with D614G and Delta variant inoculated animals, confirming that Omicron BA.1.1 is less pathogenic in a highly susceptible feline model of infection.
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Affiliation(s)
- Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gabriela M. do Nascimento
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Mohammed Nooruzzaman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Fangfeng Yuan
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Chi Chen
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Leonardo C. Caserta
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Andrew D. Miller
- Department of Biomedical Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Kim K, Calabrese P, Wang S, Qin C, Rao Y, Feng P, Chen XS. The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness. Sci Rep 2022; 12:14972. [PMID: 36100631 PMCID: PMC9470679 DOI: 10.1038/s41598-022-19067-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022] Open
Abstract
During COVID-19 pandemic, mutations of SARS-CoV-2 produce new strains that can be more infectious or evade vaccines. Viral RNA mutations can arise from misincorporation by RNA-polymerases and modification by host factors. Analysis of SARS-CoV-2 sequence from patients showed a strong bias toward C-to-U mutation, suggesting a potential mutational role by host APOBEC cytosine deaminases that possess broad anti-viral activity. We report the first experimental evidence demonstrating that APOBEC3A, APOBEC1, and APOBEC3G can edit on specific sites of SARS-CoV-2 RNA to produce C-to-U mutations. However, SARS-CoV-2 replication and viral progeny production in Caco-2 cells are not inhibited by the expression of these APOBECs. Instead, expression of wild-type APOBEC3 greatly promotes viral replication/propagation, suggesting that SARS-CoV-2 utilizes the APOBEC-mediated mutations for fitness and evolution. Unlike the random mutations, this study suggests the predictability of all possible viral genome mutations by these APOBECs based on the UC/AC motifs and the viral genomic RNA structure.
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Affiliation(s)
- Kyumin Kim
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peter Calabrese
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shanshan Wang
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chao Qin
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Youliang Rao
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA.
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.
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Yao Y, Subedi K, Liu T, Khalasawi N, Pretto-Kernahan CD, Wotring JW, Wang J, Yin C, Jiang A, Fu C, Dimitrion P, Li J, Veenstra J, Yi Q, McKinnon K, McKinnon JE, Sexton JZ, Zhou L, Mi QS. Surface translocation of ACE2 and TMPRSS2 upon TLR4/7/8 activation is required for SARS-CoV-2 infection in circulating monocytes. Cell Discov 2022; 8:89. [PMID: 36085197 PMCID: PMC9462622 DOI: 10.1038/s41421-022-00453-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/30/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractInfection of human peripheral blood cells by SARS-CoV-2 has been debated because immune cells lack mRNA expression of both angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease type 2 (TMPRSS2). Herein we demonstrate that resting primary monocytes harbor abundant cytoplasmic ACE2 and TMPRSS2 protein and that circulating exosomes contain significant ACE2 protein. Upon ex vivo TLR4/7/8 stimulation, cytoplasmic ACE2 was quickly translocated to the monocyte cell surface independently of ACE2 transcription, while TMPRSS2 surface translocation occurred in conjunction with elevated mRNA expression. The rapid translocation of ACE2 to the monocyte cell surface was blocked by the endosomal trafficking inhibitor endosidin 2, suggesting that endosomal ACE2 could be derived from circulating ACE2-containing exosomes. TLR-stimulated monocytes concurrently expressing ACE2 and TMPRSS2 on the cell surface were efficiently infected by SARS-CoV-2, which was significantly mitigated by remdesivir, TMPRSS2 inhibitor camostat, and anti-ACE2 antibody. Mass cytometry showed that ACE2 surface translocation in peripheral myeloid cells from patients with severe COVID-19 correlated with its hyperactivation and PD-L1 expression. Collectively, TLR4/7/8-induced ACE2 translocation with TMPRSS2 expression makes circulating monocytes permissive to SARS-CoV-2 infection.
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Goh D, Lim JCT, Fernaíndez SB, Joseph CR, Edwards SG, Neo ZW, Lee JN, Caballero SG, Lau MC, Yeong JPS. Case report: Persistence of residual antigen and RNA of the SARS-CoV-2 virus in tissues of two patients with long COVID. Front Immunol 2022; 13:939989. [PMID: 36131932 PMCID: PMC9483160 DOI: 10.3389/fimmu.2022.939989] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/18/2022] [Indexed: 12/12/2022] Open
Abstract
The World Health Organization has defined long COVID-19 (LC) as a condition that occurs in individuals with a history of SARS-CoV-2 infection who exhibit persistent symptoms after its acute phase that last for at least two months and cannot be explained by an alternative diagnosis. Since we had previously reported residual viral antigens in tissues of convalescent patients, we aimed to assess the presence of such antigens in long COVID tissues. Here, we established the presence of the residual virus in the appendix, skin, and breast tissues of 2 patients who exhibited LC symptoms 163 and 426 days after symptom onset. With multiplex immunohistochemistry, we detected viral nucleocapsid protein in all three tissues. The nucleocapsid protein was further observed to colocalize with macrophage marker CD68, suggesting that immune cells were direct targets of SARS-CoV-2. Additionally, using RNAscope, the presence of viral RNA was also detected. Our positive finding in the breast tissue is corroborated by the recent reports of immunocompromised patients experiencing LC symptoms and persistent viral replication. Overall, our findings and emerging LC studies raise the possibility that the gastrointestinal tract may function as a reservoir for SARS-CoV-2.
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Affiliation(s)
- Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | | | - Craig Ryan Joseph
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | | | - Zhen Wei Neo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Justina Nadia Lee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | | | - Mai Chan Lau
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- *Correspondence: Joe Poh Sheng Yeong,
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Yang D, Hansel DE, Curlin ME, Townes JM, Messer WB, Fan G, Qin X. Bimodal distribution pattern associated with the PCR cycle threshold (Ct) and implications in COVID-19 infections. Sci Rep 2022; 12:14544. [PMID: 36008543 PMCID: PMC9406279 DOI: 10.1038/s41598-022-18735-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
SARS-CoV-2 is notable for its extremely high level of viral replication in respiratory epithelial cells, relative to other cell types. This may partially explain the high transmissibility and rapid global dissemination observed during the COVID-19 pandemic. Polymerase chain reaction (PCR) cycle threshold (Ct) number has been widely used as a proxy for viral load based on the inverse relationship between Ct number and amplifiable genome copies present in a sample. We examined two PCR platforms (Centers for Disease Control and Prevention 2019-nCoV Real-time RT-PCR, Integrated DNA Technologies; and TaqPath COVID-19 multi-plex combination kit, ThermoFisher Scientific) for their performance characteristics and Ct distribution patterns based on results generated from 208,947 clinical samples obtained between October 2020 and September 2021. From 14,231 positive tests, Ct values ranged from 8 to 39 and displayed a pronounced bimodal distribution. The bimodal distribution persisted when stratified by gender, age, and time period of sample collection during which different viral variants circulated. This finding may be a result of heterogeneity in disease progression or host response to infection irrespective of age, gender, or viral variants. Quantification of respiratory mucosal viral load may provide additional insight into transmission and clinical indicators helpful for infection control.
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Affiliation(s)
- Doris Yang
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University School of Medicine, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA
| | - Donna E Hansel
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University School of Medicine, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA
| | - Marcel E Curlin
- Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University School of Medicine, Portland, OR, 97239, USA
| | - John M Townes
- Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University School of Medicine, Portland, OR, 97239, USA
| | - William B Messer
- Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University School of Medicine, Portland, OR, 97239, USA.,Department Molecular Microbiology and Immunology, Oregon Health & Science University School of Medicine, Portland, OR, 97239, USA
| | - Guang Fan
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University School of Medicine, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA
| | - Xuan Qin
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University School of Medicine, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA.
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Ju J, Su Y, Zhou Y, Wei H, Xu Q. The SARS-CoV-2 envelope protein disrupts barrier function in an in vitro human blood-brain barrier model. Front Cell Neurosci 2022; 16:897564. [PMID: 36082238 PMCID: PMC9445123 DOI: 10.3389/fncel.2022.897564] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Patients with coronavirus disease 2019 (COVID-19) have been frequently reported to exhibit neurological manifestations and disruption of the blood-brain barrier (BBB). Among the risk factors for BBB breakdown, the loss of endothelial cells and pericytes has caused widespread concern. Recent studies have revealed that severe acute respiratory syndrome coronavirus 2 envelope (S2E) protein caused cell death. We tested the hypothesis that the S2E protein alone could induce BBB dysfunction. The S2E protein bound to human BBB-related cells and inhibited cell viability in a dose- and time-dependent manner. Importantly, the S2E protein disrupted barrier function in an in vitro BBB model composed of HCMEC/D3 (brain endothelial cell line), HBVP (brain vascular pericyte), and U87MG (astrocyte cell line) cells and suppressed the expression of major genes involved in maintaining endothelial permeability and function. In addition, the S2E protein crossed the HCMEC/D3 monolayer. The S2E protein triggered inflammatory responses in HCMEC/D3 and U87MG cells. Taken together, these results show for the first time that the S2E protein has a negative impact on the BBB. Therapies targeting the S2E protein could protect against and treat central nervous system manifestations in COVID-19 patients.
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Affiliation(s)
- Jiahang Ju
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuwen Su
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - You Zhou
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Hui Wei
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Qi Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Qi Xu
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Okendo J, Musanabaganwa C, Mwangi P, Nyaga M, Onywera H. SARS-CoV-2-positive patients display considerable differences in proteome diversity in urine, nasopharyngeal, gargle solution and bronchoalveolar lavage fluid samples. PLoS One 2022; 17:e0271870. [PMID: 35939435 PMCID: PMC9359582 DOI: 10.1371/journal.pone.0271870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/09/2022] [Indexed: 11/18/2022] Open
Abstract
Proteome profile changes post-severe acute respiratory syndrome coronavirus 2 (post-SARS-CoV-2) infection in different body sites of humans remains an active scientific investigation whose solutions stand a chance of providing more information on what constitutes SARS-CoV-2 pathogenesis. While proteomics has been used to understand SARS-CoV-2 pathogenesis, there are limited data about the status of proteome profile in different human body sites infected by the SARS-CoV-2 virus. To bridge this gap, our study aims to characterize the proteins secreted in urine, bronchoalveolar lavage fluid (BALF), gargle solution, and nasopharyngeal samples and assess the proteome differences in these body samples collected from SARS-CoV-2-positive patients. We downloaded publicly available proteomic data from (https://www.ebi.ac.uk/pride/). The data we downloaded had the following identifiers: (i) PXD019423, n = 3 from Charles Tanford Protein Center in Germany. (ii) IPX0002166000, n = 15 from Beijing Proteome Research Centre, China. (iii) IPX0002429000, n = 5 from Huazhong University of Science and Technology, China, and (iv) PXD022889, n = 18 from Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA. MaxQuant was used for the human peptide spectral matching using human and SARS-CoV-2 proteome database which we downloaded from the UniProt database (access date 13th October 2021). The individuals infected with SARS-CoV-2 viruses displayed a different proteome diversity from the different body sites we investigated. Overally, we identified 1809 proteins across the four sample types we compared. Urine and BALF samples had significantly more abundant SARS-CoV-2 proteins than the other body sites we compared. Urine samples had 257(33.7%) unique proteins, followed by nasopharyngeal with 250(32.8%) unique proteins. Gargle solution and BALF had 38(5%) and 73(9.6%) unique proteins respectively. Urine, gargle solution, nasopharyngeal, and bronchoalveolar lavage fluid samples have different protein diversity in individuals infected with SARS-CoV-2. Moreover, our data also demonstrated that a given body site is characterized by a unique set of proteins in SARS-CoV-2 seropositive individuals.
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Affiliation(s)
- Javan Okendo
- Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | | | - Peter Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Martin Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Harris Onywera
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Microbiology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Research, Innovations and Academics Unit, Tunacare Services Health Providers Limited, Nairobi, Kenya
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Aknouch I, Sridhar A, Freeze E, Giugliano FP, van Keulen BJ, Romijn M, Calitz C, García-Rodríguez I, Mulder L, Wildenberg ME, Muncan V, van Gils MJ, van Goudoever JB, Stittelaar KJ, Wolthers KC, Pajkrt D. Human milk inhibits some enveloped virus infections, including SARS-CoV-2, in an intestinal model. Life Sci Alliance 2022; 5:e202201432. [PMID: 35926873 PMCID: PMC9354649 DOI: 10.26508/lsa.202201432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/24/2022] Open
Abstract
Human milk is important for antimicrobial defense in infants and has well demonstrated antiviral activity. We evaluated the protective ability of human milk against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in a human fetal intestinal cell culture model. We found that, in this model, human milk blocks SARS-CoV-2 replication, irrespective of the presence of SARS-CoV-2 spike-specific antibodies. Complete inhibition of both enveloped Middle East respiratory syndrome coronavirus and human respiratory syncytial virus infections was also observed, whereas no inhibition of non-enveloped enterovirus A71 infection was seen. Transcriptome analysis after 24 h of the intestinal monolayers treated with human milk showed large transcriptomic changes from human milk treatment, and subsequent analysis suggested that <i>ATP1A1</i> down-regulation by milk might be of importance. Inhibition of ATP1A1 blocked SARS-CoV-2 infection in our intestinal model, whereas no effect on EV-A71 infection was seen. Our data indicate that human milk has potent antiviral activity against particular (enveloped) viruses by potentially blocking the ATP1A1-mediated endocytic process.
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Affiliation(s)
- Ikrame Aknouch
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
- Department of Pediatric Infectious Diseases, Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Amsterdam, The Netherlands
- Viroclinics Xplore, Schaijk, The Netherlands
| | - Adithya Sridhar
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
- Department of Pediatric Infectious Diseases, Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Eline Freeze
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
- Department of Pediatric Infectious Diseases, Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Francesca Paola Giugliano
- Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology and Metabolism, Tytgat Institute for Intestinal and Liver Research, Amsterdam, The Netherlands
| | - Britt J van Keulen
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Vrije Universiteit Emma Children's Hospital, Dutch National Human Milk Bank, Amsterdam, The Netherlands
| | - Michelle Romijn
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Vrije Universiteit Emma Children's Hospital, Dutch National Human Milk Bank, Amsterdam, The Netherlands
| | - Carlemi Calitz
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
- Department of Pediatric Infectious Diseases, Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Inés García-Rodríguez
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
- Department of Pediatric Infectious Diseases, Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Lance Mulder
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
- Department of Pediatric Infectious Diseases, Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Manon E Wildenberg
- Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology and Metabolism, Tytgat Institute for Intestinal and Liver Research, Amsterdam, The Netherlands
| | - Vanesa Muncan
- Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology and Metabolism, Tytgat Institute for Intestinal and Liver Research, Amsterdam, The Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Johannes B van Goudoever
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Vrije Universiteit Emma Children's Hospital, Dutch National Human Milk Bank, Amsterdam, The Netherlands
| | - Koert J Stittelaar
- Department of Epidemiology, Bioinformatics and Animals Models, Wageningen University, Wageningen Bioveterinary Research, Wageningen, The Netherlands
| | - Katja C Wolthers
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
| | - Dasja Pajkrt
- Department of Pediatric Infectious Diseases, Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Amsterdam, The Netherlands
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50
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Okendo J. Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022; 23:115. [PMID: 37521832 PMCID: PMC9362069 DOI: 10.1186/s43042-022-00327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Since the COVID-19 outbreak emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved into variants with underlying mutations associated with increased transmissibility, potential escape from neutralizing antibodies, and disease severity. Although intensive research is ongoing worldwide to understand the emergence of SARS-CoV-2 variants, there is a lack of information on what constitutes the expressed RNA variants in critical and non-critical comorbidity-free young patients. The study sought to characterize the expressed RNA variants from young patients with critical and non-critical forms of SARS-CoV-2 infection. Methodology The bulk ribonucleic acid (RNA) sequencing data with the identifier GSE172114 were downloaded from the Gene Expression Omnibus (GEO) database. The study participants were divided into critical, n = 46, and non-critical, n = 23. FastQC version 0.11.9 and Cutadapt version 3.7 were used to assess the read quality and perform adapter trimming, respectively. Spliced Transcripts Alignment to a Reference (STAR) version 2.7.10a was used to align reads to the human (hg38) reference genome. Genome Analysis Tool Kit (GATK) best practice was followed to call variants using the rnavar pipeline, part of the nf-core pipelines. Results Our research demonstrates that critical and non-critical SARS-CoV-2-infected individuals are characterized by a unique set of expressed RNA variants. The expressed gene variants are enriched on the innate immune response, specifically neutrophil-mediated immune response. On the other hand, the expressed gene variants are involved in both innate and cellular immune responses. Conclusion Deeply phenotyped comorbidity-free young patients with critical and non-critical SARS-CoV-2 infection are characterized by a unique set of expressed RNA variants. The findings in this study can inform the patient classification process in health facilities globally when admitting young patients infected with SARS-CoV-2.
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Affiliation(s)
- Javan Okendo
- Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road Observatory, Cape Town, 7925 South Africa
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