1
|
Theel ES, Kirby JE, Pollock NR. Testing for SARS-CoV-2: lessons learned and current use cases. Clin Microbiol Rev 2024; 37:e0007223. [PMID: 38488364 DOI: 10.1128/cmr.00072-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.
Collapse
Affiliation(s)
- Elitza S Theel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R Pollock
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
2
|
Rischall A, Olson A. SOHO State of the Art Updates and Next Questions | CTLs for Infections Following Stem Cell Transplantation. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2024; 24:340-347. [PMID: 38267354 DOI: 10.1016/j.clml.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/26/2024]
Abstract
Allogeneic hematopoietic stem cell transplantation (AHSCT) is an important modality in the treatment of acute leukemia and other hematologic disorders. The post-transplant period is associated with prolonged periods of impaired immune function. Delayed T-cell immune reconstitution is correlated with increased risk of viral, bacterial, and fungal infections. This risk increases with high intensity inductions regimens often required for alternative donor sources. Current therapies for prophylaxis and treatment of these infections are limited by poor efficacy and significant toxicity. Adoptive cell therapy with cytotoxic T lymphocytes (CTL) has proven to be both efficacious and safe in the management of post-transplant viral infections. Recent advances have led to faster production of CTLs and broadened applications for their use. In particular, the generation of third party CTLs has helped ameliorate the problems related to donor availability and product generation time. In this review we aim to describe both the history of CTL use and current advances in the field.
Collapse
Affiliation(s)
- Ariel Rischall
- Department of Medical Oncology, The University of Texas Medical Branch, Galveston, TX
| | - Amanda Olson
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX.
| |
Collapse
|
3
|
Ge X, Zhou H, Shen F, Yang G, Zhang Y, Zhang X, Li H. SARS-CoV-2 subgenomic RNA: formation process and rapid molecular diagnostic methods. Clin Chem Lab Med 2024; 62:1019-1028. [PMID: 38000044 DOI: 10.1515/cclm-2023-0846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus disease-2019 (COVID-19) is spreading worldwide and posing enormous losses to human health and socio-economic. Due to the limitations of medical and health conditions, it is still a huge challenge to develop appropriate discharge standards for patients with COVID-19 and to use medical resources in a timely and effective manner. Similar to other coronaviruses, SARS-CoV-2 has a very complex discontinuous transcription process to generate subgenomic RNA (sgRNA). Some studies support that sgRNA of SARS-CoV-2 can only exist when the virus is active and is an indicator of virus replication. The results of sgRNA detection in patients can be used to evaluate the condition of hospitalized patients, which is expected to save medical resources, especially personal protective equipment. There have been numerous investigations using different methods, especially molecular methods to detect sgRNA. Here, we introduce the process of SARS-CoV-2 sgRNA formation and the commonly used molecular diagnostic methods to bring a new idea for clinical detection in the future.
Collapse
Affiliation(s)
- Xiao Ge
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Huizi Zhou
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Fangyuan Shen
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Guimao Yang
- Department of Medical Laboratory, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P.R. China
| | - Yubo Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Xiaoyu Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Heng Li
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| |
Collapse
|
4
|
Kavikondala S, Haeussler K, Wang X, Spellman A, Bausch-Jurken MT, Sharma P, Amiri M, Krivelyova A, Vats S, Nassim M, Kumar N, Van de Velde N. Immunogenicity of mRNA-1273 and BNT162b2 in Immunocompromised Patients: Systematic Review and Meta-analysis Using GRADE. Infect Dis Ther 2024:10.1007/s40121-024-00987-2. [PMID: 38802704 DOI: 10.1007/s40121-024-00987-2] [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: 03/14/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
INTRODUCTION Immunocompromised (IC) patients mount poor immune responses to vaccination. Higher-dose coronavirus disease 2019 (COVID-19) vaccines may offer increased immunogenicity. METHODS A pairwise meta-analysis of 98 studies reporting comparisons of mRNA-1273 (50 or 100 mcg/dose) and BNT162b2 (30 mcg/dose) in IC adults was performed. Outcomes were seroconversion, total and neutralizing antibody titers, and cellular immune responses. RESULTS mRNA-1273 was associated with a significantly higher seroconversion likelihood [relative risk, 1.11 (95% CI, 1.08, 1.14); P < 0.0001; I2 = 66.8%] and higher total antibody titers [relative increase, 50.45% (95% CI, 34.63%, 66.28%); P < 0.0001; I2 = 89.5%] versus BNT162b2. mRNA-1273 elicited higher but statistically nonsignificant relative increases in neutralizing antibody titers and cellular immune responses versus BNT162b2. CONCLUSION Higher-dose mRNA-1273 had increased immunogenicity versus BNT162b2 in IC patients.
Collapse
|
5
|
Mendes-Correa MC, Ghilardi FDR, Salomão MC, Villas-Boas LS, Paula AVD, Paiao HGO, Costa ACD, Tozetto-Mendoza TR, Freire W, Sales FCS, Claro IM, Sabino EC, Faria NR, Witkin SS. SARS-CoV-2 shedding, infectivity, and evolution in an immunocompromised adult patient. Rev Inst Med Trop Sao Paulo 2024; 66:e28. [PMID: 38747849 PMCID: PMC11095242 DOI: 10.1590/s1678-9946202466028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/25/2024] [Indexed: 05/19/2024] Open
Abstract
This study aimed to provide further insight into the evolutionary dynamics of SARS-CoV-2 by analyzing the case of a 40-year-old man who had previously undergone autologous hematopoietic stem cell transplantation due to a diffuse large B-cell lymphoma. He developed a persistent SARS-CoV-2 infection lasting at least 218 days and did not manifest a humoral immune response to the virus during this follow-up period. Whole-genome sequencing and viral cultures confirmed a persistent infection with a replication-positive virus that had undergone genetic variation for at least 196 days after symptom onset.
Collapse
Affiliation(s)
- Maria Cassia Mendes-Correa
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Fábio de Rose Ghilardi
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
| | - Matias Chiarastelli Salomão
- Hospital 9 de Julho, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, São Paulo, São Paulo, Brazil
| | - Lucy Santos Villas-Boas
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Anderson Vicente de Paula
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Tânia Regina Tozetto-Mendoza
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Wilton Freire
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Flavia Cristina Silva Sales
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
| | - Ingra Morales Claro
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
- Imperial College, Department of Infectious Disease Epidemiology, London, United Kindgom
- University of Oxford, Department of Zoology, Oxford, United Kindgom
| | - Steven Sol Witkin
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
- Weill Cornell Medicine, Department of Obstetrics and Gynecology, New York, New York, USA
| |
Collapse
|
6
|
Razonable RR. Protecting the vulnerable: addressing the COVID-19 care needs of people with compromised immunity. Front Immunol 2024; 15:1397040. [PMID: 38756784 PMCID: PMC11096526 DOI: 10.3389/fimmu.2024.1397040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
While the general population regained a certain level of normalcy with the end of the global health emergency, the risk of contracting COVID-19 with a severe outcome is still a major concern for people with compromised immunity. This paper reviews the impact of COVID-19 on people with immunocompromised status, identifies the gaps in the current management landscape, and proposes actions to address this unmet need. Observational studies have demonstrated that people with immune dysfunction have a higher risk of COVID-19-related hospitalization and death, despite vaccination, than the general population. More research is needed to define the optimal prevention and treatment strategies that are specific to people with immunocompromised status, including novel vaccination strategies, monoclonal antibodies that provide passive immunity and complement suboptimal vaccination responses, and improved and safer antiviral treatment for COVID-19. Preventive measures beyond vaccination alone are urgently needed to protect this vulnerable population.
Collapse
Affiliation(s)
- Raymund R. Razonable
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, United States
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN, United States
| |
Collapse
|
7
|
Igari H, Sakao S, Ishige T, Saito K, Murata S, Yahaba M, Taniguchi T, Suganami A, Matsushita K, Tamura Y, Suzuki T, Ido E. Dynamic diversity of SARS-CoV-2 genetic mutations in a lung transplantation patient with persistent COVID-19. Nat Commun 2024; 15:3604. [PMID: 38684722 PMCID: PMC11058237 DOI: 10.1038/s41467-024-47941-x] [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: 05/29/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Numerous SARS-CoV-2 variant strains with altered characteristics have emerged since the onset of the COVID-19 pandemic. Remdesivir (RDV), a ribonucleotide analogue inhibitor of viral RNA polymerase, has become a valuable therapeutic agent. However, immunosuppressed hosts may respond inadequately to RDV and develop chronic persistent infections. A patient with respiratory failure caused by interstitial pneumonia, who had undergone transplantation of the left lung, developed COVID-19 caused by Omicron BA.5 strain with persistent chronic viral shedding, showing viral fusogenicity. Genome-wide sequencing analyses revealed the occurrence of several viral mutations after RDV treatment, followed by dynamic changes in the viral populations. The C799F mutation in nsp12 was found to play a pivotal role in conferring RDV resistance, preventing RDV-triphosphate from entering the active site of RNA-dependent RNA polymerase. The occurrence of diverse mutations is a characteristic of SARS-CoV-2, which mutates frequently. Herein, we describe the clinical case of an immunosuppressed host in whom inadequate treatment resulted in highly diverse SARS-CoV-2 mutations that threatened the patient's health due to the development of drug-resistant variants.
Collapse
Affiliation(s)
- Hidetoshi Igari
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan.
- Future Mucosal Vaccine Research and Development Center, Chiba University Hospital, Chiba, Chiba, Japan.
- COVID-19 Vaccine Center, Chiba University Hospital, Chiba, Chiba, Japan.
- Research Institute of Disaster Medicine, Chiba University, Chiba, Chiba, Japan.
| | - Seiichiro Sakao
- Department of Respiratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
- Department of Pulmonary Medicine, School of Medicine, International University of Health and Welfare, Narita, Chiba, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan.
| | - Kengo Saito
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Shota Murata
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
| | - Misuzu Yahaba
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan
| | - Toshibumi Taniguchi
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Chiba, Japan
| | - Akiko Suganami
- Department of Bioinformatics, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
| | - Yutaka Tamura
- Department of Bioinformatics, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Takuji Suzuki
- Future Mucosal Vaccine Research and Development Center, Chiba University Hospital, Chiba, Chiba, Japan
- Department of Respiratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
- Synergy Institute for Futuristic Mucosal Vaccine Research and Development, Chiba University, Chiba, Chiba, Japan
| | - Eiji Ido
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan.
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan.
| |
Collapse
|
8
|
Acuña-Castillo C, Vidal M, Vallejos-Vidal E, Luraschi R, Barrera-Avalos C, Inostroza-Molina A, Molina-Cabrera S, Valdes D, Schafer C, Maisey K, Imarai M, Vera R, Vargas S, Rojo LE, Leiva-Salcedo E, Escobar A, Reyes-Cerpa S, Gaete A, Palma-Vejares R, Travisany D, Torres C, Reyes-López FE, Sandino AM. A retrospective study suggests 55 days of persistence of SARS-CoV-2 during the first wave of the pandemic in Santiago de Chile. Heliyon 2024; 10:e24419. [PMID: 38601544 PMCID: PMC11004068 DOI: 10.1016/j.heliyon.2024.e24419] [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: 04/04/2022] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 04/12/2024] Open
Abstract
Background As the COVID-19 pandemic persists, infections continue to surge globally. Presently, the most effective strategies to curb the disease and prevent outbreaks involve fostering immunity, promptly identifying positive cases, and ensuring their timely isolation. Notably, there are instances where the SARS-CoV-2 virus remains infectious even after patients have completed their quarantine. Objective Understanding viral persistence post-quarantine is crucial as it could account for localized infection outbreaks. Therefore, studying and documenting such instances is vital for shaping future public health policies. Design This study delves into a unique case of SARS-CoV-2 persistence in a 60-year-old female healthcare worker with a medical history of hypertension and hypothyroidism. The research spans 55 days, marking the duration between her initial and subsequent diagnosis during Chile's first COVID-19 wave, with the analysis conducted using RT-qPCR. Results Genomic sequencing-based phylogenetic analysis revealed that the SARS-CoV-2 detected in both Nasopharyngeal swab samples (NPSs) was consistent with the 20B clade of the Nextstrain classification, even after a 55-day interval. Conclusion This research underscores the need for heightened vigilance concerning cases of viral persistence. Such instances, albeit rare, might be pivotal in understanding sporadic infection outbreaks that occur post-quarantine.
Collapse
Affiliation(s)
- Claudio Acuña-Castillo
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
- Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mabel Vidal
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Concepción, Chile
| | - Eva Vallejos-Vidal
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Nanociencia y Nanotecnología CEDENNA, Universidad de Santiago de Chile, Chile
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad De Las Américas, La Florida, Santiago, Chile
| | - Roberto Luraschi
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
| | | | | | | | - Daniel Valdes
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
- Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Carolina Schafer
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
| | - Kevin Maisey
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
| | - Mónica Imarai
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
- Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Rodrigo Vera
- Hospital de Urgencia Asistencia Pública (HUAP), Santiago, Chile
| | - Sergio Vargas
- Hospital de Urgencia Asistencia Pública (HUAP), Santiago, Chile
| | - Leonel E. Rojo
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
- Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
| | | | - Alejandro Escobar
- Laboratorio Biología Celular y Molecular, Instituto de Investigación en Ciencias Odontológicas, Universidad de Chile, Santiago, Chile
| | - Sebastián Reyes-Cerpa
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de Los Alimentos, Universidad de Chile, Santiago, Chile
- Fondap Center for Genome Regulation, Universidad de Chile, Santiago, Chile
| | - Ricardo Palma-Vejares
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- Fondap Center for Genome Regulation, Universidad de Chile, Santiago, Chile
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
- Inria Chile Research Center, Santiago, Chile
| | - Claudio Torres
- Department of Neurobiology Drexel University, Philadelphia, United States
| | | | - Ana María Sandino
- Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
- Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
| |
Collapse
|
9
|
Huang L, Tong X, Cui J, Du X, Liao Y, Tan X, Ju Y, Zhong X, Zhou W, Xu X, Li Y. Recurrent and persistent fever after SARS-CoV-2 infection in patients with follicular lymphoma: A case series. Int J Infect Dis 2024; 141:106973. [PMID: 38395220 DOI: 10.1016/j.ijid.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Although persistent or recurrent COVID-19 infection is well described in some immunosuppressed patient cohort, to date, there have been no reports of this phenomenon in the context of repeatedly negative SARS-CoV-2 testing in the upper respiratory tract. We reported six patients with follicular lymphoma who developed recurrent symptomatic COVID-19 infection. They tested persistently negative for SARS-CoV-2 on pharyngeal swabs and ultimately confirmed by bronchoalveolar lavage fluid metagenomics next-generation sequencing. All six patients presented with lymphopenia and B-cell depletion, and five of them received the anti-cluster of differentiation 20 treatment in the last year. Persistent fever was the most common symptom and bilateral ground-glass opacities were the primary pattern on chest computed tomography. A relatively long course of unnecessary and ineffective antibacterial and/or antifungal treatments was administered until the definitive diagnosis. Persistent fever subsided rapidly with nirmatrelvir/ritonavir treatment. Our case highlighted that recurrent COVID-19 infection should be suspected in immunocompromised patients with persistent fever despite negative pharyngeal swabs, and urgent bronchoalveolar lavage fluid testing is necessary. Treatment with nirmatrelvir/ritonavir appeared to be very effective in these patients.
Collapse
Affiliation(s)
- Lixue Huang
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Xunliang Tong
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Jia Cui
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Xiaoman Du
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Yixuan Liao
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Xiaoming Tan
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Yang Ju
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Xuefeng Zhong
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Wei Zhou
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Xiaomao Xu
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Yanming Li
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China.
| |
Collapse
|
10
|
Sansen PY, Coche E, Hainaut P, Froidure A, Scohy A, Ghaye B, Belkhir L, De Greef J. Secondary organizing pneumonia associated with protracted COVID: A case series. Infect Dis Now 2024; 54:104888. [PMID: 38494118 DOI: 10.1016/j.idnow.2024.104888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/01/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
OBJECTIVES Immunocompromised B-cell-depleted patients are at risk of developing protracted COVID-19, a clinical syndrome characterized by prolonged viral shedding and respiratory symptoms that can lead to hypoxemic pneumonia. Our aim is to describe this unusual condition and its treatment. PATIENTS AND METHODS This monocentric retrospective study reports six cases of severe organizing pneumonia that developed during the clinical course of protracted COVID-19. RESULTS All patients developed organizing pneumonia (OP) in the setting of protracted COVID. Clinical improvement was obtained after several treatment lines including specific antiviral agents and occurred simultaneously with control of the viral load. CONCLUSION As it was the most frequent presentation of protracted COVID-19 in our survey, we believe that this specific form of organizing pneumonia warrants increased awareness. Furthermore, specific antiviral therapy seems to control this condition.
Collapse
Affiliation(s)
- P-Y Sansen
- Service de Médecine interne et Maladies Infectieuses, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium.
| | - E Coche
- Service de Radiologie, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - P Hainaut
- Service de Médecine interne et Maladies Infectieuses, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - A Froidure
- Service de Pneumologie, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - A Scohy
- Service de Microbiologie, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - B Ghaye
- Service de Radiologie, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - L Belkhir
- Service de Médecine interne et Maladies Infectieuses, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - J De Greef
- Service de Médecine interne et Maladies Infectieuses, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| |
Collapse
|
11
|
Feuth E, Nieminen V, Palomäki A, Ranti J, Sucksdorff M, Finnilä T, Oksi J, Vuorinen T, Feuth T. Prolonged viral pneumonia and high mortality in COVID-19 patients on anti-CD20 monoclonal antibody therapy. Eur J Clin Microbiol Infect Dis 2024; 43:723-734. [PMID: 38358552 DOI: 10.1007/s10096-024-04776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
PURPOSE In clinical practice, we observed an apparent overrepresentation of COVID-19 patients on anti-CD20 monoclonal antibody therapy. The aim of this study was to characterize the clinical picture of COVID-19 in these patients. METHODS All adult patients from Turku University Hospital, Turku, Finland, with COVID-19 diagnosis and/or positive SARS-CoV-2 PCR test result up to March 2023, and with anti-CD20 therapy within 12 months before COVID-19 were included. Data was retrospectively obtained from electronic patient records. RESULTS Ninety-eight patients were identified. 44/93 patients (47.3%) were hospitalized due to COVID-19. Patients with demyelinating disorder (n = 20) were youngest (median age 36.5 years, interquartile range 33-45 years), had less comorbidities, and were least likely to be hospitalized (2/20; 10.0%) or die (n = 0). COVID-19 mortality was 13.3% in the whole group, with age and male sex as independent risk factors. Persistent symptoms were documented in 33/94 patients (35.1%) alive by day 30, in 21/89 patients (23.6%) after 60 days, and in 15/85 after 90 days (17.6%), mostly in patients with haematological malignancy or connective tissue disease. Prolonged symptoms after 60 days predisposed to persistent radiological findings (odds ratio 64.0; 95% confidence interval 6.3-711; p < 0.0001) and persistently positive PCR (odds ratio 45.5, 95% confidence interval 4.0-535; p < 0.0001). Several patients displayed rapid response to late antiviral therapy. CONCLUSION Anti-CD20 monoclonal antibody therapy is associated with high COVID-19 mortality and with a phenotype consistent with prolonged viral pneumonia. Our study provides rationale for retesting of immunocompromised patients with prolonged COVID-19 symptoms and considering antiviral therapy.
Collapse
Affiliation(s)
- Eeva Feuth
- Department of Infectious Diseases, Turku University Hospital and University of Turku, Turku, Finland
| | - Valtteri Nieminen
- Department of Pulmonary Diseases and Clinical Allergology, Turku University Hospital and University of Turku, Turku, Finland
| | - Antti Palomäki
- Centre for Rheumatology and Clinical Immunology, and Department of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Juha Ranti
- Department of Haematology, Turku University Hospital, Turku, Finland
| | - Marcus Sucksdorff
- Turku PET Centre, and Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
| | - Taru Finnilä
- Department of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Jarmo Oksi
- Department of Infectious Diseases, Turku University Hospital and University of Turku, Turku, Finland
| | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital and Institute of Biomedicine, University of Turku, Turku, Finland
| | - Thijs Feuth
- Department of Pulmonary Diseases and Clinical Allergology, Turku University Hospital and University of Turku, Turku, Finland.
| |
Collapse
|
12
|
Manuelpillai B, Zendt M, Chang-Rabley E, Ricotta EE. Stuck in pandemic uncertainty: a review of the persistent effects of COVID-19 infection in immune-deficient people. Clin Microbiol Infect 2024:S1198-743X(24)00158-7. [PMID: 38552795 DOI: 10.1016/j.cmi.2024.03.027] [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: 01/17/2024] [Revised: 03/04/2024] [Accepted: 03/23/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND People who are immune-deficient/disordered (IDP) are underrepresented in COVID-19 studies. Specifically, there is limited research on post-SARS-CoV-2 infection outcomes, including viral persistence and long-term sequelae in these populations. OBJECTIVES This review aimed to examine the published literature on the occurrence of persistent SARS-CoV-2 positivity, relapse, reinfections, variant coinfection, and post-acute sequelae of COVID-19 in IDP. Although the available literature largely centred on those with secondary immunodeficiencies, studies on people with inborn errors of immunity are also included. SOURCES PubMed was searched using medical subject headings terms to identify relevant articles from the last 4 years. Articles on primary and secondary immunodeficiencies were chosen, and a special emphasis was placed on including articles that studied people with inborn errors of immunity. The absence of extensive cohort studies including these individuals has limited most articles in this review to case reports, whereas the articles focusing on secondary immunodeficiencies include larger cohort, case-control, and cross-sectional studies. Articles focusing solely on HIV/AIDS were excluded. CONTENT Scientific literature suggests that IDP of any age are more likely to experience persistent SARS-CoV-2 infections. Although adult IDP exhibits a higher rate of post-acute sequelae of COVID-19, milder COVID-19 infections in children may reduce their risk of experiencing post-acute sequelae of COVID-19. Reinfections and coinfections may occur at a slightly higher rate in IDP than in the general population. IMPLICATIONS Although IDP experience increased viral persistence and inter-host evolution, it is unlikely that enough evidence can be generated at the population-level to support or refute the hypothesis that infections in IDP are significantly more likely to result in variants of concern than infections in the general population. Additional research on the relationship between viral persistence and the rate of long-term sequelae in IDP could inform the understanding of the immune response to SARS-CoV-2 in IDP and the general population.
Collapse
Affiliation(s)
- Bevin Manuelpillai
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mackenzie Zendt
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emma Chang-Rabley
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily E Ricotta
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
13
|
Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024; 15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [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: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
Collapse
Affiliation(s)
- Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | | | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Strauss van Graan
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | | | | | | | | | - Elizabeth Venter
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Monjurul Hoque
- KwaDabeka Community Health Centre, KwaDabeka, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombulelo Magula
- Department of Internal Medicine, Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
| |
Collapse
|
14
|
Manuto L, Bado M, Cola M, Vanzo E, Antonello M, Mazzotti G, Pacenti M, Cordioli G, Sasset L, Cattelan AM, Toppo S, Lavezzo E. Immune System Deficiencies Do Not Alter SARS-CoV-2 Evolutionary Rate but Favour the Emergence of Mutations by Extending Viral Persistence. Viruses 2024; 16:447. [PMID: 38543811 PMCID: PMC10974344 DOI: 10.3390/v16030447] [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: 02/19/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 05/23/2024] Open
Abstract
During the COVID-19 pandemic, immunosuppressed patients showed prolonged SARS-CoV-2 infections, with several studies reporting the accumulation of mutations in the viral genome. The weakened immune system present in these individuals, along with the effect of antiviral therapies, are thought to create a favourable environment for intra-host viral evolution and have been linked to the emergence of new viral variants which strongly challenged containment measures and some therapeutic treatments. To assess whether impaired immunity could lead to the increased instability of viral genomes, longitudinal nasopharyngeal swabs were collected from eight immunocompromised patients and fourteen non-immunocompromised subjects, all undergoing SARS-CoV-2 infection. Intra-host viral evolution was compared between the two groups through deep sequencing, exploiting a probe-based enrichment method to minimise the possibility of artefactual mutations commonly generated in amplicon-based methods, which heavily rely on PCR amplification. Although, as expected, immunocompromised patients experienced significantly longer infections, the acquisition of novel intra-host viral mutations was similar between the two groups. Moreover, a thorough analysis of viral quasispecies showed that the variability of viral populations in the two groups is comparable not only at the consensus level, but also when considering low-frequency mutations. This study suggests that a compromised immune system alone does not affect SARS-CoV-2 within-host genomic variability.
Collapse
Affiliation(s)
- Laura Manuto
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Martina Bado
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Marco Cola
- Department of Medicine, DIMED, University of Padova, 35128 Padova, Italy;
| | - Elena Vanzo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Maria Antonello
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Giorgia Mazzotti
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Monia Pacenti
- Unit of Microbiology and Virology, University Hospital of Padova, 35128 Padova, Italy;
| | - Giampaolo Cordioli
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Lolita Sasset
- Unit of Infectious Diseases, University Hospital of Padova, 35128 Padova, Italy;
| | - Anna Maria Cattelan
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
- Unit of Infectious Diseases, University Hospital of Padova, 35128 Padova, Italy;
| | - Stefano Toppo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Enrico Lavezzo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| |
Collapse
|
15
|
Marques AD, Graham-Wooten J, Fitzgerald AS, Sobel Leonard A, Cook EJ, Everett JK, Rodino KG, Moncla LH, Kelly BJ, Collman RG, Bushman FD. SARS-CoV-2 evolution during prolonged infection in immunocompromised patients. mBio 2024; 15:e0011024. [PMID: 38364100 PMCID: PMC10936176 DOI: 10.1128/mbio.00110-24] [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: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Prolonged infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients provides an opportunity for viral evolution, potentially leading to the generation of new pathogenic variants. To investigate the pathways of viral evolution, we carried out a study on five patients experiencing prolonged SARS-CoV-2 infection (quantitative polymerase chain reaction-positive for 79-203 days) who were immunocompromised due to treatment for lymphoma or solid organ transplantation. For each timepoint analyzed, we generated at least two independent viral genome sequences to assess the heterogeneity and control for sequencing error. Four of the five patients likely had prolonged infection; the fifth apparently experienced a reinfection. The rates of accumulation of substitutions in the viral genome per day were higher in hospitalized patients with prolonged infection than those estimated for the community background. The spike coding region accumulated a significantly greater number of unique mutations than other viral coding regions, and the mutation density was higher. Two patients were treated with monoclonal antibodies (bebtelovimab and sotrovimab); by the next sampled timepoint, each virus population showed substitutions associated with monoclonal antibody resistance as the dominant forms (spike K444N and spike E340D). All patients received remdesivir, but remdesivir-resistant substitutions were not detected. These data thus help elucidate the trends of emergence, evolution, and selection of mutational variants within long-term infected immunocompromised individuals. IMPORTANCE SARS-CoV-2 is responsible for a global pandemic, driven in part by the emergence of new viral variants. Where do these new variants come from? One model is that long-term viral persistence in infected individuals allows for viral evolution in response to host pressures, resulting in viruses more likely to replicate efficiently in humans. In this study, we characterize replication in several hospitalized and long-term infected individuals, documenting efficient pathways of viral evolution.
Collapse
Affiliation(s)
- Andrew D. Marques
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | | | - Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emma J. Cook
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise H. Moncla
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
16
|
Miskovic R, Ljubicic J, Bonaci-Nikolic B, Petkovic A, Markovic V, Rankovic I, Djordjevic J, Stankovic A, Klaassen K, Pavlovic S, Stojanovic M. Case report: Rapidly progressive neurocognitive disorder with a fatal outcome in a patient with PU.1 mutated agammaglobulinemia. Front Immunol 2024; 15:1324679. [PMID: 38500873 PMCID: PMC10945545 DOI: 10.3389/fimmu.2024.1324679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction PU.1-mutated agammaglobulinemia (PU.MA) represents a recently described autosomal-dominant form of agammaglobulinemia caused by mutation of the SPI1 gene. This gene codes for PU.1 pioneer transcription factor important for the maturation of monocytes, B lymphocytes, and conventional dendritic cells. Only six cases with PU.MA, presenting with chronic sinopulmonary and systemic enteroviral infections, have been previously described. Accumulating literature evidence suggests a possible relationship between SPI1 mutation, microglial phagocytic dysfunction, and the development of Alzheimer's disease (AD). Case description We present a Caucasian female patient born from a non-consanguineous marriage, who was diagnosed with agammaglobulinemia at the age of 15 years when the immunoglobulin replacement therapy was started. During the following seventeen years, she was treated for recurrent respiratory and intestinal infections. At the age of 33 years, the diagnosis of celiac-like disease was established. Five years later progressive cognitive deterioration, unstable gait, speech disturbances, and behavioral changes developed. Comprehensive microbiological investigations were negative, excluding possible infective etiology. Brain MRI, 18FDG-PET-CT, and neuropsychological testing were suggestive for a diagnosis of a frontal variant of AD. Clinical exome sequencing revealed the presence of a novel frameshift heterozygous variant c.441dup in exon 4 of the SPI1 gene. Despite intensive therapy, the patient passed away a few months after the onset of the first neurological symptoms. Conclusion We describe the first case of PU.MA patient presenting with a rapidly progressive neurocognitive deterioration. The possible role of microglial dysfunction in patients with SPI1 mutation could explain their susceptibility to neurodegenerative diseases thus highlighting the importance of genetic testing in patients with inborn errors of immunity. Since PU.MA represents a newly described form of agammaglobulinemia, our case expands the spectrum of manifestations associated with SPI1 mutation.
Collapse
Affiliation(s)
- Rada Miskovic
- Clinic of Allergy and Immunology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena Ljubicic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Branka Bonaci-Nikolic
- Clinic of Allergy and Immunology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ana Petkovic
- Diagnostic Department, Center of Sterotaxic Radiosurgery, Clinic of Neurosurgery, University Clinical Center of Serbia, Belgrade, Serbia
| | - Vladana Markovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Ivan Rankovic
- Department of Gastroenterology and Liver Unit, Royal Cornwall Hospitals NHS Trust, University of Exeter, Truro, United Kingdom
| | - Jelena Djordjevic
- Clinic of Neurology and Psychiatry for Children and Youth, Belgrade, Serbia
- Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Ana Stankovic
- Center for Radiology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Kristel Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Stojanovic
- Clinic of Allergy and Immunology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| |
Collapse
|
17
|
Raglow Z, Surie D, Chappell JD, Zhu Y, Martin ET, Kwon JH, Frosch AE, Mohamed A, Gilbert J, Bendall EE, Bahr A, Halasa N, Talbot HK, Grijalva CG, Baughman A, Womack KN, Johnson C, Swan SA, Koumans E, McMorrow ML, Harcourt JL, Atherton LJ, Burroughs A, Thornburg NJ, Self WH, Lauring AS. SARS-CoV-2 shedding and evolution in patients who were immunocompromised during the omicron period: a multicentre, prospective analysis. THE LANCET. MICROBE 2024; 5:e235-e246. [PMID: 38286131 DOI: 10.1016/s2666-5247(23)00336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 01/31/2024]
Abstract
BACKGROUND Prolonged SARS-CoV-2 infections in people who are immunocompromised might predict or source the emergence of highly mutated variants. The types of immunosuppression placing patients at highest risk for prolonged infection have not been systematically investigated. We aimed to assess risk factors for prolonged SARS-CoV-2 infection and associated intrahost evolution. METHODS In this multicentre, prospective analysis, participants were enrolled at five US medical centres. Eligible patients were aged 18 years or older, were SARS-CoV-2-positive in the previous 14 days, and had a moderately or severely immunocompromising condition or treatment. Nasal specimens were tested by real-time RT-PCR every 2-4 weeks until negative in consecutive specimens. Positive specimens underwent viral culture and whole genome sequencing. A Cox proportional hazards model was used to assess factors associated with duration of infection. FINDINGS From April 11, 2022, to Oct 1, 2022, 156 patients began the enrolment process, of whom 150 were enrolled and included in the analyses. Participants had B-cell malignancy or anti-B-cell therapy (n=18), solid organ transplantation or haematopoietic stem-cell transplantation (HSCT; n=59), AIDS (n=5), non-B-cell malignancy (n=23), and autoimmune or autoinflammatory conditions (n=45). 38 (25%) participants were real-time RT-PCR-positive and 12 (8%) were culture-positive 21 days or longer after initial SARS-CoV-2 detection or illness onset. Compared with the group with autoimmune or autoinflammatory conditions, patients with B-cell dysfunction (adjusted hazard ratio 0·32 [95% CI 0·15-0·64]), solid organ transplantation or HSCT (0·60 [0·38-0·94]), and AIDS (0·28 [0·08-1·00]) had longer duration of infection, defined as time to last positive real-time RT-PCR test. There was no significant difference in the non-B-cell malignancy group (0·58 [0·31-1·09]). Consensus de novo spike mutations were identified in five individuals who were real-time RT-PCR-positive longer than 56 days; 14 (61%) of 23 were in the receptor-binding domain. Mutations shared by multiple individuals were rare (<5%) in global circulation. INTERPRETATION In this cohort, prolonged replication-competent omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting longer than 56 days accumulated spike mutations, which were distinct from those seen globally. Populations at high risk should be targeted for repeated testing and treatment and monitored for the emergence of antiviral resistance. FUNDING US Centers for Disease Control and Prevention.
Collapse
Affiliation(s)
- Zoe Raglow
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Diya Surie
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennie H Kwon
- Department of Medicine, Washington University, St Louis, MO, USA
| | - Anne E Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, MN, USA
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Gilbert
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily E Bendall
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Auden Bahr
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cassandra Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emilia Koumans
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Meredith L McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer L Harcourt
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lydia J Atherton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ashley Burroughs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
18
|
Vijayan A, Sukumaran A, Jones S, Paul A, Ahmed S, Mehta P, Mohanan M, Kumar S, Easwaran S, Shenoy P. Boosting Vaccine Response in Autoimmune Rheumatic Disease Patients With Inadequate Seroconversion: An Analysis of the Immunogenicity of Vector-Based and Inactivated Vaccines. Cureus 2024; 16:e55764. [PMID: 38586774 PMCID: PMC10998979 DOI: 10.7759/cureus.55764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND An additional dose of COVID-19 vaccine is being offered to vaccinated people, especially those immunocompromised. The most widely available vaccines in India are the adenoviral vector-based AZD1222 (ChAdOx1 nCoV-19) and the heat-inactivated (BBV152). This study investigated the efficacy of both vaccines in patients with autoimmune rheumatic diseases (AIRD). OBJECTIVES To compare final anti-SARS-CoV-2 antibody titers, neutralization of pseudovirions by these antibodies, and T cell responses between patients of AIRD who had received the third dose of AZD1222 and BBV152 vaccines. METHODS Patients with stable AIRD who had completed two doses of COVID-19 vaccination but had a suboptimal response (anti-receptor binding domain (RBD) antibody<212) were randomized (1:1) to receive either AZD1222 or BBV152 as a booster dose. Patients with previous hybrid immunity or those who developed COVID-19 during the trial were excluded. Antibody titers, neutralization of Wuhan and Omicron pseudovirions, and interferon release by T cells (enzyme-linked immunosorbent spot (ELISpot)) in response to the Spike antigen were measured four weeks after this booster dose. RESULTS 146 were screened, 91 were randomized, and 67 were analyzed per protocol. The third dose improved antibody titers (p<0.001), neutralization of the Wuhan strain (p<0.001), and T cell interferon release (p<0.001) but not neutralization of the Omicron strain (p=0.24). Antibody titers were higher (p<0.005) after ADZ1222 boost (2,414 IU (interquartile range (IQR): 330-10,315)) than BBV1222 (347.7 IU (0.4-973)). Neutralization of the Wuhan stain was better (AZD1222: 76.6%(23.0-95.45) versus BBV152 (32.7% (0-78.9), p=0.03 by ANCOVA). Neutralization of Omicron (0 (0-28.4) vs 0 (0-4.8)) and T cell interferon release (57.0 IU (23.5-95) vs 50.5 IU (13.2-139)) were similar. CONCLUSION The third dose improved all parameters of immunogenicity in AIRD patients with previous inadequate responses except Omicron neutralization. The vector-based vaccine exhibits notable efficacy, particularly in antibody titers and neutralizing the Wuhan strain. TRIAL REGISTRATION CTRI/2021/12/038928.
Collapse
Affiliation(s)
- Anuroopa Vijayan
- Rheumatology, Dr Shenoys CARE, Kochi, IND
- Rheumatology, Sree Sudheendra Medical Mission, Kochi, IND
| | | | - Sara Jones
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, IND
| | - Aby Paul
- Pharmacy, Dr Shenoys CARE, Kochi, IND
| | - Sakir Ahmed
- Rheumatology, Kalinga Institute of Medical Sciences, Bhubaneswar, IND
| | - Pankti Mehta
- Clinical Immunology and Rheumatology, King George's Medical University, Lucknow, IND
| | | | - Santhosh Kumar
- Cancer Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, IND
| | | | | |
Collapse
|
19
|
Meijer SE, Halutz O, Adler A, Levytskyi K, Tau L, Dekel M, Cohen-Poradosu R, Katchman E, Shasha D, Ablin J, Choshen G, Jacob G, Wasserman A, Ingbir M, Cohen YC, Perry C, Ram R, Herishanu Y, Bar On Y, van Thijn E, Rutsinsky N, Harari S, Stern A, Ben-Ami R, Paran Y. Dual anti-viral treatment for persistent COVID-19 in immunocompromised hemato-oncological patients is associated with a favorable prognosis and minor side effects. J Infect Chemother 2024; 30:271-275. [PMID: 37944697 DOI: 10.1016/j.jiac.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 10/11/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023]
Abstract
In hemato-oncological patients, COVID-19 can present as a persistent infection with ongoing symptoms and viral replication over a prolonged period of time. Data are scarce on the preferred treatment options for these patients. We describe our experience with a five-day course of dual anti-viral treatment with remdesivir and nirmatrelvir/ritonavir for hemato-oncological immunocompromised patients with persistent COVID-19. Fifteen patients with a history of lymphoma, CLL, and MM were included. Eight were male, median age was 74. All patients had an immediate clinical and virological response. In 73 % of patients, PCR for SARS-CoV-2 became negative at the end of treatment and the rest had an increase in PCR cycle threshold (CT) values, with a median increase of 6 cycles. After a follow-up of three months, 60 % of patients remained in full clinical and virological remission. None required invasive mechanical ventilation or died. The side effects we observed, neutropenia, lactatemia and elevated transaminases, were mild and almost all transient in nature. We conclude that dual anti-viral treatment appears to be a valid treatment option for persistent COVID-19.
Collapse
Affiliation(s)
- Suzy E Meijer
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Ora Halutz
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Adler
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katya Levytskyi
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Luba Tau
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Dekel
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Evgene Katchman
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David Shasha
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jacob Ablin
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Giris Jacob
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Asaf Wasserman
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Merav Ingbir
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael C Cohen
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chava Perry
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Ram
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yair Herishanu
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Bar On
- Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Natalie Rutsinsky
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ronen Ben-Ami
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Paran
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
20
|
Penrice-Randal R, Bentley EG, Sharma P, Kirby A, Donovan-Banfield I, Kipar A, Mega DF, Bramwell C, Sharp J, Owen A, Hiscox JA, Stewart JP. The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in infected and immune suppressed mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582110. [PMID: 38464327 PMCID: PMC10925244 DOI: 10.1101/2024.02.27.582110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Objectives Immunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context. Methods Mice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed. Results Treatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of A>G and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs). Conclusions Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.
Collapse
Affiliation(s)
| | - Eleanor G. Bentley
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - I’ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Daniele F. Mega
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Chloe Bramwell
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| |
Collapse
|
21
|
Port JR, Morris DH, Riopelle JC, Yinda CK, Avanzato VA, Holbrook MG, Bushmaker T, Schulz JE, Saturday TA, Barbian K, Russell CA, Perry-Gottschalk R, Shaia C, Martens C, Lloyd-Smith JO, Fischer RJ, Munster VJ. Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster. eLife 2024; 12:RP87094. [PMID: 38416804 PMCID: PMC10942639 DOI: 10.7554/elife.87094] [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] [Indexed: 03/01/2024] Open
Abstract
It remains poorly understood how SARS-CoV-2 infection influences the physiological host factors important for aerosol transmission. We assessed breathing pattern, exhaled droplets, and infectious virus after infection with Alpha and Delta variants of concern (VOC) in the Syrian hamster. Both VOCs displayed a confined window of detectable airborne virus (24-48 hr), shorter than compared to oropharyngeal swabs. The loss of airborne shedding was linked to airway constriction resulting in a decrease of fine aerosols (1-10 µm) produced, which are suspected to be the major driver of airborne transmission. Male sex was associated with increased viral replication and virus shedding in the air. Next, we compared the transmission efficiency of both variants and found no significant differences. Transmission efficiency varied mostly among donors, 0-100% (including a superspreading event), and aerosol transmission over multiple chain links was representative of natural heterogeneity of exposure dose and downstream viral kinetics. Co-infection with VOCs only occurred when both viruses were shed by the same donor during an increased exposure timeframe (24-48 hr). This highlights that assessment of host and virus factors resulting in a differential exhaled particle profile is critical for understanding airborne transmission.
Collapse
Affiliation(s)
- Julia R Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Dylan H Morris
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | - Jade C Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Victoria A Avanzato
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Myndi G Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Trenton Bushmaker
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Taylor A Saturday
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Kent Barbian
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Colin A Russell
- Department of Medical Microbiology | Amsterdam University Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Rose Perry-Gottschalk
- Rocky Mountain Visual and Medical Arts Unit, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Craig Martens
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | - Robert J Fischer
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| |
Collapse
|
22
|
Machkovech HM, Hahn AM, Garonzik Wang J, Grubaugh ND, Halfmann PJ, Johnson MC, Lemieux JE, O'Connor DH, Piantadosi A, Wei W, Friedrich TC. Persistent SARS-CoV-2 infection: significance and implications. THE LANCET. INFECTIOUS DISEASES 2024:S1473-3099(23)00815-0. [PMID: 38340735 DOI: 10.1016/s1473-3099(23)00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024]
Abstract
SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes unrecognised, and therefore might affect a substantial number of people, particularly immunocompromised individuals. Second, the formation of tissue reservoirs (including in non-respiratory tissues) might underlie the pathophysiology of the persistent SARS-CoV-2 infection and require new strategies for diagnosis and treatment. Finally, persistent SARS-CoV-2 replication, particularly in the setting of suboptimal immune responses, is a possible source of new, divergent virus variants that escape pre-existing immunity on the individual and population levels. Defining optimal diagnostic and treatment strategies for patients with persistent virus replication and monitoring viral evolution are therefore urgent medical and public health priorities.
Collapse
Affiliation(s)
- Heather M Machkovech
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | | | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
23
|
Ghafari M, Hall M, Golubchik T, Ayoubkhani D, House T, MacIntyre-Cockett G, Fryer HR, Thomson L, Nurtay A, Kemp SA, Ferretti L, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith DL, Bashton M, Nelson A, Crown M, McCann C, Young GR, Santos RAND, Richards Z, Tariq MA, Cahuantzi R, Barrett J, Fraser C, Bonsall D, Walker AS, Lythgoe K. Prevalence of persistent SARS-CoV-2 in a large community surveillance study. Nature 2024; 626:1094-1101. [PMID: 38383783 PMCID: PMC10901734 DOI: 10.1038/s41586-024-07029-4] [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: 01/29/2023] [Accepted: 01/04/2024] [Indexed: 02/23/2024]
Abstract
Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1-5, give rise to highly divergent lineages6-8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as 'persistent infections' as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1-0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people11-14. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution.
Collapse
Affiliation(s)
- Mahan Ghafari
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Pandemic Science Institute, University of Oxford, Oxford, UK.
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Daniel Ayoubkhani
- Office for National Statistics, Newport, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Helen R Fryer
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laura Thomson
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Steven A Kemp
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Angie Green
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lorne J Lonie
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | - Darren L Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - 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, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - 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, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Clare McCann
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Gregory R Young
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Rui Andre Nunes Dos Santos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Zack Richards
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Mohammad Adnan Tariq
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | | | | | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
| | - Katrina Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Pandemic Science Institute, University of Oxford, Oxford, UK.
| |
Collapse
|
24
|
Höft MA, Burgers WA, Riou C. The immune response to SARS-CoV-2 in people with HIV. Cell Mol Immunol 2024; 21:184-196. [PMID: 37821620 PMCID: PMC10806256 DOI: 10.1038/s41423-023-01087-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
This review examines the intersection of the HIV and SARS-CoV-2 pandemics. People with HIV (PWH) are a heterogeneous group that differ in their degree of immune suppression, immune reconstitution, and viral control. While COVID-19 in those with well-controlled HIV infection poses no greater risk than that for HIV-uninfected individuals, people with advanced HIV disease are more vulnerable to poor COVID-19 outcomes. COVID-19 vaccines are effective and well tolerated in the majority of PWH, though reduced vaccine efficacy, breakthrough infections and faster waning of vaccine effectiveness have been demonstrated in PWH. This is likely a result of suboptimal humoral and cellular immune responses after vaccination. People with advanced HIV may also experience prolonged infection that may give rise to new epidemiologically significant variants, but initiation or resumption of antiretroviral therapy (ART) can effectively clear persistent infection. COVID-19 vaccine guidelines reflect these increased risks and recommend prioritization for vaccination and additional booster doses for PWH who are moderately to severely immunocompromised. We recommend continued research and monitoring of PWH with SARS-CoV-2 infection, especially in areas with a high HIV burden.
Collapse
Affiliation(s)
- Maxine A Höft
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
| |
Collapse
|
25
|
Avila-Herrera A, Kimbrel JA, Manuel Martí J, Thissen J, Saada EA, Weisenberger T, Arrildt KT, Segelke BW, Allen JE, Zemla A, Borucki MK. Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PLoS One 2024; 19:e0289198. [PMID: 38271318 PMCID: PMC10810540 DOI: 10.1371/journal.pone.0289198] [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] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance.
Collapse
Affiliation(s)
- Aram Avila-Herrera
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Jeffrey A. Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jose Manuel Martí
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - James Thissen
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Edwin A. Saada
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Tracy Weisenberger
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Kathryn T. Arrildt
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Brent W. Segelke
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jonathan E. Allen
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Adam Zemla
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Monica K. Borucki
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| |
Collapse
|
26
|
Li Y, Choudhary MC, Regan J, Boucau J, Nathan A, Speidel T, Liew MY, Edelstein GE, Kawano Y, Uddin R, Deo R, Marino C, Getz MA, Reynolds Z, Barry M, Gilbert RF, Tien D, Sagar S, Vyas TD, Flynn JP, Hammond SP, Novack LA, Choi B, Cernadas M, Wallace ZS, Sparks JA, Vyas JM, Seaman MS, Gaiha GD, Siedner MJ, Barczak AK, Lemieux JE, Li JZ. SARS-CoV-2 viral clearance and evolution varies by type and severity of immunodeficiency. Sci Transl Med 2024; 16:eadk1599. [PMID: 38266109 PMCID: PMC10982957 DOI: 10.1126/scitranslmed.adk1599] [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: 08/05/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024]
Abstract
Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but the immune defects that predispose an individual to persistent coronavirus disease 2019 (COVID-19) remain incompletely understood. In this study, we performed detailed viro-immunologic analyses of a prospective cohort of participants with COVID-19. The median times to nasal viral RNA and culture clearance in individuals with severe immunosuppression due to hematologic malignancy or transplant (S-HT) were 72 and 40 days, respectively, both of which were significantly longer than clearance rates in individuals with severe immunosuppression due to autoimmunity or B cell deficiency (S-A), individuals with nonsevere immunodeficiency, and nonimmunocompromised groups (P < 0.01). Participants who were severely immunocompromised had greater SARS-CoV-2 evolution and a higher risk of developing resistance against therapeutic monoclonal antibodies. Both S-HT and S-A participants had diminished SARS-CoV-2-specific humoral responses, whereas only the S-HT group had reduced T cell-mediated responses. This highlights the varied risk of persistent COVID-19 across distinct immunosuppressive conditions and suggests that suppression of both B and T cell responses results in the highest contributing risk of persistent infection.
Collapse
Affiliation(s)
- Yijia Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Manish C. Choudhary
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Regan
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Tessa Speidel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - May Yee Liew
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gregory E. Edelstein
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yumeko Kawano
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rockib Uddin
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rinki Deo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin Marino
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Matthew A. Getz
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zahra Reynolds
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mamadou Barry
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Rebecca F. Gilbert
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Dessie Tien
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Shruti Sagar
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tammy D. Vyas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - James P. Flynn
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah P. Hammond
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lewis A. Novack
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bina Choi
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manuela Cernadas
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zachary S. Wallace
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jeffrey A. Sparks
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jatin M. Vyas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Gaurav D. Gaiha
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mark J. Siedner
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Amy K. Barczak
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jacob E. Lemieux
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan Z. Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
27
|
Farjo M, Koelle K, Martin MA, Gibson LL, Walden KKO, Rendon G, Fields CJ, Alnaji FG, Gallagher N, Luo CH, Mostafa HH, Manabe YC, Pekosz A, Smith RL, McManus DD, Brooke CB. Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection. J Virol 2024; 98:e0161823. [PMID: 38174928 PMCID: PMC10805032 DOI: 10.1128/jvi.01618-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we sequenced saliva and nasal samples collected daily from vaccinated and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.IMPORTANCEWe detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.
Collapse
Affiliation(s)
- Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Michael A. Martin
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Laura L. Gibson
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kimberly K. O. Walden
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J. Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Fadi G. Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H. Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yukari C. Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rebecca L. Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - David D. McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
28
|
Harari S, Miller D, Fleishon S, Burstein D, Stern A. Using big sequencing data to identify chronic SARS-Coronavirus-2 infections. Nat Commun 2024; 15:648. [PMID: 38245511 PMCID: PMC10799923 DOI: 10.1038/s41467-024-44803-4] [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: 09/04/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants. One leading hypothesis suggests these variants may have emerged during chronic infections of immunocompromised individuals, but limited data from these cases hinders comprehensive analyses. Here, we harnessed millions of SARS-CoV-2 genomes to identify potential chronic infections and used language models (LM) to infer chronic-associated mutations. First, we mined the SARS-CoV-2 phylogeny and identified chronic-like clades with identical metadata (location, age, and sex) spanning over 21 days, suggesting a prolonged infection. We inferred 271 chronic-like clades, which exhibited characteristics similar to confirmed chronic infections. Chronic-associated mutations were often high-fitness immune-evasive mutations located in the spike receptor-binding domain (RBD), yet a minority were unique to chronic infections and absent in global settings. The probability of observing high-fitness RBD mutations was 10-20 times higher in chronic infections than in global transmission chains. The majority of RBD mutations in BA.1/BA.2 chronic-like clades bore predictive value, i.e., went on to display global success. Finally, we used our LM to infer hundreds of additional chronic-like clades in the absence of metadata. Our approach allows mining extensive sequencing data and providing insights into future evolutionary patterns of SARS-CoV-2.
Collapse
Affiliation(s)
- Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Shay Fleishon
- Israeli Health Intelligence Agency, Public Health Division, Ministry of Health, Jerusalem, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
29
|
Adhikary S, Pathak S, Palani V, Acar A, Banerjee A, Al-Dewik NI, Essa MM, Mohammed SGAA, Qoronfleh MW. Current Technologies and Future Perspectives in Immunotherapy towards a Clinical Oncology Approach. Biomedicines 2024; 12:217. [PMID: 38255322 PMCID: PMC10813720 DOI: 10.3390/biomedicines12010217] [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: 12/04/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Immunotherapy is now established as a potent therapeutic paradigm engendering antitumor immune response against a wide range of malignancies and other diseases by modulating the immune system either through the stimulation or suppression of immune components such as CD4+ T cells, CD8+ T cells, B cells, monocytes, macrophages, dendritic cells, and natural killer cells. By targeting several immune checkpoint inhibitors or blockers (e.g., PD-1, PD-L1, PD-L2, CTLA-4, LAG3, and TIM-3) expressed on the surface of immune cells, several monoclonal antibodies and polyclonal antibodies have been developed and already translated clinically. In addition, natural killer cell-based, dendritic cell-based, and CAR T cell therapies have been also shown to be promising and effective immunotherapeutic approaches. In particular, CAR T cell therapy has benefited from advancements in CRISPR-Cas9 genome editing technology, allowing the generation of several modified CAR T cells with enhanced antitumor immunity. However, the emerging SARS-CoV-2 infection could hijack a patient's immune system by releasing pro-inflammatory interleukins and cytokines such as IL-1β, IL-2, IL-6, and IL-10, and IFN-γ and TNF-α, respectively, which can further promote neutrophil extravasation and the vasodilation of blood vessels. Despite the significant development of advanced immunotherapeutic technologies, after a certain period of treatment, cancer relapses due to the development of resistance to immunotherapy. Resistance may be primary (where tumor cells do not respond to the treatment), or secondary or acquired immune resistance (where tumor cells develop resistance gradually to ICIs therapy). In this context, this review aims to address the existing immunotherapeutic technologies against cancer and the resistance mechanisms against immunotherapeutic drugs, and explain the impact of COVID-19 on cancer treatment. In addition, we will discuss what will be the future implementation of these strategies against cancer drug resistance. Finally, we will emphasize the practical steps to lay the groundwork for enlightened policy for intervention and resource allocation to care for cancer patients.
Collapse
Affiliation(s)
- Subhamay Adhikary
- Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Surajit Pathak
- Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Vignesh Palani
- Faculty of Medicine, Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Türkiye;
| | - Antara Banerjee
- Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Nader I. Al-Dewik
- Department of Pediatrics, Women’s Wellness and Research Center, Hamad Medical Corporation, Doha 00974, Qatar;
| | - Musthafa Mohamed Essa
- College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat 123, Oman
| | | | - M. Walid Qoronfleh
- Research & Policy Division, Q3 Research Institute (QRI), Ypsilanti, MI 48917, USA
| |
Collapse
|
30
|
D’Avila H, Lima CNR, Rampinelli PG, Mateus LCO, de Sousa Silva RV, Correa JR, de Almeida PE. Lipid Metabolism Modulation during SARS-CoV-2 Infection: A Spotlight on Extracellular Vesicles and Therapeutic Prospects. Int J Mol Sci 2024; 25:640. [PMID: 38203811 PMCID: PMC10778989 DOI: 10.3390/ijms25010640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Extracellular vesicles (EVs) have a significant impact on the pathophysiological processes associated with various diseases such as tumors, inflammation, and infection. They exhibit molecular, biochemical, and entry control characteristics similar to viral infections. Viruses, on the other hand, depend on host metabolic machineries to fulfill their biosynthetic requirements. Due to potential advantages such as biocompatibility, biodegradation, and efficient immune activation, EVs have emerged as potential therapeutic targets against the SARS-CoV-2 infection. Studies on COVID-19 patients have shown that they frequently have dysregulated lipid profiles, which are associated with an increased risk of severe repercussions. Lipid droplets (LDs) serve as organelles with significant roles in lipid metabolism and energy homeostasis as well as having a wide range of functions in infections. The down-modulation of lipids, such as sphingolipid ceramide and eicosanoids, or of the transcriptional factors involved in lipogenesis seem to inhibit the viral multiplication, suggesting their involvement in the virus replication and pathogenesis as well as highlighting their potential as targets for drug development. Hence, this review focuses on the role of modulation of lipid metabolism and EVs in the mechanism of immune system evasion during SARS-CoV-2 infection and explores the therapeutic potential of EVs as well as application for delivering therapeutic substances to mitigate viral infections.
Collapse
Affiliation(s)
- Heloisa D’Avila
- Cell Biology Laboratory, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil; (H.D.); (P.G.R.); (L.C.O.M.); (R.V.d.S.S.)
| | | | - Pollianne Garbero Rampinelli
- Cell Biology Laboratory, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil; (H.D.); (P.G.R.); (L.C.O.M.); (R.V.d.S.S.)
| | - Laiza Camila Oliveira Mateus
- Cell Biology Laboratory, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil; (H.D.); (P.G.R.); (L.C.O.M.); (R.V.d.S.S.)
| | - Renata Vieira de Sousa Silva
- Cell Biology Laboratory, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil; (H.D.); (P.G.R.); (L.C.O.M.); (R.V.d.S.S.)
| | - José Raimundo Correa
- Laboratory of Microscopy and Microanalysis, University of Brasília, Brasília 70910-900, Brazil;
| | - Patrícia Elaine de Almeida
- Cell Biology Laboratory, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil; (H.D.); (P.G.R.); (L.C.O.M.); (R.V.d.S.S.)
| |
Collapse
|
31
|
Baker SJC, Nfonsam LE, Leto D, Rutherford C, Smieja M, McArthur AG. Chronic COVID-19 infection in an immunosuppressed patient shows changes in lineage over time: a case report. Virol J 2024; 21:8. [PMID: 38178158 PMCID: PMC10768205 DOI: 10.1186/s12985-023-02278-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/25/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 virus, emerged in late 2019 and spready globally. Many effects of infection with this pathogen are still unknown, with both chronic and repeated COVID-19 infection producing novel pathologies. CASE PRESENTATION An immunocompromised patient presented with chronic COVID-19 infection. The patient had history of Hodgkin's lymphoma, treated with chemotherapy and stem cell transplant. During the course of their treatment, eleven respiratory samples from the patient were analyzed by whole-genome sequencing followed by lineage identification. Whole-genome sequencing of the virus present in the patient over time revealed that the patient at various timepoints harboured three different lineages of the virus. The patient was initially infected with the B.1.1.176 lineage before coinfection with BA.1. When the patient was coinfected with both B.1.1.176 and BA.1, the viral populations were found in approximately equal proportions within the patient based on sequencing read abundance. Upon further sampling, the lineage present within the patient during the final two timepoints was found to be BA.2.9. The patient eventually developed respiratory failure and died. CONCLUSIONS This case study shows an example of the changes that can happen within an immunocompromised patient who is infected with COVID-19 multiple times. Furthermore, this case demonstrates how simultaneous coinfection with two lineages of COVID-19 can lead to unclear lineage assignment by standard methods, which are resolved by further investigation. When analyzing chronic COVID-19 infection and reinfection cases, care must be taken to properly identify the lineages of the virus present.
Collapse
Affiliation(s)
- Sheridan J C Baker
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
| | - Landry E Nfonsam
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Daniela Leto
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Candy Rutherford
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
| | - Marek Smieja
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
| |
Collapse
|
32
|
El-Baky NA, Amara AA, Uversky VN, Redwan EM. Intrinsic factors behind long COVID: III. Persistence of SARS-CoV-2 and its components. J Cell Biochem 2024; 125:22-44. [PMID: 38098317 DOI: 10.1002/jcb.30514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/27/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Considerable research has been done in investigating SARS-CoV-2 infection, its characteristics, and host immune response. However, debate is still ongoing over the emergence of post-acute sequelae of SARS-CoV-2 infection (PASC). A multitude of long-lasting symptoms have been reported several weeks after the primary acute SARS-CoV-2 infection that resemble several other viral infections. Thousands of research articles have described various post-COVID-19 conditions. Yet, the evidence around these ongoing health problems, the reasons behind them, and their molecular underpinnings are scarce. These persistent symptoms are also known as long COVID-19. The persistence of SARS-CoV-2 and/or its components in host tissues can lead to long COVID. For example, the presence of viral nucleocapsid protein and RNA was detected in the skin, appendix, and breast tissues of some long COVID patients. The persistence of viral RNA was reported in multiple anatomic sites, including non-respiratory tissues such as the adrenal gland, ocular tissue, small intestine, lymph nodes, myocardium, and sciatic nerve. Distinctive viral spike sequence variants were also found in non-respiratory tissues. Interestingly, prolonged detection of viral subgenomic RNA was observed across all tissues, sometimes in multiple tissues of the same patient, which likely reflects recent but defective viral replication. Moreover, the persistence of SARS-CoV-2 RNA was noticed throughout the brain at autopsy, as late as 230 days following symptom onset among unvaccinated patients who died of severe infection. Here, we review the persistence of SARS-CoV-2 and its components as an intrinsic factor behind long COVID. We also highlight the immunological consequences of this viral persistence.
Collapse
Affiliation(s)
- Nawal Abd El-Baky
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Egypt
| | - Amro A Amara
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Egypt
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Elrashdy M Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
33
|
Lustig G, Ganga Y, Rodel HE, Tegally H, Khairallah A, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Ndung’u T, Moosa MYS, Archary D, de Oliveira T, Lessells R, Neher RA, Abdool Karim SS, Sigal A. SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations. Virus Evol 2023; 10:vead075. [PMID: 38361824 PMCID: PMC10868398 DOI: 10.1093/ve/vead075] [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: 05/02/2023] [Revised: 11/11/2023] [Accepted: 12/21/2023] [Indexed: 02/17/2024] Open
Abstract
One mechanism of variant formation may be evolution during long-term infection in immunosuppressed people. To understand the viral phenotypes evolved during such infection, we tested SARS-CoV-2 viruses evolved from an ancestral B.1 lineage infection lasting over 190 days post-diagnosis in an advanced HIV disease immunosuppressed individual. Sequence and phylogenetic analysis showed two evolving sub-lineages, with the second sub-lineage replacing the first sub-lineage in a seeming evolutionary sweep. Each sub-lineage independently evolved escape from neutralizing antibodies. The most evolved virus for the first sub-lineage (isolated day 34) and the second sub-lineage (isolated day 190) showed similar escape from ancestral SARS-CoV-2 and Delta-variant infection elicited neutralizing immunity despite having no spike mutations in common relative to the B.1 lineage. The day 190 isolate also evolved higher cell-cell fusion and faster viral replication and caused more cell death relative to virus isolated soon after diagnosis, though cell death was similar to day 34 first sub-lineage virus. These data show that SARS-CoV-2 strains in prolonged infection in a single individual can follow independent evolutionary trajectories which lead to neutralization escape and other changes in viral properties.
Collapse
Affiliation(s)
- Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Hylton E Rodel
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa
| | - Afrah Khairallah
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Laurelle Jackson
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Sandile Cele
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Khadija Khan
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Farina Karim
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Mallory Bernstein
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Thumbi Ndung’u
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- HIV Pathogenesis Programme, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa
- Department of Global Health, University of Washington, 3980 15th Avenue NE, Seattle, WA 98105, USA
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
| | - Richard A Neher
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
- Biozentrum, University of Basel, Spitalstrasse 41 4056, Basel, Switzerland
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, United States
| | - Alex Sigal
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| |
Collapse
|
34
|
Yang Q, He Y, Zhou Y, Jia Q, Dai N, Ma S, Yang X, Zhang X, Sun J. Prolonged Viral Shedding in Cancer Patients with Asymptomatic or Mild Omicron Infection: A Retrospective Study. Infect Drug Resist 2023; 16:7735-7741. [PMID: 38144220 PMCID: PMC10749107 DOI: 10.2147/idr.s431126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/06/2023] [Indexed: 12/26/2023] Open
Abstract
Background This study aimed to investigate the risk factors for persistent viral shedding in cancer patients after Omicron infection. Methods Patients with asymptomatic or mild Omicron infection (≥18 years) who were treated in a makeshift hospital in Shanghai were enrolled from 9 Apr to 11 May, 2022. Deidentified information of all patients were collected retrospectively. Logistic regression model was used to identify risk factors associated with prolonged duration of viral shedding (defined as the time from the day of first positive SARS-CoV-2 RNA test to the first day of two consecutive negative SARS-CoV-2 RNA tests). Results A total of 1442 Omicron-infected patients were enrolled, including 129 cancer patients and 1313 non-cancer patients. The baseline clinical characteristics of cancer and non-cancer patients were balanced by propensity score matching (1:4). Compared with non-cancer patients, a higher odds ratio ([OR] 1.84, 95% CI 1.24-2.76, P = 0.003) of lasting viral shedding for ≥7 days was found in cancer patients. Further subgroup analyses found that cancer patients were at higher risk for prolonged viral shedding in a subgroup of patients without hypertension (OR 1.89), diabetes (OR 1.80), or other chronic disease (OR 2.13), unvaccinated (OR 1.97), and asymptomatic (OR 2.36). In addition, 29 patients with active cancer and 19 patients with inactive cancer were identified. The median duration of viral shedding in the active cancer group was longer than that in the inactive cancer group (10 vs 6 days, P = 0.002). The risk of persistent viral shedding ≥7 days was also increased in the active cancer group (OR 5.33, 95% CI 1.49-21.51, P = 0.013). Conclusion Cancer disease is an independent risk factor for prolonged viral shedding in Omicron infected patients, especially in patients with active cancer.
Collapse
Affiliation(s)
- Qiao Yang
- Department of Ultrasound, The 941st Hospital of the PLA Joint Logistic Support Force, Xining, 810007, People’s Republic of China
| | - Ying He
- Department of Psychiatry, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People’s Republic of China
| | - Yi Zhou
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People’s Republic of China
| | - Qinzhu Jia
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People’s Republic of China
| | - Nan Dai
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing, 400042, People’s Republic of China
| | - Siyuan Ma
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, 400038, People’s Republic of China
| | - Xiu Yang
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People’s Republic of China
| | - Xi Zhang
- Department of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People’s Republic of China
| | - Jianguo Sun
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People’s Republic of China
| |
Collapse
|
35
|
Penetra SLS, Santos HFP, Resende PC, Bastos LS, da Silva MFB, Pina-Costa A, Lopes RS, Saboia-Vahia L, de Oliveira ACA, Pereira EC, Filho FM, Wakimoto MD, Calvet GA, Fuller TL, Whitworth J, Smith C, Nielsen-Saines K, Carvalho MS, Espíndola OM, Guaraldo L, Siqueira MM, Brasil P. SARS-CoV-2 Reinfection Cases in a Household-Based Prospective Cohort in Rio de Janeiro. J Infect Dis 2023; 228:1680-1689. [PMID: 37571849 PMCID: PMC11032242 DOI: 10.1093/infdis/jiad336] [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: 03/23/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2023] Open
Abstract
This was a household-based prospective cohort study conducted in Rio de Janeiro, in which people with laboratory-confirmed coronavirus disease 2019 (COVID-19) and their household contacts were followed from April 2020 through June 2022. Ninety-eight reinfections were identified, with 71 (72.5%) confirmed by genomic analyses and lineage definition in both infections. During the pre-Omicron period, 1 dose of any COVID-19 vaccine was associated with a reduced risk of reinfection, but during the Omicron period not even booster vaccines had this effect. Most reinfections were asymptomatic or milder in comparison with primary infections, a justification for continuing active surveillance to detect infections in vaccinated individuals. Our findings demonstrated that vaccination may not prevent infection or reinfection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Therefore we highlight the need to continuously update the antigenic target of SARS CoV-2 vaccines and administer booster doses to the population regularly, a strategy well established in the development of vaccines for influenza immunization programs.
Collapse
Affiliation(s)
- Stephanie L S Penetra
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heloisa F P Santos
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Soares Bastos
- Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michele F B da Silva
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anielle Pina-Costa
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata Serrano Lopes
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Saboia-Vahia
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Any Caroline Alves de Oliveira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elisa Cavalcante Pereira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando Medeiros Filho
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mayumi D Wakimoto
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme A Calvet
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Trevon L Fuller
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- University of California, Los Angeles, Los Angeles, California, USA
| | - Jimmy Whitworth
- International Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher Smith
- International Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | | | - Marilia Sá Carvalho
- Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Otávio M Espíndola
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lusiele Guaraldo
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marilda M Siqueira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia Brasil
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
36
|
Seth-Smith H, Vesenbeckh S, Egli A, Ott S. SARS-CoV-2 in an immunocompromised host: convalescent plasma therapy and viral evolution elucidated by whole genome sequencing. BMJ Case Rep 2023; 16:e255255. [PMID: 38087481 PMCID: PMC10728978 DOI: 10.1136/bcr-2023-255255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
The evolution of SARS-CoV-2 within immunocompromised hosts who fail to clear the virus over many months has been proposed as a route to the development of Variants of Concern (VoCs). We present a case of an immunocompromised male patient with a prolonged SARS-CoV-2 infection. During hospitalisation, 7 weeks after first diagnosis, his condition worsened to require continuous ventilation support. Resolution of symptoms was observed after convalescent plasma therapy. Whole genome sequencing of the virus showed Pango lineage B.1.221. Between the first sample and the second from bronchoalveolar lavage fluid 7 weeks later, we identified eight mutations, including minor variants, which could be used to estimate the chronology of mutations. This suggests an elevated mutation rate, in-host accumulation of mutations and further evidence for sources of VoCs. Prolonged SARS-CoV-2 infections in immunocompromised hosts increase the likelihood of hospital stays and morbidity, and also pose an increased risk to global public health.
Collapse
Affiliation(s)
- Helena Seth-Smith
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Silvan Vesenbeckh
- Department of Pulmonology, University Hospital Zurich, Zurich, Switzerland
- Department of Pulmonology, Sankt Claraspital, Basel, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Sebastian Ott
- Department of Pulmonology, Sankt Claraspital, Basel, Switzerland
- Department of Pulmonology, Inselspital University Hospital Bern, Bern, Switzerland
| |
Collapse
|
37
|
Samrat SK, Bashir Q, Zhang R, Huang Y, Liu Y, Wu X, Brown T, Wang W, Zheng YG, Zhang QY, Chen Y, Li Z, Li H. A universal fluorescence polarization high throughput screening assay to target the SAM-binding sites of SARS-CoV-2 and other viral methyltransferases. Emerg Microbes Infect 2023; 12:2204164. [PMID: 37060263 PMCID: PMC10165934 DOI: 10.1080/22221751.2023.2204164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/16/2023]
Abstract
SARS-CoV-2 has caused a global pandemic with significant humanity and economic loss since 2020. Currently, only limited options are available to treat SARS-CoV-2 infections for vulnerable populations. In this study, we report a universal fluorescence polarization (FP)-based high throughput screening (HTS) assay for SAM-dependent viral methyltransferases (MTases), using a fluorescent SAM-analogue, FL-NAH. We performed the assay against a reference MTase, NSP14, an essential enzyme for SARS-CoV-2 to methylate the N7 position of viral 5'-RNA guanine cap. The assay is universal and suitable for any SAM-dependent viral MTases such as the SARS-CoV-2 NSP16/NSP10 MTase complex and the NS5 MTase of Zika virus (ZIKV). Pilot screening demonstrated that the HTS assay was very robust and identified two candidate inhibitors, NSC 111552 and 288387. The two compounds inhibited the FL-NAH binding to the NSP14 MTase with low micromolar IC50. We used three functional MTase assays to unambiguously verified the inhibitory potency of these molecules for the NSP14 N7-MTase function. Binding studies indicated that these molecules are bound directly to the NSP14 MTase with similar low micromolar affinity. Moreover, we further demonstrated that these molecules significantly inhibited the SARS-CoV-2 replication in cell-based assays at concentrations not causing cytotoxicity. Furthermore, NSC111552 significantly synergized with known SARS-CoV-2 drugs including nirmatrelvir and remdesivir. Finally, docking suggested that these molecules bind specifically to the SAM-binding site on the NSP14 MTase. Overall, these molecules represent novel and promising candidates to further develop broad-spectrum inhibitors for the management of viral infections.
Collapse
Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Qamar Bashir
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Ran Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yiding Huang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yuchen Liu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Xiangmeng Wu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Wei Wang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yin Chen
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson, AZ, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ, USA
| |
Collapse
|
38
|
Umekage Y, Hatayama M, Yagita A, Nitanai K, Yanada H, Shigaki R, Minami Y, Sasaki T. Monitoring SARS-CoV-2 Viral Load and CD4+ T-cell Count After ART in a Patient Diagnosed With AIDS Following SARS-CoV-2 Infection: A Case Report. Cureus 2023; 15:e51189. [PMID: 38283513 PMCID: PMC10817777 DOI: 10.7759/cureus.51189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2023] [Indexed: 01/30/2024] Open
Abstract
We describe the case of a 36-year-old man diagnosed with human immunodeficiency virus (HIV) following prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia. The patient had a complication of pneumocystis pneumonia. Upon initiating highly active antiretroviral therapy, we monitored HIV RNA levels, CD4+ T-cell count, SARS-CoV-2 viral load, and IgG antibodies against SARS-CoV-2. At 167 days post SARS-CoV-2 diagnosis, the patient's CD4+ T-cell count increased to 180 cells/μL. IgG antibodies against SARS-CoV-2 were undetectable despite a decreased SARS-CoV-2 viral load. HIV screening is necessary in cases of prolonged SARS-CoV-2 pneumonia or persistent SARS-CoV-2 shedding. When diagnosed with HIV infection, it is advisable to consider the possibility of pneumocystis pneumonia.
Collapse
Affiliation(s)
- Yasuhiro Umekage
- Department of Infection Control, Asahikawa Medical University Hospital, Asahikawa, JPN
| | - Mayumi Hatayama
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, JPN
| | - Akari Yagita
- Division of Respiratory Medicine and Neurology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, JPN
| | - Kiichi Nitanai
- Division of Respiratory Medicine and Neurology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, JPN
| | - Hiraku Yanada
- Division of Respiratory Medicine and Neurology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, JPN
| | - Ryota Shigaki
- Division of Respiratory Medicine and Neurology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, JPN
| | - Yoshinori Minami
- Division of Respiratory Medicine and Neurology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, JPN
| | - Takaaki Sasaki
- Division of Respiratory Medicine and Neurology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, JPN
| |
Collapse
|
39
|
Angelico R, Romano F, Coppola L, Materazzo M, Pedini D, Santicchia MS, Cacciola R, Toti L, Sarmati L, Tisone G. Effects of Anti-COVID-19 Vaccination and Pre-Exposure Prophylaxis with Tixagevimab-Cilgavimab in Kidney and Liver Transplant Recipients. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:2101. [PMID: 38138204 PMCID: PMC10744931 DOI: 10.3390/medicina59122101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
Background and Objectives: Underpowered immune response to vaccines against SARS-CoV-2 was observed in solid organ transplant (SOT) recipients. A novel combination of monoclonal antibodies tixagevimab-cilgavimab (TGM/CGM) received authorization as pre-exposure prophylaxis (PrEP) in those with reduced response to vaccine. We aimed to evaluate the response rate to COVID-19 vaccination in kidney transplant (KT), compared to liver transplant (LT) recipients, and the efficacy and safety of PrEP with TGM/CGM. Material and Methods: Between March and November 2022, adult KT and LT recipients who had completed the vaccination schedule (3 doses) were tested for anti-SARS-CoV-2 antibodies titer. SOT recipients with anti-SARS-CoV-2 titer ≥ 100 IU/mL were considered protected against infection, while those with titer < 100 UI/mL were defined non-protected. Patients with inadequate response were invited to PrEP. Results: In total, 306 patients were enrolled [KT:197 (64.4%), LT:109 (35.6%)]. After the complete scheme of vaccination, 246 (80.3%) patients developed a protective titer, while 60 (19.6%) did not have a protective titer. KT recipients had a lower rate of protective anti-COVID-19 titer compared to LT patients [149 (75.6%) vs. 97 (89.0%), p = 0.004]. Recipients with non-protective anti-COVID-19 titer received mainly tacrolimus-based regimen associated with mycophenolate mofetil (MMF) (70%) e steroids (46.7%) as maintenance immunosuppression, while those treated with everolimus were associated with higher protective titer. Of 35 (58.3%) patients who received PrEP, within 12 months, 6 (17.1%) (all KT) developed pauci-symptomatic COVID-19 disease, while 15/25 (60%) of non-responders, who did not receive the prophylaxis, developed COVID-19 disease. After PrEP, hospitalization rate was lower (2.8% vs. 16%), and no adverse events, neither graft loss nor rejection, were observed. Conclusions: Despite complete COVID-19 vaccination, SOT recipients might be not protected from the SARS-CoV-2 infection, especially after KT. In non-protected SOT patients, the subsequent pre-exposure prophylaxis with combination of monoclonal antibodies (TGM/CGM) might be an efficacy and safe strategy to prevent COVID-19 severe disease and hospitalization.
Collapse
Affiliation(s)
- Roberta Angelico
- HPB and Transplant Unit, Department of Surgical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Francesca Romano
- HPB and Transplant Unit, Department of Surgical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Luigi Coppola
- Department of System Medicine, Tor Vergata University, 00133 Rome, Italy
| | - Marco Materazzo
- HPB and Transplant Unit, Department of Surgical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Domiziana Pedini
- HPB and Transplant Unit, Department of Surgical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Maria Sara Santicchia
- HPB and Transplant Unit, Department of Surgical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Roberto Cacciola
- HPB and Transplant Unit, Department of Surgical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Luca Toti
- HPB and Transplant Unit, Department of Surgical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Loredana Sarmati
- Department of System Medicine, Tor Vergata University, 00133 Rome, Italy
- Infectious Disease Clinic, Policlinico Tor Vergata, 00133 Rome, Italy
| | - Giuseppe Tisone
- HPB and Transplant Unit, Department of Surgical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| |
Collapse
|
40
|
Ota K, Kodama H, Kawamoto Y, Sasaki D, Mitsumoto-Kaseida F, Sakamoto K, Kosai K, Hasegawa H, Takazono T, Izumikawa K, Mukae H, Tun MMN, Morita K, Yanagihara K. The evaluation of a rapid microfluidic immunofluorescence antigen test in detecting the infectiousness of COVID-19 patients. BMC Infect Dis 2023; 23:823. [PMID: 37996783 PMCID: PMC10668452 DOI: 10.1186/s12879-023-08821-9] [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: 06/08/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND A test-based strategy against coronavirus disease 2019 (COVID-19) is one of the measures to assess the need for isolation and prevention of infection. However, testing with high sensitivity methods, such as quantitative RT-PCR, leads to unnecessary isolation, whereas the lateral flow antigen test shows low sensitivity and false negative results. The purpose of this study was to evaluate the performance of the LumiraDx SARS-CoV-2 Ag test (Lumira Ag), a rapid microfluidic immunofluorescence method, in assessing infectivity. METHODS This study was performed from March 2022 to July 2022. A pair of nasopharyngeal swab samples were obtained from each patient with mild COVID-19. One swab was used for Lumira Ag testing, and the other for quantitative RT-PCR testing and virus culture. RESULTS A total of 84 patients were included in the study. Among them, PCR, Lumira Ag test, and virus culture indicated positivity for 82, 66, and 24 patients, respectively. When comparing the Lumira Ag test to virus culture, its sensitivity was 100.0% (24/24), specificity, 30.0% (18/60); positive predictive value, 36.3% (24/66); and negative predictive value (NPV), 100.0% (18/18). The positive sample for virus culture was observed until the ninth day from the onset of symptoms, while the Lumira Ag test was observed until day 11. CONCLUSIONS The Lumira Ag test showed high sensitivity and NPV (100% each) compared to virus culture. A test-based strategy using the Lumira Ag test can effectively exclude COVID-19 infectiousness.
Collapse
Affiliation(s)
- Kenji Ota
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan.
| | - Hina Kodama
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Yasuhide Kawamoto
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Daisuke Sasaki
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Fujiko Mitsumoto-Kaseida
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Kei Sakamoto
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
- Department of Microbiology, Graduate School of Medicine, Yamaguchi University, 1-1-1, Minami-Kogushi, Ube, 755-8505, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Takahiro Takazono
- Department of Respiratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Koichi Izumikawa
- Infection Control and Education Center, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
- Dejima Infectious Disease Research Alliance, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| |
Collapse
|
41
|
Hirotsu Y, Kobayashi H, Kakizaki Y, Saito A, Tsutsui T, Kawaguchi M, Shimamura S, Hata K, Hanawa S, Toyama J, Miyashita Y, Omata M. Multidrug-resistant mutations to antiviral and antibody therapy in an immunocompromised patient infected with SARS-CoV-2. MED 2023; 4:813-824.e4. [PMID: 37683636 DOI: 10.1016/j.medj.2023.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/19/2023] [Accepted: 08/15/2023] [Indexed: 09/10/2023]
Abstract
BACKGROUND Antiviral and antibody therapies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being recommended for high-risk patients, but the potential for the development of multidrug-resistant mutations in immunocompromised patients is unclear. METHODS To investigate the treatment course in cases of prolonged viral shedding in an immunocompromised patient with SARS-CoV-2 infection, we conducted longitudinal measurements of laboratory tests, chest computed tomography (CT) image evaluations, antibody titers, and antigen levels in nasopharyngeal swabs. Furthermore, we performed whole-genome sequencing and digital PCR analysis to examine the mechanisms of drug resistance. FINDINGS We present a case of a 65-year-old man with a history of malignant lymphoma who was treated with multiple antiviral and antibody therapies, including sotrovimab, remdesivir, paxlovid (nirmatrelvir/ritonavir), and molnupiravir. Initially, viral antigen levels decreased after treatments. However, after the virus rebounded, the patient showed no virologic response. The viral genome analysis revealed a single Omicron subvariant (BA.1.1), which evolved within the host during the disease progression. The viruses had acquired multiple resistance mutations to nirmatrelvir (3 chymotrypsin-like protease [3CLpro] E166 A/V), sotrovimab (spike P337L and E340K), and remdesivir (RNA-dependent RNA polymerase [RdRp] V166L). CONCLUSIONS Our results indicate that viruses with multidrug-resistant mutations and survival fitness persist in the infected subpopulation after drug selection pressure. FUNDING This study was supported by the JSPS KAKENHI Early-Career Scientists 18K16292 (Y.H.), Grant-in-Aid for Scientific Research (B) 20H03668 and 23H02955 (Y.H.), the YASUDA Medical Foundation (Y.H.), the Uehara Memorial Foundation (Y.H.), the Takeda Science Foundation (Y.H.), and Kato Memorial Bioscience Foundation (Y.H.).
Collapse
Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
| | - Hiroaki Kobayashi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Akitoshi Saito
- Department of Radiology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Makoto Kawaguchi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Sou Shimamura
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Kouki Hata
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Syunya Hanawa
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Jun Toyama
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| |
Collapse
|
42
|
Shimazu H, Wada D, Maruyama S, Inoue A, Kashihara M, Yoshihara T, Saito F, Yoshiya K, Nakamori Y, Kuwagata Y. Clinical experience of treatment of immunocompromised individuals with persistent SARS-CoV-2 infection based on drug resistance mutations determined by genomic analysis: a descriptive study. BMC Infect Dis 2023; 23:780. [PMID: 37946111 PMCID: PMC10636837 DOI: 10.1186/s12879-023-08797-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The efficacy of antiviral drugs that neutralize antibody drugs and fight against SARS-COV-2 is reported to be attenuated by genetic mutations of the virus in vitro. When B-cell immunocompromised patients are infected with SARS-COV-2, the infection can be prolonged, and genetic mutations can occur during the course of treatment. Therefore, for refractory patients with persistent COVID-19 infection, genomic analysis was performed to obtain data on drug resistance mutations as a reference to determine which antiviral drugs and antibody therapies might be effective in their treatment. METHODS This was a descriptive analysis with no controls. Patients were diagnosed as having COVID-19, examined, and treated in the Kansai Medical University General Medical Center between January 2022 and January 2023. The subjects of the study were B-cell immunocompromised patients in whom genome analysis of SARS-CoV-2 was performed. RESULTS During the study period, 984 patients with COVID-19 were treated at our hospital. Of those, 17 refractory cases underwent genomic analysis. All 17 patients had factors related to immunodeficiency, such as malignant lymphoma or post-organ transplantation. Eleven patients started initial treatment for COVID-19 at our hospital, developed persistent infection, and underwent genomic analysis. Six patients who were initially treated for COVID-19 at other hospitals became persistently infected and were transferred to our hospital. Before COVID-19 treatment, genomic analysis showed no intrahost mutations in the NSP5, the NSP12, and the RBD regions. After COVID-19 treatment, mutations in these regions were found in 12 of 17 cases (71%). Sixteen patients survived the quarantine, but one died of sepsis. CONCLUSIONS In genomic analysis, more mutations were found to be drug-resistant after COVID-19 treatment than before COVID-19 treatment. Although it was not possible to demonstrate the usefulness of genome analysis for clinical application, the change of the treatment drug with reference to drug resistance indicated by genomic analysis may lead to good outcome of immunocompromised COVID-19 patients.
Collapse
Affiliation(s)
- Haruka Shimazu
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Daiki Wada
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan.
| | - Shuhei Maruyama
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Akira Inoue
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Masami Kashihara
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Tomoyuki Yoshihara
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Fukuki Saito
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Kazuhisa Yoshiya
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yasushi Nakamori
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yasuyuki Kuwagata
- Department of Emergency and Critical Care Medicine, Kansai Medical University Hospital, 2-3-1 Shinmachi, Hirakata, Osaka, 573-1191, Japan
| |
Collapse
|
43
|
Galipeau Y, Xavier A, Dyks A, Cooper C, Langlois MA. Continuous false positive results by SARS-CoV-2 rapid antigen testing: a case report. Front Public Health 2023; 11:1240308. [PMID: 38026284 PMCID: PMC10657208 DOI: 10.3389/fpubh.2023.1240308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/29/2023] [Indexed: 12/01/2023] Open
Abstract
Efficient and rapid identification of active SARS-CoV-2 infections has been key to monitoring and mitigating the spread of the virus. The implementation of nucleic acid testing (e.g., RT-PCR) was broadly adopted by most public health organizations at the national and community levels across the globe, which was followed by more accessible means of home testing including lateral flow immunochromatographic assay (LFA), also known as a rapid antigen test. Here we report the case of an adult female who repeatedly and consecutively tested positive by RAT (BTNX inc). This sustained false positive was not linked with an active SARS-CoV-2 infection, which was ruled out by RT-PCR and serological analyses. SARS-CoV-2 serology revealed no detectable levels of antibodies against the nucleocapsid suggesting no recent prior infection by SARS-CoV-2. This continuous false positive was limited to BTNX testing devices. This case report aims to describe that such continuous false positives can occur and describes alternative testing approaches that can be performed to confirm RAT results. In addition, broader awareness of such occurrences is warranted in the healthcare and public health community to avoid unnecessary negative impacts on individual's day to day life.
Collapse
Affiliation(s)
- Yannick Galipeau
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Abishek Xavier
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Aaron Dyks
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Curtis Cooper
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- University of Ottawa Centre for Infection, Immunity and Inflammation (CI3), Ottawa, ON, Canada
| |
Collapse
|
44
|
Kim D, Kim J, Kim M, Park H, Park S, Maharjan S, Baek K, Kang BM, Kim S, Park MS, Lee Y, Kwon HJ. Analysis of spike protein variants evolved in a novel in vivo long-term replication model for SARS-CoV-2. Front Cell Infect Microbiol 2023; 13:1280686. [PMID: 38029235 PMCID: PMC10655031 DOI: 10.3389/fcimb.2023.1280686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The spectrum of SARS-CoV-2 mutations have increased over time, resulting in the emergence of several variants of concern. Persistent infection is assumed to be involved in the evolution of the variants. Calu-3 human lung cancer cells persistently grow without apoptosis and release low virus titers after infection. Methods We established a novel in vivo long-term replication model using xenografts of Calu-3 human lung cancer cells in immunodeficient mice. Virus replication in the tumor was monitored for 30 days and occurrence of mutations in the viral genome was determined by whole-genome deep sequencing. Viral isolates with mutations were selected after plaque forming assays and their properties were determined in cells and in K18-hACE2 mice. Results After infection with parental SARS-CoV-2, viruses were found in the tumor tissues for up to 30 days and acquired various mutations, predominantly in the spike (S) protein, some of which increased while others fluctuated for 30 days. Three viral isolates with different combination of mutations produced higher virus titers than the parental virus in Calu-3 cells without cytopathic effects. In K18-hACE2 mice, the variants were less lethal than the parental virus. Infection with each variant induced production of cross-reactive antibodies to the receptor binding domain of parental SARS-CoV-2 S protein and provided protective immunity against subsequent challenge with parental virus. Discussion These results suggest that most of the SARS-CoV-2 variants acquired mutations promoting host adaptation in the Calu-3 xenograft mice. This model can be used in the future to further study SARS-CoV-2 variants upon long-term replication in vivo.
Collapse
Affiliation(s)
- Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| |
Collapse
|
45
|
Swan CL, Dushimiyimana V, Ndishimye P, Buchanan R, Yourkowski A, Semafara S, Nsanzimana S, Francis ME, Thivierge B, Lew J, Facciuolo A, Gerdts V, Falzarano D, Sjaarda C, Kelvin DJ, Bitunguhari L, Kelvin AA. Third COVID-19 vaccine dose boosts antibody function in Rwandans with high HIV viral load. iScience 2023; 26:107959. [PMID: 37810226 PMCID: PMC10558770 DOI: 10.1016/j.isci.2023.107959] [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: 06/28/2023] [Revised: 08/18/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) causing COVID-19 (coronavirus disease 2019) poses a greater health risk to immunocompromized individuals including people living with HIV (PLWH). However, most studies on PLWH have been conducted in higher-income countries. We investigated the post-vaccination antibody responses of PLWH in Rwanda by collecting peripheral blood from participants after receiving a second or third COVID-19 vaccine. Virus-binding antibodies as well as antibody neutralization ability against all major SARS-CoV-2 variants of concern were analyzed. We found that people with high HIV viral loads and two COVID-19 vaccine doses had lower levels of binding antibodies that were less virus neutralizing and less cross-reactive compared to control groups. A third vaccination increased neutralizing antibody titers. Our data suggest that people with high HIV viral loads require a third dose of vaccine to neutralize SARS-CoV-2 virus and new variants as they emerge.
Collapse
Affiliation(s)
- Cynthia L. Swan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | | | - Pacifique Ndishimye
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- African Institute for Mathematical Sciences, Kigali, Rwanda
| | - Rachelle Buchanan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Anthony Yourkowski
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Sage Semafara
- Rwanda Network of the People living with HIV (RRP+), Kigali, Rwanda
| | | | - Magen E. Francis
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Brittany Thivierge
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Calvin Sjaarda
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
- Queen’s Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Centre, Kingston, ON K7M 8A6, Canada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | - Alyson A. Kelvin
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| |
Collapse
|
46
|
Port JR, Yinda CK, Riopelle JC, Weishampel ZA, Saturday TA, Avanzato VA, Schulz JE, Holbrook MG, Barbian K, Perry-Gottschalk R, Haddock E, Martens C, Shaia CI, Lambe T, Gilbert SC, van Doremalen N, Munster VJ. Infection- or AZD1222 vaccine-mediated immunity reduces SARS-CoV-2 transmission but increases Omicron competitiveness in hamsters. Nat Commun 2023; 14:6592. [PMID: 37852960 PMCID: PMC10584863 DOI: 10.1038/s41467-023-42346-8] [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: 01/19/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Limited data is available on the effect of vaccination and previous virus exposure on the nature of SARS-CoV-2 transmission and immune-pressure on variants. To understand the impact of pre-existing immunity on SARS-CoV-2 airborne transmission efficiency, we perform a transmission chain experiment using naïve, intranasally or intramuscularly AZD1222 vaccinated, and previously infected hamsters. A clear gradient in transmission efficacy is observed: Transmission in hamsters vaccinated via the intramuscular route was reduced over three airborne chains (approx. 60%) compared to naïve animals, whereas transmission in previously infected hamsters and those vaccinated via the intranasal route was reduced by 80%. We also find that the Delta B.1.617.2 variant outcompeted Omicron B.1.1.529 after dual infection within and between hosts in naïve, vaccinated, and previously infected transmission chains, yet an increase in Omicron B.1.1.529 competitiveness is observed in groups with pre-existing immunity against Delta B.1.617.2. This correlates with an increase in the strength of the humoral response against Delta B.1.617.2, with the strongest response seen in previously infected animals. These data highlight the continuous need to improve vaccination strategies and address the additional evolutionary pressure pre-existing immunity may exert on SARS-CoV-2.
Collapse
Affiliation(s)
- Julia R Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jade C Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Zachary A Weishampel
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Taylor A Saturday
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Victoria A Avanzato
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Myndi G Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kent Barbian
- Genomics Research Section, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Rose Perry-Gottschalk
- Rocky Mountain Visual and Medical Arts Unit, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Elaine Haddock
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Genomics Research Section, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Carl I Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sarah C Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Neeltje van Doremalen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
| |
Collapse
|
47
|
Port JR, Morris DH, Riopelle JC, Yinda CK, Avanzato VA, Holbrook MG, Bushmaker T, Schulz JE, Saturday TA, Barbian K, Russell CA, Perry-Gottschalk R, Shaia CI, Martens C, Lloyd-Smith JO, Fischer RJ, Munster VJ. Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.08.15.504010. [PMID: 36032963 PMCID: PMC9413705 DOI: 10.1101/2022.08.15.504010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
It remains poorly understood how SARS-CoV-2 infection influences the physiological host factors important for aerosol transmission. We assessed breathing pattern, exhaled droplets, and infectious virus after infection with Alpha and Delta variants of concern (VOC) in the Syrian hamster. Both VOCs displayed a confined window of detectable airborne virus (24-48 h), shorter than compared to oropharyngeal swabs. The loss of airborne shedding was linked to airway constriction resulting in a decrease of fine aerosols (1-10μm) produced, which are suspected to be the major driver of airborne transmission. Male sex was associated with increased viral replication and virus shedding in the air. Next, we compared the transmission efficiency of both variants and found no significant differences. Transmission efficiency varied mostly among donors, 0-100% (including a superspreading event), and aerosol transmission over multiple chain links was representative of natural heterogeneity of exposure dose and downstream viral kinetics. Co-infection with VOCs only occurred when both viruses were shed by the same donor during an increased exposure timeframe (24-48 h). This highlights that assessment of host and virus factors resulting in a differential exhaled particle profile is critical for understanding airborne transmission.
Collapse
Affiliation(s)
- Julia R. Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Dylan H. Morris
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Jade C. Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Victoria A. Avanzato
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Myndi G. Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Trenton Bushmaker
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jonathan E. Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Taylor A. Saturday
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kent Barbian
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Colin A. Russell
- Department of Medical Microbiology | Amsterdam University Medical Center, University of Amsterdam
| | - Rose Perry-Gottschalk
- Rocky Mountain Visual and Medical Arts Unit, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Carl I. Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Robert J. Fischer
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Vincent J. Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| |
Collapse
|
48
|
Piñana JL, Heras I, Aiello TF, García-Cadenas I, Vazquez L, Lopez-Jimenez J, Chorão P, Aroca C, García-Vidal C, Arroyo I, Soler-Espejo E, López-Corral L, Avendaño-Pita A, Arrufat A, Garcia-Gutierrez V, Arellano E, Hernández-Medina L, González-Santillana C, Morell J, Hernández-Rivas JÁ, Rodriguez-Galvez P, Mico-Cerdá M, Guerreiro M, Campos D, Navarro D, Cedillo Á, Martino R, Solano C. Remdesivir or Nirmatrelvir/Ritonavir Therapy for Omicron SARS-CoV-2 Infection in Hematological Patients and Cell Therapy Recipients. Viruses 2023; 15:2066. [PMID: 37896843 PMCID: PMC10612015 DOI: 10.3390/v15102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Scarce data exist that analyze the outcomes of hematological patients with SARS-CoV-2 infection during the Omicron variant period who received treatment with remdesivir or nirmatrelvir/ritonavir. METHODS This study aims to address this issue by using a retrospective observational registry, created by the Spanish Hematopoietic Stem Cell Transplantation and Cell Therapy Group, spanning from 27 December 2021 to 30 April 2023. RESULTS This study included 466 patients, 243 (52%) who were treated with remdesivir and 223 (48%) with nirmatrelvir/ritonavir. Nirmatrelvir/ritonavir was primarily used for mild cases, resulting in a lower COVID-19-related mortality rate (1.3%), while remdesivir was preferred for moderate to severe cases (40%), exhibiting a higher mortality rate (9%). A multivariate analysis in the remdesivir cohort showed that male gender (odds ratio (OR) 0.35, p = 0.042) correlated with a lower mortality risk, while corticosteroid use (OR 9.4, p < 0.001) and co-infection (OR 2.8, p = 0.047) were linked to a higher mortality risk. Prolonged virus shedding was common, with 52% of patients shedding the virus for more than 25 days. In patients treated with remdesivir, factors associated with prolonged shedding included B-cell malignancy as well as underlying disease, severe disease, a later onset of and shorter duration of remdesivir treatment and a higher baseline viral load. Nirmatrelvir/ritonavir demonstrated a comparable safety profile to remdesivir, despite a higher risk of drug interactions. CONCLUSIONS Nirmatrelvir/ritonavir proved to be a safe and effective option for treating mild cases in the outpatient setting, while remdesivir was preferred for severe cases, where corticosteroids and co-infection significantly predicted worse outcomes. Despite antiviral therapy, prolonged shedding remains a matter of concern.
Collapse
Affiliation(s)
- José Luis Piñana
- Hematology Department, Hospital Clínico Universitario, 46017 Valencia, Spain; (I.A.); (J.M.); (P.R.-G.); (M.M.-C.); (D.C.); (C.S.)
- INCLIVA, Biomedical Research Institute, 46017 Valencia, Spain
| | - Inmaculada Heras
- Hematology Division, Hospital Morales Meseguer, 30100 Murcia, Spain; (I.H.); (C.A.); (E.S.-E.)
| | | | - Irene García-Cadenas
- Hematology Division, Hospital de la Santa Creu i Sant Pau, 08193 Barcelona, Spain; (I.G.-C.); (A.A.); (R.M.)
| | - Lourdes Vazquez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (L.V.); (L.L.-C.); (A.A.-P.); (L.H.-M.)
| | - Javier Lopez-Jimenez
- Hematology Division, Hospital Ramon y Cajal, 28029 Madrid, Spain; (J.L.-J.); (V.G.-G.)
| | - Pedro Chorão
- Hematology Division, Hospital Universitario y Politécnico La Fe, 46017 Valencia, Spain; (P.C.); (M.G.)
| | - Cristina Aroca
- Hematology Division, Hospital Morales Meseguer, 30100 Murcia, Spain; (I.H.); (C.A.); (E.S.-E.)
| | - Carolina García-Vidal
- Infectious Disease Division, Hospital Clinic, 08193 Barcelona, Spain; (T.F.A.); (C.G.-V.)
| | - Ignacio Arroyo
- Hematology Department, Hospital Clínico Universitario, 46017 Valencia, Spain; (I.A.); (J.M.); (P.R.-G.); (M.M.-C.); (D.C.); (C.S.)
- INCLIVA, Biomedical Research Institute, 46017 Valencia, Spain
| | - Eva Soler-Espejo
- Hematology Division, Hospital Morales Meseguer, 30100 Murcia, Spain; (I.H.); (C.A.); (E.S.-E.)
| | - Lucia López-Corral
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (L.V.); (L.L.-C.); (A.A.-P.); (L.H.-M.)
| | - Alejandro Avendaño-Pita
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (L.V.); (L.L.-C.); (A.A.-P.); (L.H.-M.)
| | - Anna Arrufat
- Hematology Division, Hospital de la Santa Creu i Sant Pau, 08193 Barcelona, Spain; (I.G.-C.); (A.A.); (R.M.)
| | | | - Elena Arellano
- Hematology Division, Hospital Universitario Virgen Macarena, 41092 Sevilla, Spain;
| | - Lorena Hernández-Medina
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (L.V.); (L.L.-C.); (A.A.-P.); (L.H.-M.)
| | | | - Julia Morell
- Hematology Department, Hospital Clínico Universitario, 46017 Valencia, Spain; (I.A.); (J.M.); (P.R.-G.); (M.M.-C.); (D.C.); (C.S.)
- INCLIVA, Biomedical Research Institute, 46017 Valencia, Spain
| | | | - Paula Rodriguez-Galvez
- Hematology Department, Hospital Clínico Universitario, 46017 Valencia, Spain; (I.A.); (J.M.); (P.R.-G.); (M.M.-C.); (D.C.); (C.S.)
- INCLIVA, Biomedical Research Institute, 46017 Valencia, Spain
| | - Mireia Mico-Cerdá
- Hematology Department, Hospital Clínico Universitario, 46017 Valencia, Spain; (I.A.); (J.M.); (P.R.-G.); (M.M.-C.); (D.C.); (C.S.)
- INCLIVA, Biomedical Research Institute, 46017 Valencia, Spain
| | - Manuel Guerreiro
- Hematology Division, Hospital Universitario y Politécnico La Fe, 46017 Valencia, Spain; (P.C.); (M.G.)
| | - Diana Campos
- Hematology Department, Hospital Clínico Universitario, 46017 Valencia, Spain; (I.A.); (J.M.); (P.R.-G.); (M.M.-C.); (D.C.); (C.S.)
- INCLIVA, Biomedical Research Institute, 46017 Valencia, Spain
- Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Brain, Behavior and Metabolism (CBBM), University of Lübeck, 23562 Lübeck, Germany
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
- Department of Medicine, School of Medicine. University of Valencia, 46010 Valencia, Spain
| | - Ángel Cedillo
- Hematopoietic Stem Cell Transplantation and Cell Therapy Group (GETH-TC) Office, 28029 Madrid, Spain;
| | - Rodrigo Martino
- Hematology Division, Hospital de la Santa Creu i Sant Pau, 08193 Barcelona, Spain; (I.G.-C.); (A.A.); (R.M.)
| | - Carlos Solano
- Hematology Department, Hospital Clínico Universitario, 46017 Valencia, Spain; (I.A.); (J.M.); (P.R.-G.); (M.M.-C.); (D.C.); (C.S.)
- INCLIVA, Biomedical Research Institute, 46017 Valencia, Spain
- Department of Medicine, School of Medicine. University of Valencia, 46010 Valencia, Spain
| |
Collapse
|
49
|
Furie N, Mandelboim M, Zuckerman N, Belkin A, Seluk L, Shafran I, Mass R, Levy L, Chatterji S, Baltaxe E, Peled M, Shulimzon T, Avigdor A, Amit S, Onn A, Marom EM, Rahav G, Segel MJ. Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Pneumonia in Patients Treated With Anti-CD20 Monoclonal Antibodies. Open Forum Infect Dis 2023; 10:ofad464. [PMID: 37808896 PMCID: PMC10551847 DOI: 10.1093/ofid/ofad464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
We report 8 cases of persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia in patients previously treated with anti-CD20 monoclonal antibodies. Polymerase chain reaction of nasopharyngeal swabs for SARS-CoV-2 was negative in most cases; viral cell cultures confirmed that viable SARS-Co-2 virus was present. Four patients were treated with anti-SARS-CoV-2 hyperimmune globulins with rapid resolution of disease.
Collapse
Affiliation(s)
- Nadav Furie
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Michal Mandelboim
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Neta Zuckerman
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Ana Belkin
- Internal Medicine D, Sheba Medical Center, Tel Hashomer, Israel
- Infectious Diseases Unit, Sheba Medical Center, Tel Hashomer, Israel
| | - Lior Seluk
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Inbal Shafran
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Ronen Mass
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
| | - Liran Levy
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Sumit Chatterji
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
| | - Erik Baltaxe
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Michael Peled
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Tiberiu Shulimzon
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
| | - Abraham Avigdor
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
- Division of Hematology and Bone-Marrow Transplantation, Sheba Medical Center, Ramat Gan, Israel
| | - Sharon Amit
- Microbiology Laboratory, Sheba Medical Center, Tel Hashomer, Israel
| | - Amir Onn
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Edith M Marom
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
- Department of Diagnostic Radiology, Sheba Medical Center, Tel Hashomer, Israel
| | - Galia Rahav
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
- Infectious Diseases Unit, Sheba Medical Center, Tel Hashomer, Israel
| | - Michael J Segel
- Institute of Pulmonology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| |
Collapse
|
50
|
El-Haddad K, Adhikari TM, Tu ZJ, Cheng YW, Leng X, Zhang X, Rhoads D, Ko JS, Worley S, Li J, Rubin BP, Esper FP. Intra-host mutation rate of acute SARS-CoV-2 infection during the initial pandemic wave. Virus Genes 2023; 59:653-661. [PMID: 37310519 DOI: 10.1007/s11262-023-02011-0] [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: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 mutation is minimized through a proofreading function encoded by NSP-14. Most estimates of the SARS-CoV-2 mutation rate are derived from population based sequence data. Our understanding of SARS-CoV-2 evolution might be enhanced through analysis of intra-host viral mutation rates in specific populations. Viral genome analysis was performed between paired samples and mutations quantified at allele frequencies (AF) ≥ 0.25, ≥ 0.5 and ≥ 0.75. Mutation rate was determined employing F81 and JC69 evolution models and compared between isolates with (ΔNSP-14) and without (wtNSP-14) non-synonymous mutations in NSP-14 and by patient comorbidity. Forty paired samples with median interval of 13 days [IQR 8.5-20] were analyzed. The estimated mutation rate by F81 modeling was 93.6 (95%CI 90.8-96.4], 40.7 (95%CI 38.9-42.6) and 34.7 (95%CI 33.0-36.4) substitutions/genome/year at AF ≥ 0.25, ≥ 0.5, ≥ 0.75 respectively. Mutation rate in ΔNSP-14 were significantly elevated at AF ≥ 0.25 vs wtNSP-14. Patients with immune comorbidities had higher mutation rate at all allele frequencies. Intra-host SARS-CoV-2 mutation rates are substantially higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated mutation rate at low AF. Immunosuppressed patients have elevated mutation rate at all AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling.
Collapse
Affiliation(s)
- Kim El-Haddad
- Center for Pediatric Infectious Disease, Cleveland Clinic Children's, R3, 9500 Euclid Avenue, Cleveland, 44195 , OH, USA.
| | - Thamali M Adhikari
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Zheng Jin Tu
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaoyi Leng
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Xiangyi Zhang
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Daniel Rhoads
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer S Ko
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sarah Worley
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jing Li
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Frank P Esper
- Center for Pediatric Infectious Disease, Cleveland Clinic Children's, R3, 9500 Euclid Avenue, Cleveland, 44195 , OH, USA.
| |
Collapse
|