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Kuroda Y, Ozaki M, Sakai Y, Uchida-Fujii E, Hanada I, Yamamoto T, Tatemoto K, Hirata Y, Sato Y, Katano H, Nagata N, Kato H, Shimada T, Suzuki T, Nakao T, Maeda K. An outbreak of SARS-CoV-2 omicron variant and deaths of three lions in a zoo. One Health 2024; 19:100870. [PMID: 39206254 PMCID: PMC11350503 DOI: 10.1016/j.onehlt.2024.100870] [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: 06/27/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
There have been reports of the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to various mammalian species. Some infected animals show clinical signs and may even die in rare cases. Outbreaks of SARS-CoV-2 have been reported in zoos where susceptible animals are bred in high population densities. However, there have been few reports of omicron variant outbreaks in zoo animals. From late 2022 to 2023, an outbreak of the SARS-CoV-2 omicron variant occurred in one Japanese zoo. A total of 24 lions were housed in the zoo; 13 of them showed respiratory symptoms, and the three oldest lions died. Molecular and histopathological analyses revealed that the deceased lions were infected with SARS-CoV-2 omicron BF.7.15. Virus-neutralization tests showed that all 21 lions were positive for antibodies against the omicron variant, but not against the delta variant. In addition, three tigers and one bear in the same or neighboring building as the lions possessed antibodies against the omicron variant. This is a very rare report on the outbreak of a SARS-CoV-2 omicron variant infection that resulted in the death of animals. This finding demonstrates the importance of continuous countermeasures to protect non-vaccinated animals from SARS-CoV-2 infection.
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Affiliation(s)
- Yudai Kuroda
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Miki Ozaki
- Adventure World, 2399 Katada, Shirahama-cho, Nishimuro-gun, Wakayama 649-2201, Japan
| | - Yusuke Sakai
- Department of Pathology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Eri Uchida-Fujii
- Center for Field Epidemic Intelligence Research and Professional Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ikumi Hanada
- Adventure World, 2399 Katada, Shirahama-cho, Nishimuro-gun, Wakayama 649-2201, Japan
| | - Tsukasa Yamamoto
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Kango Tatemoto
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hirofumi Kato
- Center for Field Epidemic Intelligence Research and Professional Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomoe Shimada
- Center for Field Epidemic Intelligence Research and Professional Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tatsuko Nakao
- Adventure World, 2399 Katada, Shirahama-cho, Nishimuro-gun, Wakayama 649-2201, Japan
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
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Miyashita N, Nakamori Y, Ogata M, Fukuda N, Yamura A, Ito T. Efficacy of ensitrelvir for cough due to COVID-19 Omicron variant in medical healthcare workers. Antimicrob Agents Chemother 2024; 68:e0106424. [PMID: 39207153 PMCID: PMC11459974 DOI: 10.1128/aac.01064-24] [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: 09/04/2024] Open
Abstract
We evaluated the efficacy of ensitrelvir for the treatment of cough due to coronavirus disease 2019 Omicron variant in medical healthcare workers. A total of 633 patients were registered in this study: 206 patients chose ensitrelvir and 427 patients chose symptomatic treatment. Difference in score changes using the Leicester Cough Questionnaire between groups was 3.17 on day 4, 3.24 on day 7, and 2.46 on day 14. The analysis demonstrated a significant difference at all time points.
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Affiliation(s)
- Naoyuki Miyashita
- First Department of Internal Medicine, Division of Respiratory Medicine, Infectious Disease and Allergology, Kansai Medical University, Hirakata, Japan
| | - Yasushi Nakamori
- Department of Emergency Medicine, Kansai Medical University Medical Center, Moriguchi, Japan
| | - Makoto Ogata
- First Department of Internal Medicine, Division of Respiratory Medicine, Infectious Disease and Allergology, Kansai Medical University, Hirakata, Japan
| | - Naoki Fukuda
- First Department of Internal Medicine, Division of Respiratory Medicine, Infectious Disease and Allergology, Kansai Medical University, Hirakata, Japan
| | - Akihisa Yamura
- First Department of Internal Medicine, Division of Respiratory Medicine, Infectious Disease and Allergology, Kansai Medical University, Hirakata, Japan
| | - Tomoki Ito
- First Department of Internal Medicine, Division of Respiratory Medicine, Infectious Disease and Allergology, Kansai Medical University, Hirakata, Japan
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3
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Bang LL, Madsen LW, Pedersen RM, Nilsson AC, Johansen IS, Andersen TE. Sotrovimab lost neutralization efficacy against SARS-CoV-2 subvariants but remained clinically effective: Were monoclonal antibodies against COVID-19 rejected too early? J Infect Public Health 2024; 17:102512. [PMID: 39137507 DOI: 10.1016/j.jiph.2024.102512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/15/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Affiliation(s)
- Line Lundegaard Bang
- Department of Clinical Microbiology, Odense University Hospital, and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark.
| | - Lone Wulff Madsen
- Department of Infectious Diseases, Odense University Hospital and Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark; Unit for Infectious Diseases, Department of Medicine, Sygehus Lillebælt, Kolding, Denmark; Department of Regional Health Research, University of Southern Denmark, Denmark.
| | - Rune Micha Pedersen
- Department of Clinical Microbiology, Odense University Hospital, and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark.
| | - Anna Christine Nilsson
- Department of Clinical Immunology, Odense University Hospital, and Research Unit for Clinical Immunology, University of Southern Denmark, Odense, Denmark.
| | - Isik Somuncu Johansen
- Department of Infectious Diseases, Odense University Hospital and Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark.
| | - Thomas Emil Andersen
- Department of Clinical Microbiology, Odense University Hospital, and Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark.
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4
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Barroso-Arévalo S, Sánchez-Morales L, Porras N, Díaz-Frutos M, Barasona JA, Isla J, López D, Gortázar C, Domínguez L, Sánchez-Vizcaíno JM. Comparative SARS-CoV-2 Omicron BA.5 variant and D614G-Wuhan strain infections in ferrets: insights into attenuation and disease progression during subclinical to mild COVID-19. Front Vet Sci 2024; 11:1435464. [PMID: 39211479 PMCID: PMC11358085 DOI: 10.3389/fvets.2024.1435464] [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: 05/20/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction As the SARS-CoV-2 virus continues to evolve and new variants emerge, it becomes crucial to understand the comparative pathological and immunological responses elicited by different strains. This study focuses on the original Wuhan strain and the Omicron variant, which have demonstrated significant differences in clinical outcomes and immune responses. Methods We employed ferrets as an experimental model to assess the D614G variant (a derivative of the Wuhan strain) and the Omicron BA.5 variant. Each variant was inoculated into separate groups of ferrets to compare disease severity, viral dissemination, and immune responses. Results The D614G variant induced more severe disease and greater viral spread than the Omicron variant. Notably, ferrets infected with the D614G variant exhibited a robust neutralizing antibody response, whereas those infected with the Omicron variant failed to produce a detectable neutralizing antibody response. Despite the clearance of the virus from nearly all tissues by 7 days post-infection, an increase in pathological lesions was observed from 14 to 21 days, particularly in those infected with the D614G variant, suggesting a sustained immune response even after viral clearance. Discussion These findings underscore the adaptability of SARS-CoV-2 and illuminate how susceptibility and clinical manifestations vary across different strains and species. The results emphasize the necessity of considering both the direct effects of viral infection and the indirect, often prolonged, impacts of the immune response in evaluating the outcomes of SARS-CoV-2 infections.
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Affiliation(s)
- Sandra Barroso-Arévalo
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Lidia Sánchez-Morales
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Néstor Porras
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Marta Díaz-Frutos
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Jose A. Barasona
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Débora López
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Lucas Domínguez
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Jose M. Sánchez-Vizcaíno
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
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He Y, Hao M, Yang M, Guo H, Rayman MP, Zhang X, Zhang J. Influence of EGCG oxidation on inhibitory activity against the SARS-CoV-2 main protease. Int J Biol Macromol 2024; 274:133451. [PMID: 38944088 DOI: 10.1016/j.ijbiomac.2024.133451] [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: 11/28/2023] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
SARS-CoV-2 main protease (Mpro) is a well-recognized target for COVID-19 therapy. Green tea (-)-epigallocatechin-3-gallate (EGCG) possesses Mpro-inhibitory activity; however, the influence of EGCG oxidation on its inhibition activity remains obscure, given its high oxidation propensity. This study reveals that prolonged EGCG oxidation in the presence of Mpro dramatically increases its inhibitory activity with an IC50 of 0.26 μM. The inhibitory mechanism is that EGCG-quinone preferentially binds the active site Mpro-Cys145-SH, which forms a quinoprotein. Though Mpro is present in the cell lysate, EGCG preferentially depletes its thiols. Non-cytotoxic EGCG effectively generates a quinoprotein in living cells, thus EGCG might selectively inhibit Mpro in SARS-CoV-2 infected cells. Chlorogenic acid facilitates EGCG oxidation. Together, they synergistically deplete multiple Mpro thiols though this is not more beneficial than EGCG alone. By contrast, excessive EGCG oxidation prior to incubation with Mpro largely compromises its inhibitory activity. Overall, the low IC50 and the high selectivity imply that EGCG is a promising dietary Mpro inhibitor. While EGCG oxidation in the presence of Mpro has a pivotal role in inhibition, enhancing EGCG oxidation by chlorogenic acid no longer increases its inhibitory potential. EGCG oxidation in the absence of Mpro should be avoided to maximize its Mpro-inhibitory activity.
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Affiliation(s)
- Yufeng He
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Joint Research Center for Food Nutrition and Health of IHM, Anhui Agricultural University, Hefei 230036, China
| | - Meng Hao
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Joint Research Center for Food Nutrition and Health of IHM, Anhui Agricultural University, Hefei 230036, China
| | - Mingchuan Yang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Joint Research Center for Food Nutrition and Health of IHM, Anhui Agricultural University, Hefei 230036, China
| | - Huimin Guo
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Joint Research Center for Food Nutrition and Health of IHM, Anhui Agricultural University, Hefei 230036, China; Center for Biological Technology, Anhui Agricultural University, Hefei 230036, China
| | - Margaret P Rayman
- Department of Nutritional Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Xiangchun Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China.
| | - Jinsong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Joint Research Center for Food Nutrition and Health of IHM, Anhui Agricultural University, Hefei 230036, China.
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6
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Liu X, Zhou M, Fang M, Xie Y, Chen P, Chen R, Wu K, Ye J, Liu C, Zhu H, Cheng T, Yuan L, Zhao H, Guan Y, Xia N. Decisive reversal of lethal coronavirus disease 2019 in senescent hamster by synchronic antiviral and immunoregulatory intervention. MedComm (Beijing) 2024; 5:e642. [PMID: 39036342 PMCID: PMC11258460 DOI: 10.1002/mco2.642] [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: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/23/2024] Open
Abstract
The poor prognosis observed in elderly individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a serious clinical burden and the underlying mechanism is unclear, which necessities detailed investigation of disease characteristics and research for efficient countermeasures. To simulate lethal coronavirus disease 2019 (COVID-19) in senescent human patients, 80-week-old male hamsters are intranasally inoculated with different doses of SARS-CoV-2 Omicron BA.5 variant. Exposure to a low dose of the Omicron BA.5 variant results in early activation of the innate immune response, followed by rapid viral clearance and minimal lung damage. However, a high dose of BA.5 results in impaired interferon signaling, cytokine storm, uncontrolled viral replication, and severe lung injury. To decrease viral load and reverse the deterioration of COVID-19, a new bio-mimic decoy called CoVR-MV is used as a preventive or therapeutic agent. Administration of CoVR-MV as a preventive or therapeutic intervention in the early stages of infection can effectively suppress viral load, regulate the immune response, and rescue animals from death and critical illness. These findings underscore the risk associated with SARS-CoV-2 Omicron BA.5 exposure in senescent hamsters and highlight the importance of early intervention to prevent disease progression.
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Affiliation(s)
- Xuan Liu
- Clinical Center for Bio‐TherapyZhongshan HospitalFudan University (Xiamen Branch)XiamenFujianChina
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
| | - Ming Zhou
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
| | - Mujing Fang
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
| | - Ying Xie
- National Institute for Food and Drug ControlBeijingChina
- Institute of Medical BiologyChinese Academy of Medical Science and Peking Union Medical CollegeKunmingChina
| | - Peiwen Chen
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
- Guangdong‐Hong Kong Joint Laboratory of Emerging Infectious Diseases/Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU)Shantou UniversityShantouGuangdongChina
| | - Rirong Chen
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
- Guangdong‐Hong Kong Joint Laboratory of Emerging Infectious Diseases/Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU)Shantou UniversityShantouGuangdongChina
| | - Kun Wu
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
| | - Jianghui Ye
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
| | - Che Liu
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
- Guangdong‐Hong Kong Joint Laboratory of Emerging Infectious Diseases/Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU)Shantou UniversityShantouGuangdongChina
| | - Tong Cheng
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
| | - Lunzhi Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
| | - Hui Zhao
- National Institute for Food and Drug ControlBeijingChina
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
- Guangdong‐Hong Kong Joint Laboratory of Emerging Infectious Diseases/Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU)Shantou UniversityShantouGuangdongChina
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Life Sciences & School of Public HealthXiamen UniversityXiamenFujianChina
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7
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Patel V, Yarwood MJ, Levick B, Gibbons DC, Drysdale M, Kerr W, Watkins JD, Young S, Pierce BF, Lloyd EJ, Birch HJ, Kamalati T, Brett SJ. Characteristics and outcomes of patients with COVID-19 at high risk of disease progression receiving sotrovimab, oral antivirals or no treatment in England: a retrospective cohort study. Curr Med Res Opin 2024; 40:1323-1334. [PMID: 38975862 DOI: 10.1080/03007995.2024.2376144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/08/2024] [Accepted: 03/29/2024] [Indexed: 07/09/2024]
Abstract
OBJECTIVE To describe characteristics and acute clinical outcomes for patients with COVID-19 treated with sotrovimab, nirmatrelvir/ritonavir or molnupiravir, or untreated patients at highest risk per National Health Service (NHS) criteria. METHODS Retrospective study of non-hospitalized patients between 1 December 2021 and 31 May 2022, using data from the Discover-NOW dataset (North-West London). Included patients were aged ≥12 years and treated with sotrovimab, nirmatrelvir/ritonavir or molnupiravir, or untreated but expected to be eligible for early treatment per NHS highest-risk criteria. COVID-19-related and all-cause hospitalizations were reported for 28 days from COVID-19 diagnosis (index). Subgroup analyses were conducted in patients with advanced renal disease, those aged 18-64 and ≥65 years, and by period of Omicron BA.1, BA.2 and BA.5 (post-hoc exploratory) predominance. RESULTS Overall, 1503 treated and 4044 eligible high-risk untreated patients were included. A high proportion of patients on sotrovimab had advanced renal disease (29.3%), ≥3 high-risk comorbidities (47.6%) and were aged ≥65 years (36.9%). Five of 696 (0.7%) patients on sotrovimab, <5/337 (0.3-1.2%) on nirmatrelvir/ritonavir, 10/470 (2.1%) on molnupiravir and 114/4044 (2.8%) untreated patients were hospitalized with COVID-19. Similar results were observed across all subgroups. The proportion of patients dying within 28 days of the index period was similarly low across all cohorts (<2%). CONCLUSION Patients receiving sotrovimab appeared to show evidence of multiple high-risk comorbidities. Low hospitalization rates were observed for all treated cohorts across subgroups and periods of predominant variants of concern. These results require confirmation with comparative effectiveness analyses adjusting for differences in underlying patient characteristics.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Stephen J Brett
- Department of Surgery and Cancer, Imperial College, London, UK
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8
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Zhang J. Immune responses in COVID-19 patients: Insights into cytokine storms and adaptive immunity kinetics. Heliyon 2024; 10:e34577. [PMID: 39149061 PMCID: PMC11325674 DOI: 10.1016/j.heliyon.2024.e34577] [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: 01/29/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 08/17/2024] Open
Abstract
SARS-CoV-2 infection can trigger cytokine storm in some patients, which characterized by an excessive production of cytokines and chemical mediators. This hyperactive immune response may cause significant tissue damage and multiple organ failure (MOF). The severity of COVID-19 correlates with the intensity of cytokine storm, involving elements such as IFN, NF-κB, IL-6, HMGB1, etc. It is imperative to rapidly engage adaptive immunity to effectively control the disease progression. CD4+ T cells facilitate an immune response by improving B cells in the production of neutralizing antibodies and activating CD8+ T cells, which are instrumental in eradicating virus-infected cells. Meanwhile, antibodies from B cells can neutralize virus, obstructing further infection of host cells. In individuals who have recovered from the disease, virus-specific antibodies and memory T cells were observed, which could confer a level of protection, reducing the likelihood of re-infection or attenuating severity. This paper discussed the roles of macrophages, IFN, IL-6 and HMGB1 in cytokine release syndrome (CRS), the intricacies of adaptive immunity, and the persistence of immune memory, all of which are critical for the prevention and therapeutic strategies against COVID-19.
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Affiliation(s)
- Junguo Zhang
- Pulmonology Department, Fengdu General Hospital, Chongqing, 408200, China
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9
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Liu H, Brostoff T, Ramirez A, Wong T, Rowland DJ, Heffner M, Flores A, Willis B, Evans JJ, Lanoue L, Lloyd KCK, Coffey LL. Establishment and characterization of an h ACE2/hTMPRSS2 knock-in mouse model to study SARS-CoV-2. Front Immunol 2024; 15:1428711. [PMID: 39050847 PMCID: PMC11266032 DOI: 10.3389/fimmu.2024.1428711] [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: 05/06/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Despite a substantial body of research, we lack fundamental understanding of the pathophysiology of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including pulmonary and cardiovascular outcomes, in part due to limitations of murine models. Most models use transgenic mice (K18) that express the human (h) angiotensin converting enzyme 2 (ACE2), ACE2 knock-in (KI) mice, or mouse-adapted strains of SARS-CoV-2. Further, many SARS-CoV-2 variants produce fatal neurologic disease in K18 mice and most murine studies focus only on acute disease in the first 14 days post inoculation (dpi). To better enable understanding of both acute (<14 dpi) and post-acute (>14 dpi) infection phases, we describe the development and characterization of a novel non-lethal KI mouse that expresses both the ACE2 and transmembrane serine protease 2 (TMPRSS2) genes (hACE2/hTMPRSS2). The human genes were engineered to replace the orthologous mouse gene loci but remain under control of their respective murine promoters, resulting in expression of ACE2 and TMPRSS2 instead of their murine counterparts. After intranasal inoculation with an omicron strain of SARS-CoV-2, hACE2/hTMPRSS2 KI mice transiently lost weight but recovered by 7 dpi. Infectious SARS-CoV-2 was detected in nasopharyngeal swabs 1-2 dpi and in lung tissues 2-6 dpi, peaking 4 dpi. These outcomes were similar to those in K18 mice that were inoculated in parallel. To determine the extent to which hACE2/hTMPRSS2 KI mice are suitable to model pulmonary and cardiovascular outcomes, physiological assessments measuring locomotion, behavior and reflexes, biomonitoring to measure cardiac activity and respiration, and micro computed tomography to assess lung function were conducted frequently to 6 months post inoculation. Male but not female SARS-CoV-2 inoculated hACE2/hTMPRSS2 KI mice showed a transient reduction in locomotion compared to control saline treated mice. No significant changes in respiration, oxygen saturation, heart rate variability, or conductivity were detected in SARS-CoV-2 inoculated mice of either sex. When re-inoculated 6 months after the first inoculation, hACE2/hTMPRSS2 KI became re-infected with disease signs similar to after the first inoculation. Together these data show that a newly generated hACE2/hTMPRSS2 KI mouse can be used to study mild COVID-19.
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Affiliation(s)
- Hongwei Liu
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Terza Brostoff
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Ana Ramirez
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Talia Wong
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Douglas J. Rowland
- Center for Molecular and Genomic Imaging, College of Engineering, University of California, Davis, Davis, CA, United States
| | - Mollie Heffner
- Mouse Biology Program, University of California, Davis, Davis, CA, United States
| | - Arturo Flores
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Brandon Willis
- Mouse Biology Program, University of California, Davis, Davis, CA, United States
| | - Jeffrey J. Evans
- Mouse Biology Program, University of California, Davis, Davis, CA, United States
| | - Louise Lanoue
- Mouse Biology Program, University of California, Davis, Davis, CA, United States
| | - K. C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, Davis, CA, United States
- Department of Surgery, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Lark L. Coffey
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
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10
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Liang L, Wang B, Zhang Q, Zhang S, Zhang S. Antibody drugs targeting SARS-CoV-2: Time for a rethink? Biomed Pharmacother 2024; 176:116900. [PMID: 38861858 DOI: 10.1016/j.biopha.2024.116900] [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: 02/14/2024] [Revised: 04/20/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) heavily burdens human health. Multiple neutralizing antibodies (nAbs) have been issued for emergency use or tested for treating infected patients in the clinic. However, SARS-CoV-2 variants of concern (VOC) carrying mutations reduce the effectiveness of nAbs by preventing neutralization. Uncoding the mutation profile and immune evasion mechanism of SARS-CoV-2 can improve the outcome of Ab-mediated therapies. In this review, we first outline the development status of anti-SARS-CoV-2 Ab drugs and provide an overview of SARS-CoV-2 variants and their prevalence. We next focus on the failure causes of anti-SARS-CoV-2 Ab drugs and rethink the design strategy for developing new Ab drugs against COVID-19. This review provides updated information for the development of therapeutic Ab drugs against SARS-CoV-2 variants.
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Affiliation(s)
- Likeng Liang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Bo Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Qing Zhang
- Department of Laboratory Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China.
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11
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Singh J, Anantharaj A, Kumar P, Pandey R, Pandey AK, Medigeshi GR. The Effective Inhibitory Concentration of Interferon-β Correlates with Infectivity and Replication Fitness of SARS-CoV-2 Variants. J Interferon Cytokine Res 2024; 44:325-333. [PMID: 38557204 DOI: 10.1089/jir.2024.0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
India saw a spike in COVID-19 cases in early 2023, and this wave of infection was attributed to XBB sublineages of SARS-CoV-2 Omicron variant. The impact of XBB wave was significantly shorter with low burden of severe cases or hospitalization as compared with previous SARS-CoV-2 variants of concern. Although a combination of old and new mutations in the spike region of XBB.1.16 variant led to a drastic reduction in the ability of antibodies from prior immunity to neutralize this virus, additional nonspike mutations suggested a possible change in its ability to suppress innate immune responses. In this study, we tested the sensitivity of Delta, BA.2.75, and XBB.1.16 variants to interferon-β (IFN-β) treatment and found that XBB.1.16 variant was most sensitive to IFN-β. We next tested the ability of serum antibodies from healthy individuals to neutralize XBB.1.16. We showed that most of the individuals with hybrid immunity maintained a low but significant level of neutralizing antibodies to XBB.1.16 variant. Therefore, our observations indicated that both hybrid immunity because of natural infection and enhanced sensitivity to IFNs may have contributed to the low impact of XBB.1.16 infections in India.
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Affiliation(s)
- Janmejay Singh
- Bioassay Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Anbalagan Anantharaj
- Bioassay Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Parveen Kumar
- Bioassay Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anil Kumar Pandey
- Academic Block, Employees State Insurance Corporation Medical College and Hospital, Faridabad, Haryana, India
| | - Guruprasad R Medigeshi
- Bioassay Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India
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12
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Focosi D, Franchini M, Maggi F, Shoham S. COVID-19 therapeutics. Clin Microbiol Rev 2024; 37:e0011923. [PMID: 38771027 PMCID: PMC11237566 DOI: 10.1128/cmr.00119-23] [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: 05/22/2024] Open
Abstract
SUMMARYSince the emergence of COVID-19 in 2020, an unprecedented range of therapeutic options has been studied and deployed. Healthcare providers have multiple treatment approaches to choose from, but efficacy of those approaches often remains controversial or compromised by viral evolution. Uncertainties still persist regarding the best therapies for high-risk patients, and the drug pipeline is suffering fatigue and shortage of funding. In this article, we review the antiviral activity, mechanism of action, pharmacokinetics, and safety of COVID-19 antiviral therapies. Additionally, we summarize the evidence from randomized controlled trials on efficacy and safety of the various COVID-19 antivirals and discuss unmet needs which should be addressed.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Massimo Franchini
- Division of Hematology and Transfusion Medicine, Carlo Poma Hospital, Mantua, Italy
| | - Fabrizio Maggi
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Shmuel Shoham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Singh UB, Deb S, Rani L, Gupta R, Verma S, Kumari L, Bhardwaj D, Bala K, Ahmed J, Gaurav S, Perumalla S, Nizam M, Mishra A, Stephenraj J, Shukla J, Nayer J, Aggarwal P, Kabra M, Ahuja V, Chaudhry R, Sinha S, Guleria R. Phylogeny and evolution of SARS-CoV-2 during Delta and Omicron variant waves in India. J Biomol Struct Dyn 2024; 42:4769-4781. [PMID: 37318006 DOI: 10.1080/07391102.2023.2222832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/02/2023] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was reported in patients without comorbidity (97%), while Omicron BA.2 was reported in patients with comorbidity (77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2. Higher propensity of Omicron variants to bronchial tissue, probably ensured increased transmission while Omicron BA.2 became the prevalent variant possibly due to evolutionary trade-off. Virus evolution continues to shape the epidemic and its culmination.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sushanta Deb
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Rani
- Central Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Sunita Verma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Kumari
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepika Bhardwaj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Kiran Bala
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jawed Ahmed
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sudesh Gaurav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sowjanya Perumalla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Md Nizam
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Anwita Mishra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - J Stephenraj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Shukla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jamshed Nayer
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care & Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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14
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Drysdale M, Hautekiet T, Singh M, Hautekiet J, Ludikhuyze L, Patel V, Gibbons DC, De Roeck D, Colpaert K, Lloyd EJ, Van Braeckel E. Characteristics and outcomes of patients treated with sotrovimab to prevent progression to severe COVID-19 in Belgium. Acta Clin Belg 2024; 79:174-183. [PMID: 39081095 DOI: 10.1080/17843286.2024.2381272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/13/2024] [Indexed: 08/30/2024]
Abstract
OBJECTIVE Sotrovimab, a dual-action, engineered human monoclonal antibody, has been demonstrated to significantly reduce the risk of hospitalisation and death in high-risk patients with COVID-19. Here, we describe the real-world use of, and outcomes from, sotrovimab treatment in Belgium during the Delta and Omicron waves among patients with COVID-19 at high risk of developing severe disease. METHODS This was a multicentric, single-arm observational cohort study of non-hospitalised patients receiving outpatient sotrovimab treatment between 1 November 2021 and 2 August 2022 at nine hospitals in Belgium. The primary outcomes were all-cause and COVID-19-related hospitalisations and all-cause deaths during the 29-day acute follow-up period from first administration of sotrovimab. RESULTS A total of 634 patients were included (63.4% aged < 65 years; 50.3% male). A high proportion (67.7%; n = 429/634) of patients were immunocompromised, with 36.9% (n = 234/634) actively treated for malignancy. During the 29-day acute period, 12.5% (n = 79/634) of sotrovimab-treated patients were hospitalised due to any cause (median duration 4 days; median time to hospitalisation 14 days) and 1.1% (n = 7/634) died due to any cause. The proportion of sotrovimab-treated patients experiencing COVID-19-related hospitalisation was highest during the Delta predominance and Delta/BA.1 codominance (both 6.3%) periods. During the BA.1 predominance, BA.1/BA.2 codominance and BA.2/BA.5 codominance periods, COVID-19-related hospitalisations were consistently low (all ≤2.7%). CONCLUSION This study indicated low rates of COVID-19-related hospitalisations and all-cause deaths in sotrovimab-treated patients in Belgium, including during Omicron subvariant periods, despite over two-thirds of the study population being immunocompromised.
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Affiliation(s)
| | - Thor Hautekiet
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | | | | | | | | | | | - Kirsten Colpaert
- Department of Intensive Care, Ghent University Hospital, Ghent, Belgium
| | | | - Eva Van Braeckel
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Respiratory Infection and Defense Lab, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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15
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Li Z, Wang L, Zheng Q, Xu T, Yang K, Wang X, Wen X, Zhang C, Wang J, Song Y, Zhao Y, Zheng X, Wu T. Identifying risk factors for severe omicron infection in allogeneic hematopoietic stem cell transplant recipients with hematologic malignancies. Cancer Rep (Hoboken) 2024; 7:e2103. [PMID: 39031740 PMCID: PMC11190581 DOI: 10.1002/cnr2.2103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 07/22/2024] Open
Abstract
BACKGROUND In December 2022, a large-scale epidemic occurred in China due to Omicron variant of SARS-CoV-2. This study explored risk factors for Omicron infection in transplant recipients at our institution and investigated the factors influencing the severity of SARS-CoV-2 Omicron infection among recipients of allo-HSCT. METHODS This single-center study investigated totally 63 allogeneic hematopoietic stem cell transplant patients infected with Omicron variant at the Beijing GoBroad Boren Hospital Transplant Center during December 2022 and analyzed their risk factors. RESULTS The study included 63 allogeneic hematopoietic stem cell transplant patients who developed Omicron infection. There were 34 mild and 29 moderate to severe cases. Their median age was 22 years (range, 1-65 years), with the male-to-female ratio being 1:1.1. Acute myeloid leukemia (53.97%), acute lymphoblastic leukemia (42.86%), and non-Hodgkin lymphoma (3.17%) were underlying diseases. The median time between HCT and Omicron infection was 8.45 months. Significant predictive factors for moderate to severe Omicron infection included older age (p < .0001), cGVHD (p = .0195), concurrent bacterial infection (p < .0001), low absolute lymphocyte count (p = .026), low CD4/CD8 ratio (p = .0091), high CRP (p < .0001), high serum ferritin (p = .0023), high D-dimer (p < .0001), low CD4 absolute count (p = .0057), and low B-cell absolute count (p = .0154). A moderate to high HCT-CI score tended to be associated with moderate to severe infection (p = .0596). CONCLUSION This study indicates that risk factors for severe Omicron infection include certain clinical characteristics, such as age, cGVHD, and inflammatory response.
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Affiliation(s)
- Zhihui Li
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
| | - Lei Wang
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
| | - Qinlong Zheng
- Department of Medical LaboratoryBeijing GoBroad Boren HospitalBeijingChina
| | - Teng Xu
- Gobroad Research CenterGobroad Healthcare GroupBeijingChina
| | - Keyan Yang
- Department of Medical LaboratoryBeijing GoBroad Boren HospitalBeijingChina
| | - Xianxuan Wang
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
| | - Xiaopei Wen
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
| | - Caiyan Zhang
- Department of Medical LaboratoryBeijing GoBroad Boren HospitalBeijingChina
| | - Jingjing Wang
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
| | - Yanzhi Song
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
| | - Yongqiang Zhao
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
| | - Xiaoyu Zheng
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
| | - Tong Wu
- Department of Bone Marrow TransplantationBeijing GoBroad Boren HospitalBeijingChina
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16
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Rong N, Wu J, Zhao B, Peng W, Yang H, Zhang G, Ruan D, Wei X, Liu J. Comparison of the pathogenicity and neutrophil and monocyte response between SARS-CoV-2 prototype and Omicron BA.1 in a lethal mouse model. Animal Model Exp Med 2024. [PMID: 38760905 DOI: 10.1002/ame2.12419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/02/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND SARS-CoV-2, first identified in late 2019, has given rise to numerous variants of concern (VOCs), posing a significant threat to human health. The emergence of Omicron BA.1.1 towards the end of 2021 led to a pandemic in early 2022. At present, the lethal mouse model for the study of SARS-CoV-2 needs supplementation, and the alterations in neutrophils and monocytes caused by different strains remain to be elucidated. METHODS Human ACE2 transgenic mice were inoculated with the SARS-CoV-2 prototype and Omicron BA.1, respectively. The pathogenicity of the two strains was evaluated by observing clinical symptoms, viral load and pathology. Complete blood count, immunohistochemistry and flow cytometry were performed to detect the alterations of neutrophils and monocytes caused by the two strains. RESULTS Our findings revealed that Omicron BA.1 exhibited significantly lower virulence compared to the SARS-CoV-2 prototype in the mouse model. Additionally, we observed a significant increase in the proportion of neutrophils late in infection with the SARS-CoV-2 prototype and Omicron BA.1. We found that the proportion of monocytes increased at first and then decreased. The trends in the changes in the proportions of neutrophils and monocytes induced by the two strains were similar. CONCLUSION Our study provides valuable insights into the utility of mouse models for simulating the severe disease of SARS-CoV-2 prototype infection and the milder manifestation associated with Omicron BA.1. SARS-CoV-2 prototype and Omicron BA.1 resulted in similar trends in the changes in neutrophils and monocytes.
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Affiliation(s)
- Na Rong
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Jing Wu
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Binbin Zhao
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Wanjun Peng
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Hekai Yang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Gengxin Zhang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | | | - Xiaohui Wei
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Jiangning Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
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17
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Desautels TA, Arrildt KT, Zemla AT, Lau EY, Zhu F, Ricci D, Cronin S, Zost SJ, Binshtein E, Scheaffer SM, Dadonaite B, Petersen BK, Engdahl TB, Chen E, Handal LS, Hall L, Goforth JW, Vashchenko D, Nguyen S, Weilhammer DR, Lo JKY, Rubinfeld B, Saada EA, Weisenberger T, Lee TH, Whitener B, Case JB, Ladd A, Silva MS, Haluska RM, Grzesiak EA, Earnhart CG, Hopkins S, Bates TW, Thackray LB, Segelke BW, Lillo AM, Sundaram S, Bloom JD, Diamond MS, Crowe JE, Carnahan RH, Faissol DM. Computationally restoring the potency of a clinical antibody against Omicron. Nature 2024; 629:878-885. [PMID: 38720086 PMCID: PMC11111397 DOI: 10.1038/s41586-024-07385-1] [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: 10/21/2022] [Accepted: 04/04/2024] [Indexed: 05/21/2024]
Abstract
The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3 and revealed how quickly viral escape can curtail effective options4,5. When the SARS-CoV-2 Omicron variant emerged in 2021, many antibody drug products lost potency, including Evusheld and its constituent, cilgavimab4-6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign and renew the efficacy of COV2-2130 against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and subsequent variants of concern, and provides protection in vivo against the strains tested: WA1/2020, BA.1.1 and BA.5. Deep mutational scanning of tens of thousands of pseudovirus variants reveals that 2130-1-0114-112 improves broad potency without increasing escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Our computational approach does not require experimental iterations or pre-existing binding data, thus enabling rapid response strategies to address escape variants or lessen escape vulnerabilities.
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Affiliation(s)
- Thomas A Desautels
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kathryn T Arrildt
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Adam T Zemla
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Edmond Y Lau
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Fangqiang Zhu
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Dante Ricci
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Stephanie Cronin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suzanne M Scheaffer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brenden K Petersen
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Taylor B Engdahl
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elaine Chen
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura S Handal
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lynn Hall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John W Goforth
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Denis Vashchenko
- Applications Simulations and Quality Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Sam Nguyen
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Google, Alphabet Inc., Mountain View, CA, USA
| | - Dina R Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jacky Kai-Yin Lo
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Bonnee Rubinfeld
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Edwin A Saada
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Tracy Weisenberger
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Tek-Hyung Lee
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Bradley Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Vir Biotechnology, San Francisco, CA, USA
| | - James B Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexander Ladd
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Mary S Silva
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Rebecca M Haluska
- Applications Simulations and Quality Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Emilia A Grzesiak
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christopher G Earnhart
- Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense, US Department of Defense, Frederick, MD, USA
| | | | - Thomas W Bates
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brent W Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Shivshankar Sundaram
- Center for Bioengineering, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel M Faissol
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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18
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Li X, Xu M, Yang J, Zhou L, Liu L, Li M, Wang S, Liu MQ, Huang Z, Zhang Z, Liu S, Hu Y, Lin H, Liu B, Sun Y, Wu Q, Shi ZL, Lan K, Chen Y, Yan H, Chen YQ. Nasal vaccination of triple-RBD scaffold protein with flagellin elicits long-term protection against SARS-CoV-2 variants including JN.1. Signal Transduct Target Ther 2024; 9:114. [PMID: 38678055 PMCID: PMC11055866 DOI: 10.1038/s41392-024-01822-3] [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: 12/11/2023] [Revised: 03/06/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024] Open
Abstract
Developing a mucosal vaccine against SARS-CoV-2 is critical for combatting the epidemic. Here, we investigated long-term immune responses and protection against SARS-CoV-2 for the intranasal vaccination of a triple receptor-binding domain (RBD) scaffold protein (3R-NC) adjuvanted with a flagellin protein (KFD) (3R-NC + KFDi.n). In mice, the vaccination elicited RBD-specific broad-neutralizing antibody responses in both serum and mucosal sites sustained at high level over a year. This long-lasting humoral immunity was correlated with the presence of long-lived RBD-specific IgG- and IgA-producing plasma cells, alongside the Th17 and Tfh17-biased T-cell responses driven by the KFD adjuvant. Based upon these preclinical findings, an open labeled clinical trial was conducted in individuals who had been primed with the inactivated SARS-CoV-2 (IAV) vaccine. With a favorable safety profile, the 3R-NC + KFDi.n boost elicited enduring broad-neutralizing IgG in plasma and IgA in salivary secretions. To meet the challenge of frequently emerged variants, we further designed an updated triple-RBD scaffold protein with mutated RBD combinations, which can induce adaptable antibody responses to neutralize the newly emerging variants, including JN.1. Our findings highlight the potential of the KFD-adjuvanted triple-RBD scaffold protein is a promising prototype for the development of a mucosal vaccine against SARS-CoV-2 infection.
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Affiliation(s)
- Xian Li
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Vaccine and Immunology Research Center, Translational Medical Research Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengxin Xu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jingyi Yang
- Vaccine and Immunology Research Center, Translational Medical Research Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Li Zhou
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Min Li
- Vaccine and Immunology Research Center, Translational Medical Research Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shasha Wang
- Vaccine and Immunology Research Center, Translational Medical Research Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Mei-Qin Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhixiang Huang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhen Zhang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shuning Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yunqi Hu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Haofeng Lin
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bowen Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Vaccine and Immunology Research Center, Translational Medical Research Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Sun
- Aerosol Bio-Tech (Suzhou) Co., LTD, Suzhou, Jiangsu, China
| | - Qingguo Wu
- Vaccine and Immunology Research Center, Translational Medical Research Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zheng-Li Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ke Lan
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Huimin Yan
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
- Vaccine and Immunology Research Center, Translational Medical Research Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China.
- National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Sun Yat-sen University, Guanzhou, China.
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19
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Willem L, Abrams S, Franco N, Coletti P, Libin PJK, Wambua J, Couvreur S, André E, Wenseleers T, Mao Z, Torneri A, Faes C, Beutels P, Hens N. The impact of quality-adjusted life years on evaluating COVID-19 mitigation strategies: lessons from age-specific vaccination roll-out and variants of concern in Belgium (2020-2022). BMC Public Health 2024; 24:1171. [PMID: 38671366 PMCID: PMC11047051 DOI: 10.1186/s12889-024-18576-w] [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: 10/27/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND When formulating and evaluating COVID-19 vaccination strategies, an emphasis has been placed on preventing severe disease that overburdens healthcare systems and leads to mortality. However, more conventional outcomes such as quality-adjusted life years (QALYs) and inequality indicators are warranted as additional information for policymakers. METHODS We adopted a mathematical transmission model to describe the infectious disease dynamics of SARS-COV-2, including disease mortality and morbidity, and to evaluate (non)pharmaceutical interventions. Therefore, we considered temporal immunity levels, together with the distinct transmissibility of variants of concern (VOCs) and their corresponding vaccine effectiveness. We included both general and age-specific characteristics related to SARS-CoV-2 vaccination. Our scenario study is informed by data from Belgium, focusing on the period from August 2021 until February 2022, when vaccination for children aged 5-11 years was initially not yet licensed and first booster doses were administered to adults. More specifically, we investigated the potential impact of an earlier vaccination programme for children and increased or reduced historical adult booster dose uptake. RESULTS Through simulations, we demonstrate that increasing vaccine uptake in children aged 5-11 years in August-September 2021 could have led to reduced disease incidence and ICU occupancy, which was an essential indicator for implementing non-pharmaceutical interventions and maintaining healthcare system functionality. However, an enhanced booster dose regimen for adults from November 2021 onward could have resulted in more substantial cumulative QALY gains, particularly through the prevention of elevated levels of infection and disease incidence associated with the emergence of Omicron VOC. In both scenarios, the need for non-pharmaceutical interventions could have decreased, potentially boosting economic activity and mental well-being. CONCLUSIONS When calculating the impact of measures to mitigate disease spread in terms of life years lost due to COVID-19 mortality, we highlight the impact of COVID-19 on the health-related quality of life of survivors. Our study underscores that disease-related morbidity could constitute a significant part of the overall health burden. Our quantitative findings depend on the specific setup of the interventions under review, which is open to debate or should be contextualised within future situations.
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Affiliation(s)
- Lander Willem
- Department of Family Medicine and Population Health, Antwerp, Belgium.
- Centre for Health Economic Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium.
| | - Steven Abrams
- Department of Family Medicine and Population Health, Antwerp, Belgium
- Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Nicolas Franco
- Data Science Institute, Hasselt University, Hasselt, Belgium
- Namur Institute for Complex Systems (naXys) and Department of Mathematics, University of Namur, Namur, Belgium
| | - Pietro Coletti
- Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Pieter J K Libin
- Data Science Institute, Hasselt University, Hasselt, Belgium
- Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
- Rega Institute for Medical Research, Clinical and Epidemiological Virology, University of Leuven, Leuven, Belgium
| | - James Wambua
- Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Simon Couvreur
- Department of Epidemiology and public health, Sciensano, Brussel, Belgium
| | - Emmanuel André
- National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, University of Leuven, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, University of Leuven, Leuven, Belgium
| | - Zhuxin Mao
- Centre for Health Economic Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium
| | - Andrea Torneri
- Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Christel Faes
- Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Philippe Beutels
- Centre for Health Economic Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium
- School of Public Health and Community Medicine, The University of New South Wales, Sydney, Australia
| | - Niel Hens
- Centre for Health Economic Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium
- Data Science Institute, Hasselt University, Hasselt, Belgium
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20
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [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: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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21
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Halfmann PJ, Iwatsuki-Horimoto K, Kuroda M, Hirata Y, Yamayoshi S, Iida S, Uraki R, Ito M, Ueki H, Furusawa Y, Sakai-Tagawa Y, Kiso M, Armbrust T, Spyra S, Maeda K, Wang Z, Imai M, Suzuki T, Kawaoka Y. Characterization of Omicron BA.4.6, XBB, and BQ.1.1 subvariants in hamsters. Commun Biol 2024; 7:331. [PMID: 38491227 PMCID: PMC10943235 DOI: 10.1038/s42003-024-06015-w] [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: 04/30/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
During the Omicron wave, previous variants such as BA.2, BA.4, and BA.5 were replaced by newer variants with additional mutations in the spike protein. These variants, BA.4.6, BQ.1.1, and XBB, have spread in different countries with different degrees of success. Here, we evaluated the replicative ability and pathogenicity of BA.4.6, BQ1.1, and XBB clinical isolates in male Syrian hamsters. Although we found no substantial differences in weight change among hamsters infected with these Omicron subvariants, the replicative ability of BQ.1.1 and XBB in lung tissue was higher than that of BA.4.6 and BA.5. Of note, BQ.1.1 was lethal in both male and female transgenic human ACE2 hamsters. In competition assays, XBB replicated better than BQ.1.1 in the nasal turbinate tissues of female hamsters previously infected with Omicron BA.2. These results suggest that newer Omicron subvariants in the XBB family are still evolving and should be closely monitored.
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Affiliation(s)
- Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | | | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Ryuta Uraki
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Mutsumi Ito
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Hiroshi Ueki
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Maki Kiso
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Tammy Armbrust
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Sam Spyra
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Zhongde Wang
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, 84322, USA
| | - Masaki Imai
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA.
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
- The University of Tokyo, Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), Tokyo, 162-8655, Japan.
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22
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Bell CF, Bobbili P, Desai R, Gibbons DC, Drysdale M, DerSarkissian M, Patel V, Birch HJ, Lloyd EJ, Zhang A, Duh MS. Real-World Effectiveness of Sotrovimab for the Early Treatment of COVID-19: Evidence from the US National COVID Cohort Collaborative (N3C). Clin Drug Investig 2024; 44:183-198. [PMID: 38379107 PMCID: PMC10912146 DOI: 10.1007/s40261-024-01344-4] [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] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND AND OBJECTIVE The coronavirus disease 2019 (COVID-19) pandemic has been an unprecedented healthcare crisis, one that threatened to overwhelm health systems and prompted an urgent need for early treatment options for patients with mild-to-moderate COVID-19 at high risk for progression to severe disease. Randomised clinical trials established the safety and efficacy of monoclonal antibodies (mAbs) early in the pandemic; in vitro data subsequently led to use of the mAbs being discontinued, without clear evidence on how these data were linked to outcomes. In this study, we describe and compare real-world outcomes for patients with mild-to-moderate COVID-19 at high risk for progression to severe COVID-19 treated with sotrovimab versus untreated patients. METHODS Electronic health records from the National COVID Cohort Collaborative (N3C) were used to identify US patients (aged ≥ 12 years) diagnosed with COVID-19 (positive test or ICD-10: U07.1) in an ambulatory setting (27 September 2021-30 April 2022) who met Emergency Use Authorization (EUA) high-risk criteria. Patients receiving the mAb sotrovimab within 10 days of diagnosis were assigned to the sotrovimab cohort, with the day of infusion as the index date. Untreated patients (no evidence of early mAb treatment, prophylactic mAb or oral antiviral treatment) were assigned to the untreated cohort, with an imputed index date based on the time distribution between diagnosis and sotrovimab infusion in the sotrovimab cohort. The primary endpoint was hospitalisation or death (both all-cause) within 29 days of index, reported as descriptive rate and adjusted [via inverse probability of treatment weighting (IPTW)] odds ratio (OR) and 95% confidence interval (CI). RESULTS Of nearly 2.9 million patients diagnosed with COVID-19 during the analysis period, 4992 met the criteria for the sotrovimab cohort, and 541,325 were included in the untreated cohort. Before weighting, significant differences were noted between the cohorts; for example, patients in the sotrovimab cohort were older (60 years versus 54 years), were more likely to be white (85% versus 75%) and met more EUA criteria (mean 3.1 versus 2.2) versus the untreated cohort. The proportions of patients with 29-day hospitalisation or death were 3.5% (176/4992) and 4.5% (24,163/541,325) in the sotrovimab and untreated cohorts, respectively (unadjusted OR: 0.78; 95% CI: 0.67, 0.91; p = 0.001). In adjusted analysis, sotrovimab was associated with a 25% reduction in the odds of hospitalisation or death compared with the untreated cohort (IPTW-adjusted OR: 0.75; 95% CI: 0.61, 0.92; p = 0.005). CONCLUSIONS Sotrovimab demonstrated clinical effectiveness in preventing severe outcomes (hospitalisation, mortality) in the period 27 September 2021-30 April 2022, which included Delta and Omicron BA.1 variants and an early surge of Omicron BA.2 variant.
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Affiliation(s)
- Christopher F Bell
- GSK, Research Triangle Park, 410 Blackwell Street, Durham, NC, 27701, USA.
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23
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Ying B, Darling TL, Desai P, Liang CY, Dmitriev IP, Soudani N, Bricker T, Kashentseva EA, Harastani H, Raju S, Liu M, Schmidt AG, Curiel DT, Boon ACM, Diamond MS. Mucosal vaccine-induced cross-reactive CD8 + T cells protect against SARS-CoV-2 XBB.1.5 respiratory tract infection. Nat Immunol 2024; 25:537-551. [PMID: 38337035 PMCID: PMC10907304 DOI: 10.1038/s41590-024-01743-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: 07/13/2023] [Accepted: 01/08/2024] [Indexed: 02/12/2024]
Abstract
A nasally delivered chimpanzee adenoviral-vectored severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine (ChAd-SARS-CoV-2-S) is currently used in India (iNCOVACC). Here, we update this vaccine by creating ChAd-SARS-CoV-2-BA.5-S, which encodes a prefusion-stabilized BA.5 spike protein. Whereas serum neutralizing antibody responses induced by monovalent or bivalent adenoviral vaccines were poor against the antigenically distant XBB.1.5 strain and insufficient to protect in passive transfer experiments, mucosal antibody and cross-reactive memory T cell responses were robust, and protection was evident against WA1/2020 D614G and Omicron variants BQ.1.1 and XBB.1.5 in mice and hamsters. However, depletion of memory CD8+ T cells before XBB.1.5 challenge resulted in loss of protection against upper and lower respiratory tract infection. Thus, nasally delivered vaccines stimulate mucosal immunity against emerging SARS-CoV-2 strains, and cross-reactive memory CD8+ T cells mediate protection against lung infection by antigenically distant strains in the setting of low serum levels of cross-reactive neutralizing antibodies.
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Affiliation(s)
- Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Tamarand L Darling
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pritesh Desai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Chieh-Yu Liang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Igor P Dmitriev
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Nadia Soudani
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Traci Bricker
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Elena A Kashentseva
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Houda Harastani
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Saravanan Raju
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Meizi Liu
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Aaron G Schmidt
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - David T Curiel
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA.
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24
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Zhang D, Li X, Zhang M, Huang A, Yang L, Wang C, Yuan T, Lei Y, Liu H, Hua Y, Zhang L, Zhang J. The mediating effect of resilience and COVID-19 anxiety on the relationship between social support and insomnia among healthcare workers: a cross-sectional study. Front Psychiatry 2024; 15:1328226. [PMID: 38414504 PMCID: PMC10896830 DOI: 10.3389/fpsyt.2024.1328226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
Background Insomnia in healthcare workers has become a topic of concern in the health system. The high infectivity and longevity of the COVID-19 pandemic have resulted in great pressure and a high incidence of insomnia among healthcare workers. Insomnia among healthcare workers has a negative impact on high-quality healthcare services in addition to their health. Thus, it's necessary to explore insomnia's underlying mechanisms. Object The present research's aims were threefold: explored the association between social support, resilience, COVID-19 anxiety, and insomnia among healthcare workers during the pandemic, elucidated the underlying mechanism of insomnia, and offered recommendations for improving the health of these workers. Materials and methods A cross-sectional design was adopted. From May 20 to 30, 2022, 1038 healthcare workers were selected to fill out the Oslo 3-item Social Support Scale, the eight-item Athens Insomnia Scale, the Coronavirus Anxiety Scale, and the Brief Resilience Scale. Descriptive statistics and correlations were analyzed by SPSS 25.0. Mediation analysis was conducted by Mplus 8.3 using 5000 bootstrap samples. Results Of the participating 1038 healthcare workers, the prevalence of insomnia was 41.62% (432/1038). Significant associations were found involving insomnia, resilience, COVID-19 anxiety, and social support. Insomnia was directly affected by social support. Moreover, three indirect pathways explain how social support affected insomnia: resilience's mediating role, COVID-19 anxiety's mediating role, and the chain-mediation role of resilience and COVID-19 anxiety. Conclusion The results validated our hypotheses and supported the opinion of Spielman et al. 's three-factor model of insomnia. Social support of healthcare workers has an indirect impact on insomnia in addition to its direct one via independent and chain-mediation effects of resilience and COVID-19 anxiety.
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Affiliation(s)
- Dongmei Zhang
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Xiaoping Li
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Ming Zhang
- School of Innovation and Entrepreneurship, Wannan Medical College, Wuhu, Anhui, China
| | - Anle Huang
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Liu Yang
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Congzhi Wang
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Ting Yuan
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Yunxiao Lei
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Haiyang Liu
- Student Health Center, Wannan Medical College, Wuhu, Anhui, China
| | - Ying Hua
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Lin Zhang
- School of Nursing, Wannan Medical College, Wuhu, Anhui, China
| | - Jing Zhang
- Nursing Department, The People's Hospital of Yingshang, Yingshang, Anhui, China
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25
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Yotsuyanagi H, Ohmagari N, Doi Y, Yamato M, Bac NH, Cha BK, Imamura T, Sonoyama T, Ichihashi G, Sanaki T, Tsuge Y, Uehara T, Mukae H. Efficacy and Safety of 5-Day Oral Ensitrelvir for Patients With Mild to Moderate COVID-19: The SCORPIO-SR Randomized Clinical Trial. JAMA Netw Open 2024; 7:e2354991. [PMID: 38335000 PMCID: PMC10858401 DOI: 10.1001/jamanetworkopen.2023.54991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/14/2023] [Indexed: 02/10/2024] Open
Abstract
Importance Treatment options for COVID-19 are warranted irrespective of the presence of risk factors for severe disease. Objective To assess the efficacy and safety of ensitrelvir in patients with mild to moderate COVID-19. Design, Setting, and Participants This phase 3 part of a phase 2/3, double-blind, placebo-controlled randomized clinical trial was conducted from February 10 to July 10, 2022, with a 28-day follow-up period, at 92 institutions in Japan, Vietnam, and South Korea. Patients (aged 12 to <70 years) with mild to moderate COVID-19 within 120 hours of positive viral test results were studied. Interventions Patients were randomized (1:1:1) to receive 125 mg of once-daily ensitrelvir (375 mg on day 1), 250 mg of once-daily ensitrelvir (750 mg on day 1), or placebo for 5 days. Main Outcomes and Measures The primary end point was the time to resolution of the composite of 5 characteristic symptoms of SARS-CoV-2 Omicron infection, assessed using a Peto-Prentice generalized Wilcoxon test stratified by vaccination history. Virologic efficacy and safety were also assessed. Results A total of 1821 patients were randomized, of whom 1030 (347 in the 125-mg ensitrelvir group, 340 in the 250-mg ensitrelvir group, and 343 in the placebo group) were randomized in less than 72 hours of disease onset (primary analysis population). The mean (SD) age in this population was 35.2 (12.3) years, and 552 (53.6%) were men. A significant difference was observed between the 125-mg ensitrelvir group and the placebo group (P = .04 with a Peto-Prentice generalized Wilcoxon test). The difference in median time was approximately 1 day between the 125-mg ensitrelvir group and the placebo group (167.9 vs 192.2 hours; difference, -24.3 hours; 95% CI, -78.7 to 11.7 hours). Adverse events were observed in 267 of 604 patients (44.2%) in the 125-mg ensitrelvir group, 321 of 599 patients (53.6%) in the 250-mg ensitrelvir group, and 150 of 605 patients (24.8%) in the placebo group, which included a decrease in high-density lipoprotein level (188 [31.1%] in the 125-mg ensitrelvir group, 231 [38.6%] in the 250-mg ensitrelvir group, and 23 [3.8%] in the placebo group). No treatment-related serious adverse events were reported. Conclusions and Relevance In this randomized clinical trial, 125-mg ensitrelvir treatment reduced the time to resolution of the 5 typical COVID-19 symptoms compared with placebo in patients treated in less than 72 hours of disease onset; the absolute difference in median time to resolution was approximately 1 day. Ensitrelvir demonstrated clinical and antiviral efficacy without new safety concerns. Generalizability to populations outside Asia should be confirmed. Trial Registration Japan Registry of Clinical Trials Identifier: jRCT2031210350.
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Affiliation(s)
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masaya Yamato
- Infectious Diseases Center, Rinku General Medical Center, Izumisano, Japan
| | - Nguyen Hoang Bac
- Endoscopic Surgery Training Center, University Medical Center, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Bong Ki Cha
- Department of Internal Medicine, Chung-Ang Medical Health Care System Hyundae Hospital, Gyeonggi-do, Republic of Korea
| | - Takumi Imamura
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Takuhiro Sonoyama
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Genki Ichihashi
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Takao Sanaki
- Research Division, Shionogi & Co, Ltd, Toyonaka, Japan
| | - Yuko Tsuge
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Takeki Uehara
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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26
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Hao X, Bao Z, Dai R, Wu X, Li X, Zhang M, Li H, Xu L, Qiao P, Liu X, Hu W, Zhang Z, Fang J, Zhou M, Wang W, Qu J. A pilot study on Paxlovid therapy for hemodialysis patients with severe acute respiratory syndrome coronavirus 2 infections. Front Med 2024; 18:169-179. [PMID: 37978164 DOI: 10.1007/s11684-023-1011-0] [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: 01/01/2023] [Accepted: 05/19/2023] [Indexed: 11/19/2023]
Abstract
We aimed to investigate the safety and efficacy of nirmatrelvir/ritonavir (Paxlovid) therapy for hemodialysis-dependent patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Thirteen hemodialysis patients infected with the Omicron variant of SARS-CoV-2 from April 3 to May 30, 2022, were recruited. Laboratory parameters and chest CT (computed tomography) imaging were analyzed. The treatment group included six patients who received 150 mg/100 mg of Paxlovid orally once daily for 5 days, whereas the control group included seven patients who received basic treatment. No serious adverse reactions or safety events were recorded. Four control patients progressed to moderate disease, and none in the treatment group showed progression of chest CT findings (P < 0.05). Paxlovid therapy tended toward early viral clearance and low viral load on Day 8. Moreover, 83.3% of the patients in the treatment group and 57.1% of the patients in the control group turned negative within 22 days. In the Paxlovid treatment group, we found significantly increased levels of lymphocytes (P=0.03) and eosinophils (P=0.02) and decreased levels of D-dimer on Day 8 compared with those on Day 1. Paxlovid therapy showed a potential therapeutic effect with good tolerance in hemodialysis patients. The optimal dose and effectiveness evaluation must be further investigated in a largeer cohort.
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Affiliation(s)
- Xu Hao
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhiyao Bao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ranran Dai
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaojing Wu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Li
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Muyin Zhang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hao Li
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lili Xu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Panpan Qiao
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xuefei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Weiting Hu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ze Zhang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jie Fang
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Weiming Wang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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27
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Belongia EA, Petrie JG, Feldstein LR, Guan L, Halfmann PJ, King JP, Neumann G, Pattinson D, Rolfes MA, McLean HQ, Kawaoka Y. Neutralizing Immunity Against Antigenically Advanced Omicron BA.5 in Children After SARS-CoV-2 Infection. J Pediatric Infect Dis Soc 2024; 13:100-104. [PMID: 38142128 DOI: 10.1093/jpids/piad109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
We assessed serum neutralization of Omicron BA.5 in children following SARS-CoV-2 infection during the Delta or Omicron BA.1/BA.2 variant period. Convalescent BA.5 titers were higher following infections during the Omicron BA.1/BA.2 vs Delta variant period, and in vaccinated vs unvaccinated children. Titers against BA.5 did not differ by age group.
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Affiliation(s)
- Edward A Belongia
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Joshua G Petrie
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Leora R Feldstein
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lizheng Guan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Jennifer P King
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - David Pattinson
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Melissa A Rolfes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Huong Q McLean
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
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28
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Kim SH, Kim J, Jung S, Noh JY, Kim J, Park H, Song YG, Peck KR, Park SH, Park MS, Ko JH, Song JY, Choi JY, Jung MK, Shin EC. Omicron BA.2 breakthrough infection elicits CD8 + T cell responses recognizing the spike of later Omicron subvariants. Sci Immunol 2024; 9:eade6132. [PMID: 38241400 DOI: 10.1126/sciimmunol.ade6132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
Here, we examine peripheral blood memory T cell responses against the SARS-CoV-2 BA.4/BA.5 variant spike among vaccinated individuals with or without Omicron breakthrough infections. We provide evidence supporting a lack of original antigenic sin in CD8+ T cell responses targeting the spike. We show that BNT162b2-induced memory T cells respond to the BA.4/BA.5 spike. Among individuals with BA.1/BA.2 breakthrough infections, IFN-γ-producing CD8+ T cell responses against the BA.4/BA.5 spike increased. In a subgroup with BA.2 breakthrough infections, IFN-γ-producing CD8+ T cell responses against the BA.2-mutated spike region increased and correlated directly with responses against the BA.4/BA.5 spike, indicating that BA.2 spike-specific CD8+ T cells elicited by BA.2 breakthrough infection cross-react with the BA.4/BA.5 spike. We identified CD8+ T cell epitope peptides that are present in the spike of BA.2 and BA.4/BA.5 but not the original spike. These peptides are fully conserved in the spike of now-dominant XBB lineages. Our study shows that breakthrough infection by early Omicron subvariants elicits CD8+ T cell responses that recognize epitopes within the spike of newly emerging subvariants.
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Affiliation(s)
- Sang-Hoon Kim
- Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Jihye Kim
- Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Sungmin Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ji Yun Noh
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Jinnam Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Young Goo Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Su-Hyung Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Jae-Hoon Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Min Kyung Jung
- Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Eui-Cheol Shin
- Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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29
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Li H, Zhao X, Peng S, Li Y, Li J, Zheng H, Zhang Y, Zhao Y, Tian Y, Yang J, Wang Y, Zhang X, Liu L. The Abundant Distribution and Duplication of SARS-CoV-2 in the Cerebrum and Lungs Promote a High Mortality Rate in Transgenic hACE2-C57 Mice. Int J Mol Sci 2024; 25:997. [PMID: 38256071 PMCID: PMC10815841 DOI: 10.3390/ijms25020997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Patients with COVID-19 have been reported to experience neurological complications, although the main cause of death in these patients was determined to be lung damage. Notably, SARS-CoV-2-induced pathological injuries in brains with a viral presence were also found in all fatal animal cases. Thus, an appropriate animal model that mimics severe infections in the lungs and brain needs to be developed. In this paper, we compared SARS-CoV-2 infection dynamics and pathological injuries between C57BL/6Smoc-Ace2em3(hACE2-flag-Wpre-pA)Smoc transgenic hACE2-C57 mice and Syrian hamsters. Importantly, the greatest viral distribution in mice occurred in the cerebral cortex neuron area, where pathological injuries and cell death were observed. In contrast, in hamsters, viral replication and distribution occurred mainly in the lungs but not in the cerebrum, although obvious ACE2 expression was validated in the cerebrum. Consistent with the spread of the virus, significant increases in IL-1β and IFN-γ were observed in the lungs of both animals. However, in hACE2-C57 mice, the cerebrum showed noticeable increases in IL-1β but only mild increases in IFN-γ. Notably, our findings revealed that both the cerebrum and the lungs were prominent infection sites in hACE2 mice infected with SARS-CoV-2 with obvious pathological damage. Furthermore, hamsters exhibited severe interstitial pneumonia from 3 dpi to 5 dpi, followed by gradual recovery. Conversely, all the hACE2-C57 mice experienced severe pathological injuries in the cerebrum and lungs, leading to mortality before 5 dpi. According to these results, transgenic hACE2-C57 mice may be valuable for studying SARS-CoV-2 pathogenesis and clearance in the cerebrum. Additionally, a hamster model could serve as a crucial resource for exploring the mechanisms of recovery from infection at different dosage levels.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Longding Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China; (H.L.); (X.Z.); (S.P.); (Y.L.); (J.L.); (H.Z.); (Y.Z.); (Y.Z.); (Y.T.); (J.Y.); (Y.W.); (X.Z.)
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30
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Li J, Zhang K, Lin G, Li J. CRISPR-Cas system: A promising tool for rapid detection of SARS-CoV-2 variants. J Med Virol 2024; 96:e29356. [PMID: 38180237 DOI: 10.1002/jmv.29356] [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: 06/04/2023] [Revised: 12/05/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
COVID-19, caused by SARS-CoV-2, remains a global health crisis. The emergence of multiple variants with enhanced characteristics necessitates their detection and monitoring. Genome sequencing, the gold standard, faces implementation challenges due to complexity, cost, and limited throughput. The CRISPR-Cas system offers promising potential for rapid variant detection, with advantages such as speed, sensitivity, specificity, and programmability. This review provides an in-depth examination of the applications of CRISPR-Cas in mutation detection specifically for SARS-CoV-2. It begins by introducing SARS-CoV-2 and existing variant detection platforms. The principles of the CRISPR-Cas system are then clarified, followed by an exploration of three CRISPR-Cas-based mutation detection platforms, which are evaluated from different perspectives. The review discusses strategies for mutation site selection and the utilization of CRISPR-Cas, offering valuable insights for the development of mutation detection methods. Furthermore, a critical analysis of the clinical applications, advantages, disadvantages, challenges, and prospects of the CRISPR-Cas system is provided.
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Affiliation(s)
- Jing Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
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31
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Hu B, Chan JFW, Liu Y, Liu H, Chen YX, Shuai H, Hu YF, Hartnoll M, Chen L, Xia Y, Hu JC, Yuen TTT, Yoon C, Hou Y, Huang X, Chai Y, Zhu T, Shi J, Wang Y, He Y, Cai JP, Zhou J, Yuan S, Zhang J, Huang JD, Yuen KY, To KKW, Zhang BZ, Chu H. Divergent trajectory of replication and intrinsic pathogenicity of SARS-CoV-2 Omicron post-BA.2/5 subvariants in the upper and lower respiratory tract. EBioMedicine 2024; 99:104916. [PMID: 38101297 PMCID: PMC10733096 DOI: 10.1016/j.ebiom.2023.104916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Earlier Omicron subvariants including BA.1, BA.2, and BA.5 emerged in waves, with a subvariant replacing the previous one every few months. More recently, the post-BA.2/5 subvariants have acquired convergent substitutions in spike that facilitated their escape from humoral immunity and gained ACE2 binding capacity. However, the intrinsic pathogenicity and replication fitness of the evaluated post-BA.2/5 subvariants are not fully understood. METHODS We systemically investigated the replication fitness and intrinsic pathogenicity of representative post-BA.2/5 subvariants (BL.1, BQ.1, BQ.1.1, XBB.1, CH.1.1, and XBB.1.5) in weanling (3-4 weeks), adult (8-10 weeks), and aged (10-12 months) mice. In addition, to better model Omicron replication in the human nasal epithelium, we further investigated the replication capacity of the post-BA.2/5 subvariants in human primary nasal epithelial cells. FINDINGS We found that the evaluated post-BA.2/5 subvariants are consistently attenuated in mouse lungs but not in nasal turbinates when compared with their ancestral subvariants BA.2/5. Further investigations in primary human nasal epithelial cells revealed a gained replication fitness of XBB.1 and XBB.1.5 when compared to BA.2 and BA.5.2. INTERPRETATION Our study revealed that the post-BA.2/5 subvariants are attenuated in lungs while increased in replication fitness in the nasal epithelium, indicating rapid adaptation of the circulating Omicron subvariants in the human populations. FUNDING The full list of funding can be found at the Acknowledgements section.
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Affiliation(s)
- Bingjie Hu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huan Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yan-Xia Chen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ye-Fan Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Madeline Hartnoll
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Li Chen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yao Xia
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jing-Chu Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Terrence Tsz-Tai Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Chaemin Yoon
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yuxin Hou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yue Chai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Tianrenzheng Zhu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yang Wang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yixin He
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jinxia Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Bao-Zhong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
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Zeng Y, Xia F, Guo C, Hu C, Li Y, Wang X, Wu Q, Chen Z, Lu J, Wang Z. Virological Characteristics of Five SARS-CoV-2 Variants, Including Beta, Delta and Omicron BA.1, BA.2, BA.5. Viruses 2023; 15:2394. [PMID: 38140635 PMCID: PMC10747097 DOI: 10.3390/v15122394] [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: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) show increasing transmissibility and infectivity and induce substantial injuries to human health and the ecology. Therefore, it is vital to understand the related features for controlling infection. In this study, SARS-CoV-2 WIV04 (prototype) and five VOCs (Beta, Delta, Omicron BA.1, BA.2 and BA.5 variants) were inoculated in Vero cells to observe their growth activities. Apart from evaluating the environmental stability at different temperatures, residual virus titers and infectivity at different temperatures (4 °C, room temperature (RT) and 37 °C) were measured over 7 days. The experiment also assessed the infectivity for different incubation durations. The growth capacity assay suggested that the WIV04, Beta and Delta variants replicated efficiently in Vero cells compared with Omicron Variants, and BA.2 replicated more efficiently in Vero cells than BA.1 and BA.5. In addition, all variants exhibited longer survivals at 4 °C and could remain infectious after 7 days, compared to RT' survival after 5 days and at 37 °C after 1 day. The virus infection assay indicated that the Omicron variant had a weaker ability to infect cells compared to the WIV04, Beta and Delta strains, and a longer infection time was required for these strains, except for BA.2.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jia Lu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (Y.Z.); (F.X.); (C.G.); (C.H.); (Y.L.); (X.W.); (Q.W.); (Z.C.)
| | - Zejun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (Y.Z.); (F.X.); (C.G.); (C.H.); (Y.L.); (X.W.); (Q.W.); (Z.C.)
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Strizki JM, Grobler JA, Murgolo N, Fridman A, Johnson MG, Du J, Carmelitano P, Brown ML, Paschke A, De Anda C. Virologic Outcomes with Molnupiravir in Non-hospitalized Adult Patients with COVID-19 from the Randomized, Placebo-Controlled MOVe-OUT Trial. Infect Dis Ther 2023; 12:2725-2743. [PMID: 37995070 PMCID: PMC10746688 DOI: 10.1007/s40121-023-00891-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
INTRODUCTION The randomized, placebo-controlled, double-blind MOVe-OUT trial demonstrated molnupiravir (800 mg every 12 h for 5 days) as safe and effective for outpatient treatment of mild-to-moderate COVID-19, significantly reducing the risk of hospitalization/death in high-risk adults. At the time of that report, virologic assessments from the trial were partially incomplete as a result of their time-intensive nature. Here we present final results from all prespecified virology endpoints in MOVe-OUT based on the full trial dataset. METHODS Nasopharyngeal swabs were collected at baseline (day 1, prior to first dose) and days 3, 5 (end-of-treatment visit), 10, 15, and 29. From these samples, change from baseline in SARS-CoV-2 RNA titers (determined by quantitative PCR), detection of infectious SARS-CoV-2 (by plaque assay), and SARS-CoV-2 viral error induction (determined by whole genome next-generation sequencing) were assessed as exploratory endpoints. RESULTS Molnupiravir was associated with greater mean reductions from baseline in SARS-CoV-2 RNA than placebo (including 50% relative reduction at end-of-treatment) through day 10. Among participants with infectious virus detected at baseline (n = 96 molnupiravir, n = 97 placebo) and evaluable post-baseline samples, no molnupiravir-treated participant had infectious SARS-CoV-2 by day 3, whereas infectious virus was recovered from 21% of placebo-arm participants on day 3 and 2% at end-of-treatment. Consistent with molnupiravir's mechanism of action, sequence analysis demonstrated that molnupiravir was associated with an increased number of low-frequency transition errors randomly distributed across the SARS-CoV-2 RNA genome compared with placebo (median 143.5 molnupiravir, 15 placebo), while transversion errors were infrequent overall (median 2 in both arms). Outcomes were consistent regardless of baseline SARS-CoV-2 clade, presence of SARS-CoV-2-specific immune response, or viral load. CONCLUSIONS A 5-day course of orally administered molnupiravir demonstrated a consistently greater virologic effect than placebo, including rapidly eliminating infectious SARS-CoV-2, in high-risk outpatients with mild-to-moderate COVID-19. TRIAL REGISTRATION ClinicalTrials.gov, NCT04575597.
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Affiliation(s)
| | - Jay A Grobler
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | | | - Arthur Fridman
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | | | - Jiejun Du
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | | | | | - Amanda Paschke
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | - Carisa De Anda
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
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Yao H, Wang H, Zhang Z, Lu Y, Zhang Z, Zhang Y, Xiong X, Wang Y, Wang Z, Yang H, Zhao J, Xu W. A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains. MedComm (Beijing) 2023; 4:e397. [PMID: 37901798 PMCID: PMC10600506 DOI: 10.1002/mco2.397] [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: 04/21/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023] Open
Abstract
SARS-CoV-2 viruses are highly transmissible and immune evasive. It is critical to develop broad-spectrum prophylactic and therapeutic antibodies for potential future pandemics. Here, we used the phage display method to discover nanobodies (Nbs) for neutralizing SARS-CoV-2 viruses especially Omicron strains. The leading nanobody (Nb), namely, Nb4, with excellent physicochemical properties, can neutralize Delta and Omicron subtypes, including BA.1, BA.1.1 (BA.1 + R346K), BA.2, BA.5, BQ.1, and XBB.1. The crystal structure of Nb4 in complex with the receptor-binding domain (RBD) of BA.1 Spike protein reveals that Nb4 interacts with an epitope on the RBD overlapping with the receptor-binding motif, and thus competes with angiotensin-converting enzyme 2 (ACE2) binding. Nb4 is expected to be effective for neutralizing most recent Omicron variants, since the epitopes are evolutionarily conserved among them. Indeed, trivalent Nb4 interacts with the XBB1.5 Spike protein with low nM affinity and competes for ACE2 binding. Prophylactic and therapeutic experiments in mice indicated that Nb4 could reduce the Omicron virus loads in the lung. In particular, in prophylactic experiments, intranasal administration of multivalent Nb4 completely protected mice from Omicron infection. Taken together, these results demonstrated that Nb4 could serve as a potent and broad-spectrum prophylactic and therapeutic Nb for COVID-19.
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Affiliation(s)
- Hebang Yao
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Hongyang Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Yuchi Lu
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghaiChina
| | - Zhiying Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Xinyi Xiong
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yanqun Wang
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Zhizhi Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Haitao Yang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghaiChina
| | - Jincun Zhao
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghaiChina
- Guangzhou LaboratoryBio‐IslandGuangzhouGuangdongChina
- Institute of Infectious DiseaseGuangzhou Eighth People's Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
- Institute for HepatologyNational Clinical Research Center for Infectious Disease, Shenzhen Third People's HospitalShenzhenGuangdongChina
| | - Wenqing Xu
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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Chen K, Wang F. Cell-specific genome-scale metabolic modeling of SARS-CoV-2-infected lung to identify antiviral enzymes. FEBS Open Bio 2023; 13:2172-2186. [PMID: 37734920 PMCID: PMC10699103 DOI: 10.1002/2211-5463.13710] [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: 06/21/2023] [Revised: 08/09/2023] [Accepted: 09/19/2023] [Indexed: 09/23/2023] Open
Abstract
Computational systems biology plays a key role in the discovery of suitable antiviral targets. We designed a cell-specific, constraint-based modeling technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected lungs. We used the gene sequence of the alpha variant of SARS-CoV-2 to build a viral biomass reaction (VBR). We also used the mass proportion of lipids between the viral biomass and its host cell to estimate the stoichiometric coefficients of viral lipids in the reaction. We then integrated the VBR, the gene expression of the alpha variant of SARS-CoV-2, and the generic human metabolic network Recon3D to reconstruct a cell-specific genome-scale metabolic model. An antiviral target discovery (AVTD) platform was introduced using this model to identify therapeutic drug targets for combating COVID-19. The AVTD platform not only identified antiviral genes for eliminating viral replication but also predicted side effects of treatments. Our computational results revealed that knocking out dihydroorotate dehydrogenase (DHODH) might reduce the synthesis rate of cytidine-5'-triphosphate and uridine-5'-triphosphate, which terminate the viral building blocks of DNA and RNA for SARS-CoV-2 replication. Our results also indicated that DHODH is a promising antiviral target that causes minor side effects, which is consistent with the results of recent reports. Moreover, we discovered that the genes that participate in the de novo biosynthesis of glycerophospholipids and ceramides become unidentifiable if the VBR does not involve the stoichiometry of lipids.
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Affiliation(s)
- Ke‐Lin Chen
- Department of Chemical EngineeringNational Chung Cheng UniversityChiayiTaiwan
| | - Feng‐Sheng Wang
- Department of Chemical EngineeringNational Chung Cheng UniversityChiayiTaiwan
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Johnson TV, Baranov P, Di Polo A, Fortune B, Gokoffski KK, Goldberg JL, Guido W, Kolodkin AL, Mason CA, Ou Y, Reh TA, Ross AG, Samuels BC, Zack DJ. The Retinal Ganglion Cell Repopulation, Stem Cell Transplantation, and Optic Nerve Regeneration Consortium. OPHTHALMOLOGY SCIENCE 2023; 3:100390. [PMID: 38025164 PMCID: PMC10630665 DOI: 10.1016/j.xops.2023.100390] [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] [Received: 06/01/2023] [Revised: 07/24/2023] [Accepted: 08/18/2023] [Indexed: 12/01/2023]
Abstract
Purpose The Retinal Ganglion Cell (RGC) Repopulation, Stem Cell Transplantation, and Optic Nerve Regeneration (RReSTORe) consortium was founded in 2021 to help address the numerous scientific and clinical obstacles that impede development of vision-restorative treatments for patients with optic neuropathies. The goals of the RReSTORe consortium are: (1) to define and prioritize the most critical challenges and questions related to RGC regeneration; (2) to brainstorm innovative tools and experimental approaches to meet these challenges; and (3) to foster opportunities for collaborative scientific research among diverse investigators. Design and Participants The RReSTORe consortium currently includes > 220 members spanning all career stages worldwide and is directed by an organizing committee comprised of 15 leading scientists and physician-scientists of diverse backgrounds. Methods Herein, we describe the structure and organization of the RReSTORe consortium, its activities to date, and the perceived impact that the consortium has had on the field based on a survey of participants. Results In addition to helping propel the field of regenerative medicine as applied to optic neuropathies, the RReSTORe consortium serves as a framework for developing large collaborative groups aimed at tackling audacious goals that may be expanded beyond ophthalmology and vision science. Conclusions The development of innovative interventions capable of restoring vision for patients suffering from optic neuropathy would be transformative for the ophthalmology field, and may set the stage for functional restoration in other central nervous system disorders. By coordinating large-scale, international collaborations among scientists with diverse and complementary expertise, we are confident that the RReSTORe consortium will help to accelerate the field toward clinical translation. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Thomas V. Johnson
- Wilmer Eye Institute and Cellular & Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Petr Baranov
- Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Maryland
| | - Adriana Di Polo
- Department of Neuroscience, University of Montreal, Montreal, QC, Canada, Neuroscience Division, Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Brad Fortune
- Discoveries in Sight Research Laboratories, Devers Eye Institute and Legacy Research Institute, Legacy Health, Portland, Oregon
| | | | - Jeffrey L. Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California
| | - William Guido
- Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, Louisville, Kentucky
| | - Alex L. Kolodkin
- Solomon H Snyder Department of Neuroscience and Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Carol A. Mason
- Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Department of Pathology & Cell Biology, and Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Yvonne Ou
- Department of Ophthalmology, University of California, San Francisco, California
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Ahmara G. Ross
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Brian C. Samuels
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, Alabama
| | - Donald J. Zack
- Departments of Ophthalmology (Wilmer Eye Institute), Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Pastorio C, Noettger S, Nchioua R, Zech F, Sparrer KM, Kirchhoff F. Impact of mutations defining SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 on Spike function and neutralization. iScience 2023; 26:108299. [PMID: 38026181 PMCID: PMC10661123 DOI: 10.1016/j.isci.2023.108299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/04/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Additional mutations in the viral Spike protein helped the BA.2.12.1 and BA.4/5 SARS-CoV-2 Omicron subvariants to outcompete the parental BA.2 subvariant. Here, we determined the functional impact of mutations that newly emerged in the BA.2.12.1 (L452Q, S704L) and BA.4/5 (Δ69-70, L452R, F486V, R493Q) Spike proteins. Our results show that mutation of L452Q/R or F486V typically increases and R493Q or S704L impair BA.2 Spike-mediated infection. In combination, changes of Δ69-70, L452R, and F486V contribute to the higher infectiousness and fusogenicity of the BA.4/5 Spike. L452R/Q and F486V in Spike are mainly responsible for reduced sensitivity to neutralizing antibodies. However, the combined mutations are required for full infectivity, reduced TMPRSS2 dependency, and immune escape of BA.4/5 Spike. Thus, it is the specific combination of mutations in BA.4/5 Spike that allows increased functionality and immune evasion, which helps to explain the temporary dominance and increased pathogenicity of these Omicron subvariants.
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Affiliation(s)
- Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Sabrina Noettger
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
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Meehan GR, Herder V, Allan J, Huang X, Kerr K, Mendonca DC, Ilia G, Wright DW, Nomikou K, Gu Q, Molina Arias S, Hansmann F, Hardas A, Attipa C, De Lorenzo G, Cowton V, Upfold N, Palmalux N, Brown JC, Barclay WS, Filipe ADS, Furnon W, Patel AH, Palmarini M. Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning. PLoS Pathog 2023; 19:e1011589. [PMID: 37934791 PMCID: PMC10656012 DOI: 10.1371/journal.ppat.1011589] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/17/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to evolve throughout the coronavirus disease-19 (COVID-19) pandemic, giving rise to multiple variants of concern (VOCs) with different biological properties. As the pandemic progresses, it will be essential to test in near real time the potential of any new emerging variant to cause severe disease. BA.1 (Omicron) was shown to be attenuated compared to the previous VOCs like Delta, but it is possible that newly emerging variants may regain a virulent phenotype. Hamsters have been proven to be an exceedingly good model for SARS-CoV-2 pathogenesis. Here, we aimed to develop robust quantitative pipelines to assess the virulence of SARS-CoV-2 variants in hamsters. We used various approaches including RNAseq, RNA in situ hybridization, immunohistochemistry, and digital pathology, including software assisted whole section imaging and downstream automatic analyses enhanced by machine learning, to develop methods to assess and quantify virus-induced pulmonary lesions in an unbiased manner. Initially, we used Delta and Omicron to develop our experimental pipelines. We then assessed the virulence of recent Omicron sub-lineages including BA.5, XBB, BQ.1.18, BA.2, BA.2.75 and EG.5.1. We show that in experimentally infected hamsters, accurate quantification of alveolar epithelial hyperplasia and macrophage infiltrates represent robust markers for assessing the extent of virus-induced pulmonary pathology, and hence virus virulence. In addition, using these pipelines, we could reveal how some Omicron sub-lineages (e.g., BA.2.75 and EG.5.1) have regained virulence compared to the original BA.1. Finally, to maximise the utility of the digital pathology pipelines reported in our study, we developed an online repository containing representative whole organ histopathology sections that can be visualised at variable magnifications (https://covid-atlas.cvr.gla.ac.uk). Overall, this pipeline can provide unbiased and invaluable data for rapidly assessing newly emerging variants and their potential to cause severe disease.
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Affiliation(s)
- Gavin R. Meehan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jay Allan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Xinyi Huang
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Karen Kerr
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Diogo Correa Mendonca
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Georgios Ilia
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Derek W. Wright
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Sergi Molina Arias
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Florian Hansmann
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Germany
| | - Alexandros Hardas
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, North Mymms, United Kingdom
| | - Charalampos Attipa
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, United Kingdom
| | | | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Nicole Upfold
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, United Kingdom
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
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Kimura I, Yamasoba D, Nasser H, Ito H, Zahradnik J, Wu J, Fujita S, Uriu K, Sasaki J, Tamura T, Suzuki R, Deguchi S, Plianchaisuk A, Yoshimatsu K, Kazuma Y, Mitoma S, Schreiber G, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Takaori-Kondo A, Ito J, Shirakawa K, Takayama K, Irie T, Hashiguchi T, Nakagawa S, Fukuhara T, Saito A, Ikeda T, Sato K. Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics. J Virol 2023; 97:e0101123. [PMID: 37796123 PMCID: PMC10781145 DOI: 10.1128/jvi.01011-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/16/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non-spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Medicine, Kobe University, Kobe, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuya Mitoma
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - The Genotype to Phenotype Japan (G2P-Japan) Consortium
MisawaNaoko1KosugiYusuke1PanLin1SuganamiMai1ChibaMika1YoshimuraRyo1YasudaKyoko1IidaKeiko1OhsumiNaomi1StrangeAdam P.1KakuYu1PlianchaisukArnon1GuoZiyi1HinayAlfredo Jr. Amolong1Mendoza TolentinoJarel Elgin1ChenLuo1ShimizuRyo2Monira BegumM. S. T.2TakahashiOtowa2IchiharaKimiko2JonathanMichael2MugitaYuka2SuzukiSaori3SuzukiTateki4KimuraKanako4NakajimaYukari4YajimaHisano4HashimotoRina4WatanabeYukio4SakamotoAyaka4YasuharaNaoko4NagataKayoko4NomuraRyosuke4HorisawaYoshihito4TashiroYusuke4KawaiYugo4ShibataniYuki5NishiuchiTomoko5YoshidaIsao6KawabataRyoko7MatsunoKeita8NaoNaganori9SawaHirofumi9TanakaShinya10TsudaMasumi10WangLei10OdaYoshikata10FerdousZannatul10ShishidoKenji10MotozonoChihiro11ToyodaMako11UenoTakamasa11TabataKaori12Institute of Medical Science, University of Tokyo, Tokyo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, JapanHokkaido University, Sapporo, JapanKyoto University, Kyoto, JapanUniversity of Miyazaki, Miyazaki, JapanTokyo Metropolitan Institute of Public Health, Tokyo, JapanHiroshima University, Hiroshima, JapanOne Health Research Center, Hokkaido University, Sapporo, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo, JapanHokkaido University, Sapporo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto, JapanKyushu University, Fukuoka, Japan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Medicine, Kobe University, Kobe, Japan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
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Rasmussen HB, Hansen PR. Molnupiravir Revisited-Critical Assessment of Studies in Animal Models of COVID-19. Viruses 2023; 15:2151. [PMID: 38005828 PMCID: PMC10675540 DOI: 10.3390/v15112151] [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: 08/31/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 11/26/2023] Open
Abstract
Molnupiravir, a prodrug known for its broad antiviral activity, has demonstrated efficacy in animal models of COVID-19, prompting clinical trials, in which initial results indicated a significant effect against the disease. However, subsequent clinical studies did not confirm these findings, leading to the refusal of molnupiravir for permanent market authorization in many countries. This report critically assessed 22 studies published in 18 reports that investigated the efficacy of molnupiravir in animal models of COVID-19, with the purpose of determining how well the design of these models informed human studies. We found that the administered doses of molnupiravir in most studies involving animal COVID-19 models were disproportionately higher than the dose recommended for human use. Specifically, when adjusted for body surface area, over half of the doses of molnupiravir used in the animal studies exceeded twice the human dose. Direct comparison of reported drug exposure across species after oral administration of molnupiravir indicated that the antiviral efficacy of the dose recommended for human use was underestimated in some animal models and overestimated in others. Frequently, molnupiravir was given prophylactically or shortly after SARS-CoV-2 inoculation in these models, in contrast to clinical trials where such timing is not consistently achieved. Furthermore, the recommended five-day treatment duration for humans was exceeded in several animal studies. Collectively, we suggest that design elements in the animal studies under examination contributed to a preference favoring molnupiravir, and thus inflated expectations for its efficacy against COVID-19. Addressing these elements may offer strategies to enhance the clinical efficacy of molnupiravir for the treatment of COVID-19. Such strategies include dose increment, early treatment initiation, administration by inhalation, and use of the drug in antiviral combination therapy.
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Affiliation(s)
- Henrik Berg Rasmussen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, 4000 Roskilde, Denmark
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Peter Riis Hansen
- Department of Cardiology, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2900 Hellerup, Denmark;
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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Guo Y, Guo Y, Ying H, Yu W, Chen S, Zhang Y, Zhang S, Lin Y, Sun F, Zhang Y, Yu J, Ma K, Qin L, Long F, Zhu H, Mao R, Xue J, Zhang J. In-hospital adverse outcomes and risk factors among chronic kidney disease patients infected with the omicron variant of SARS-CoV-2: a single-center retrospective study. BMC Infect Dis 2023; 23:698. [PMID: 37853317 PMCID: PMC10585898 DOI: 10.1186/s12879-023-08620-2] [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: 02/08/2023] [Accepted: 09/18/2023] [Indexed: 10/20/2023] Open
Abstract
INTRODUCTION The SARS-CoV-2 Omicron variant has decreased virulence and pathogenicity, yet the number of Omicron infections worldwide is unprecedentedly high, with rather high mortality and severe disease rate. Chronic kidney disease (CKD) patients are particularly vulnerable to the SARS-CoV-2 Omicron variant and have unique clinical outcomes. METHODS We retrospectively collected data from 2140 hospitalized patients with SARS-CoV-2 Omicron variant infection from March 29, 2022, to May 17, 2022. Demographic characteristics, ancillary examination results, and clinical treatments were described. Occurrence of critical COVID-19 or death and time of positive-to-negative conversion was defined as primary outcomes. The presence of COVID-19 pneumonia and the usage of respiratory or circulatory support was defined as secondary outcomes. Univariate or multivariate logistic regression analyses were performed to identify risk factors for primary outcomes. RESULTS 15.74% of CKD patients infected with the SARS-CoV-2 Omicron variant ended up with critical COVID-19 or death. Pre-existing CKD was a risk factor for critical COVID-19 or death and prolonged time of positive-to-negative conversion of SARS-CoV-2. Nirmatrelvir-ritonavir facilitated viral clearance among COVID-19 patients with non-severe CKD. CONCLUSION We found patients with CKD and COVID-19 due to Omicron experienced worse clinical outcomes and prolonged time of positive-to-negative conversion of SARS-CoV-2 compared to patients without CKD, which helps rationalize limited medical resources and offers guidance for appropriate clinical treatments.
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Affiliation(s)
- Yue Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Yifei Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Huajian Ying
- Department of Nephrology, Huashan Hospital Fudan University, Shanghai, China
| | - Weien Yu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Shiqi Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Yao Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Shenyan Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Yanxue Lin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Feng Sun
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Yongmei Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Jie Yu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Ke Ma
- Department of Emergency and Acute Critical Care, Huashan Hospital North, Fudan University, Shanghai, China
| | - Lunxiu Qin
- Department of General Surgery, Cancer Metastasis Institute, Huashan Hospital, Fudan University, Shanghai, China
| | - Feng Long
- Department of Respiratory Medicine, Huashan Hospital North, Fudan University, Shanghai, China
| | - Haoxiang Zhu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Richeng Mao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
| | - Jun Xue
- Department of Nephrology, Huashan Hospital Fudan University, Shanghai, China
| | - Jiming Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, Huashan Hospital, National Medical Center for Infectious Diseases, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
- Department of Infectious Diseases, Jing’An Branch of Huashan Hospital, Fudan University, Shanghai, China
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Creisher PS, Perry JL, Zhong W, Lei J, Mulka KR, Ryan WH, Zhou R, Akin EH, Liu A, Mitzner W, Burd I, Pekosz A, Klein SL. Adverse outcomes in SARS-CoV-2-infected pregnant mice are gestational age-dependent and resolve with antiviral treatment. J Clin Invest 2023; 133:e170687. [PMID: 37581940 PMCID: PMC10575736 DOI: 10.1172/jci170687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023] Open
Abstract
SARS-CoV-2 infection during pregnancy is associated with severe COVID-19 and adverse fetal outcomes, but the underlying mechanisms remain poorly understood. Moreover, clinical studies assessing therapeutics against SARS-CoV-2 in pregnancy are limited. To address these gaps, we developed a mouse model of SARS-CoV-2 infection during pregnancy. Outbred CD1 mice were infected at E6, E10, or E16 with a mouse-adapted SARS-CoV-2 (maSCV2) virus. Outcomes were gestational age-dependent, with greater morbidity, reduced antiviral immunity, greater viral titers, and impaired fetal growth and neurodevelopment occurring with infection at E16 (third trimester equivalent) than with infection at either E6 (first trimester equivalent) or E10 (second trimester equivalent). To assess the efficacy of ritonavir-boosted nirmatrelvir, which is recommended for individuals who are pregnant with COVID-19, we treated E16-infected dams with mouse-equivalent doses of nirmatrelvir and ritonavir. Treatment reduced pulmonary viral titers, decreased maternal morbidity, and prevented offspring growth restriction and neurodevelopmental impairments. Our results highlight that severe COVID-19 during pregnancy and fetal growth restriction is associated with heightened virus replication in maternal lungs. Ritonavir-boosted nirmatrelvir mitigated maternal morbidity along with fetal growth and neurodevelopment restriction after SARS-CoV-2 infection. These findings prompt the need for further consideration of pregnancy in preclinical and clinical studies of therapeutics against viral infections.
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Affiliation(s)
- Patrick S. Creisher
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jamie L. Perry
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Weizhi Zhong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jun Lei
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kathleen R. Mulka
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - W. Hurley Ryan
- Department of Environmental Health and Engineering, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Elgin H. Akin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Anguo Liu
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Wayne Mitzner
- Department of Environmental Health and Engineering, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Irina Burd
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Environmental Health and Engineering, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Sabra L. Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Guruprasad L, Naresh GKRS, Boggarapu G. Taking stock of the mutations in human SARS-CoV-2 spike proteins: From early days to nearly the end of COVID-19 pandemic. Curr Res Struct Biol 2023; 6:100107. [PMID: 37841365 PMCID: PMC10569959 DOI: 10.1016/j.crstbi.2023.100107] [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: 09/10/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causative agent of the coronavirus disease-2019 (COVID-19) has resulted in several deaths and severe economic losses throughout the world. The spike protein in the virus binds to the human ACE-2 receptor in order to mediate virus-host interactions required for the viral transmission. Since first report of the SARS-CoV-2 sequence during December 2019 from patient infected with the virus in Wuhan, China, the virus has undergone rapid changes leading to mutations comprising substitutions, deletions and insertions in the sequence resulting in several variants of the virus that were more virulent and transmissible or less virulent but highly transmissible. The timely intervention with COVID-19 vaccines proved to be effective in controlling the number of infections. However, rapid mutations in the virus led to the lowering of vaccine efficacies being administered to people. In May 2023, the World Health Organization declared COVID-19 was not a public health emergency of international concern anymore. In order to take stock of mutations in the virus from early days to nearly end of COVID-19 pandemic, sequence analyses of the SARS-CoV-2 spike proteins available in the NCBI Virus database was carried out. The mutations and invariant residues in the SARS-CoV-2 spike protein sequences relative to the reference sequence were analysed. The location of the invariant residues and residues at interface of the protein chains in the spike protein trimer complex structure were examined. A total of 111,298 non-redundant SARS-CoV-2 spike protein sequences representing 2,345,585 spike proteins in the NCBI Virus database showed mutations at 1252 of the 1273 positions in the amino acid sequence. The mutations represented 6129 different mutation types in the sequences analysed. Besides, some sequences also contained insertion mutations. The SARS-CoV-2 spike protein sequences represented 1435 lineages. In addition, several spike protein sequences with mutations whose lineages were either 'not classified' or were 'unclassifiable' indicated the virus could still be evolving.
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Shimizu R, Sonoyama T, Fukuhara T, Kuwata A, Matsuo Y, Kubota R. A Phase 1 Study of Ensitrelvir Fumaric Acid Tablets Evaluating the Safety, Pharmacokinetics and Food Effect in Healthy Adult Populations. Clin Drug Investig 2023; 43:785-797. [PMID: 37798608 PMCID: PMC10575992 DOI: 10.1007/s40261-023-01309-z] [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] [Accepted: 09/17/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND A reported clinical pharmacokinetics and safety study of suspension formulation of ensitrelvir, a therapeutic agent used in severe acute respiratory syndrome coronavirus 2 infection, demonstrated favorable pharmacokinetics and was well tolerated in healthy male Japanese and White participants. Understanding the safety and pharmacokinetic features of ensitrelvir (using the formulation approved for clinical use) in various populations, and the effect of food, is crucial for optimal clinical use. OBJECTIVES The objectives of this study were to (1) assess the safety, tolerability, and pharmacokinetics of ensitrelvir following multiple-dose administration of ensitrelvir tablets in populations with different races, ages, and sex; and (2) assess the effect of food on the pharmacokinetics of ensitrelvir tablets in the fasted or fed state. METHODS A phase 1, multicenter, double-blinded, randomized, placebo-controlled study was conducted to evaluate the safety and pharmacokinetics of once-daily ensitrelvir tablets at loading/maintenance doses of 375/125 mg or 750/250 mg for 5 days in healthy Japanese females, Japanese elderly (only 375/125 mg), and White male and female participants. An open-label, two-group, two-period crossover study was also conducted to estimate the effect of food on the pharmacokinetics of ensitrelvir at single dose of 375 mg. The nature, frequency, and severity of treatment-emergent adverse events were evaluated and recorded in safety assessments in both studies. RESULTS The maximum plasma concentration (Cmax) and area under the plasma concentration-time curve (AUC) were similar within these populations. The geometric mean half-life of ensitrelvir following multiple-dose administration was 48.7-58.9 h across all cohorts. The Cmax and AUC increased in a dose-proportional manner in Japanese female participants, and increased in a less than dose-proportional manner in White participants. Furthermore, there was no clear relationship between the dose and geometric mean half-life of ensitrelvir. The plasma concentration at 24 h (C24) after an initial dose of 375/125 mg exceeded the target plasma concentration (6.09 µg/mL) in all populations. Regarding the effect of food on the pharmacokinetics of ensitrelvir, although time to Cmax in the fed state was delayed, there was no clinically meaningful difference in the exposure levels (Cmax and AUC) of ensitrelvir between the fasted and fed states. Most treatment-emergent adverse events were mild in nature and had resolved. CONCLUSION Ensitrelvir (375/125 mg and 750/250 mg tablet formulation) was well tolerated, without any major safety concerns. The pharmacokinetics of ensitrelvir between all populations in the study were similar and C24 exceeded the target plasma concentration at 375/125 mg. These results suggest that ensitrelvir can be effectively administered with no necessity for dose adjustment for age, sex, and race without food restriction. CLINICAL TRIAL REGISTRATION Japan Registry of Clinical Trials identifier: jRCT2031210202, registered on 16 July 2021.
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Affiliation(s)
- Ryosuke Shimizu
- Project Management Division, Clinical Pharmacology and Pharmacokinetics Department, Shionogi & Co., Ltd, 8F, Nissay Yodoyabashi East, 3-3-13 Imabashi, Chuo-ku, Osaka, 541-0042, Japan.
| | | | | | - Aya Kuwata
- Clinical Research Department, Shionogi & Co., Ltd, Osaka, Japan
| | - Yumiko Matsuo
- Project Management Division, Clinical Pharmacology and Pharmacokinetics Department, Shionogi & Co., Ltd, 8F, Nissay Yodoyabashi East, 3-3-13 Imabashi, Chuo-ku, Osaka, 541-0042, Japan
- Quantitative Clinical Pharmacology, Takeda Pharmaceuticals, Osaka, Japan
| | - Ryuji Kubota
- Project Management Division, Clinical Pharmacology and Pharmacokinetics Department, Shionogi & Co., Ltd, 8F, Nissay Yodoyabashi East, 3-3-13 Imabashi, Chuo-ku, Osaka, 541-0042, Japan
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Vardhan S, Sahoo SK. Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols. PHYTOCHEMICAL ANALYSIS : PCA 2023; 34:800-815. [PMID: 36606391 DOI: 10.1002/pca.3204] [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: 11/01/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The SARS-CoV-2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes caused by mutations, we conducted a comparative analysis of BA.2 with variants BA.1 and BA.3. OBJECTIVE In the present study, we aimed to investigate the interactions of the spike glycoprotein receptor-binding domain (SGp RBD) of Omicron variants BA.1, BA.2, and BA.3 with the human receptor hACE2. Further, a library of 233 polyphenols was screened by molecular docking with the SGp RBDs of Omicron variants BA.1, BA.2, and BA.3. METHODS Protein-protein and protein-ligand molecular docking simulations were performed with AutoDock Vina and the ClusPro 2.0 server, respectively. The protein-ligand interactions were evaluated by BIOVIA Discovery Studio and ChimeraX 1.4. The molecular dynamics simulations for 100 ns were performed using GROMACS 2021. RESULTS Compared to other variants of concern, the structural changes in Omicron caused by mutations at key positions improved its ability to cause infection. Despite multiple mutations, many important polyphenols bind effectively at the RBDs of Omicron variants, with the required pharmacokinetic and ADME features and obeying the Lipinski rule. CONCLUSION Even though Omicron variants have multiple mutations and their transmission rate is relatively high, the computed binding affinities of lead polyphenols like epigallocatechin-3-O-gallate (EGCG) and luteolin-7-O-glucuronide (L7G) indicate that traditional medicines and proper immunity booster diets may be useful in the long-term fight against SARS-CoV-2.
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Affiliation(s)
- Seshu Vardhan
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, Gujarat, India
| | - Suban K Sahoo
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, Gujarat, India
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Imbiakha B, Ezzatpour S, Buchholz DW, Sahler J, Ye C, Olarte-Castillo XA, Zou A, Kwas C, O’Hare K, Choi A, Adeleke RA, Khomandiak S, Goodman L, Jager MC, Whittaker GR, Martinez-Sobrido L, August A, Aguilar HC. Age-dependent acquisition of pathogenicity by SARS-CoV-2 Omicron BA.5. SCIENCE ADVANCES 2023; 9:eadj1736. [PMID: 37738347 PMCID: PMC10516498 DOI: 10.1126/sciadv.adj1736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/23/2023] [Indexed: 09/24/2023]
Abstract
Pathology studies of SARS-CoV-2 Omicron variants of concern (VOC) are challenged by the lack of pathogenic animal models. While Omicron BA.1 and BA.2 replicate in K18-hACE2 transgenic mice, they cause minimal to negligible morbidity and mortality, and less is known about more recent Omicron VOC. Here, we show that in contrast to Omicron BA.1, BA.5-infected mice exhibited high levels of morbidity and mortality, correlating with higher early viral loads. Neither Omicron BA.1 nor BA.5 replicated in brains, unlike most prior VOC. Only Omicron BA.5-infected mice exhibited substantial weight loss, high pathology scores in lungs, and high levels of inflammatory cells and cytokines in bronchoalveolar lavage fluid, and 5- to 8-month-old mice exhibited 100% fatality. These results identify a rodent model for pathogenesis or antiviral countermeasure studies for circulating SARS-CoV-2 Omicron BA.5. Further, differences in morbidity and mortality between Omicron BA.1 and BA.5 provide a model for understanding viral determinants of pathogenicity.
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Affiliation(s)
- Brian Imbiakha
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Shahrzad Ezzatpour
- Department of Microbiology, Cornell University, College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
| | - David W. Buchholz
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Julie Sahler
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ximena A. Olarte-Castillo
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- James A. Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Anna Zou
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Cole Kwas
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Katelyn O’Hare
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Annette Choi
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Richard Ayomide Adeleke
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Solomiia Khomandiak
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Laura Goodman
- James A. Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public & Ecosystem Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Mason C. Jager
- Department of Population Medicine and Diagnostic Sciences, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public & Ecosystem Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | | | - Avery August
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Microbiology, Cornell University, College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
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Shuai H, Chan JFW, Hu B, Chai Y, Yoon C, Liu H, Liu Y, Shi J, Zhu T, Hu JC, Hu YF, Hou Y, Huang X, Yuen TTT, Wang Y, Zhang J, Xia Y, Chen LL, Cai JP, Zhang AJ, Yuan S, Zhou J, Zhang BZ, Huang JD, Yuen KY, To KKW, Chu H. The viral fitness and intrinsic pathogenicity of dominant SARS-CoV-2 Omicron sublineages BA.1, BA.2, and BA.5. EBioMedicine 2023; 95:104753. [PMID: 37579626 PMCID: PMC10448076 DOI: 10.1016/j.ebiom.2023.104753] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Among the Omicron sublineages that have emerged, BA.1, BA.2, BA.5, and their related sublineages have resulted in the largest number of infections. While recent studies demonstrated that all Omicron sublineages robustly escape neutralizing antibody response, it remains unclear on whether these Omicron sublineages share any pattern of evolutionary trajectory on their replication efficiency and intrinsic pathogenicity along the respiratory tract. METHODS We compared the virological features, replication capacity of dominant Omicron sublineages BA.1, BA.2 and BA.5 in the human nasal epithelium, and characterized their pathogenicity in K18-hACE2, A129, young C57BL/6, and aged C57BL/6 mice. FINDINGS We found that BA.5 replicated most robustly, followed by BA.2 and BA.1, in the differentiated human nasal epithelium. Consistently, BA.5 infection resulted in higher viral gene copies, infectious viral titres and more abundant viral antigen expression in the nasal turbinates of the infected K18-hACE2 transgenic mice. In contrast, the Omicron sublineages are continuously attenuated in lungs of infected K18-hACE2 and C57BL/6 mice, leading to decreased pathogenicity. Nevertheless, lung manifestations remain severe in Omicron sublineages-infected A129 and aged C57BL/6 mice. INTERPRETATION Our results suggested that the Omicron sublineages might be gaining intrinsic replication fitness in the upper respiratory tract, therefore highlighting the importance of global surveillance of the emergence of hyper-transmissive Omicron sublineages. On the contrary, replication and intrinsic pathogenicity of Omicron is suggested to be further attenuated in the lower respiratory tract. Effective vaccination and other precautions should be in place to prevent severe infections in the immunocompromised populations at risk. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.
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Affiliation(s)
- Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Bingjie Hu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yue Chai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Chaemin Yoon
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huan Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Tianrenzheng Zhu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jing-Chu Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ye-Fan Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yuxin Hou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Terrence Tsz-Tai Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yang Wang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jinjin Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yao Xia
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lin-Lei Chen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Anna Jinxia Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Bao-Zhong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
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Chen S, Huang Z, Guo Y, Guo H, Jian L, Xiao J, Yao X, Yu H, Cheng T, Zhang Y, Guan M, Mao R, Zhang J, Xia N, Yuan Q. Evolving spike mutations in SARS-CoV-2 Omicron variants facilitate evasion from breakthrough infection-acquired antibodies. Cell Discov 2023; 9:86. [PMID: 37596249 PMCID: PMC10439137 DOI: 10.1038/s41421-023-00584-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/08/2023] [Indexed: 08/20/2023] Open
Affiliation(s)
- Shiqi Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Yue Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Huilin Guo
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Lijuan Jian
- Department of Pulmonary Diseases, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jin Xiao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Xiangyang Yao
- Department of Pulmonary Diseases, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Hai Yu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Tong Cheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Yali Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China.
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Richeng Mao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
| | - Jiming Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China.
| | - Quan Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China.
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49
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Zhang D, Wang C, Yuan T, Li X, Yang L, Huang A, Li J, Liu M, Lei Y, Sun L, Zhang J, Zhang L. Psychometric properties of the Coronavirus Anxiety Scale based on Classical Test Theory (CTT) and Item Response Theory (IRT) models among Chinese front-line healthcare workers. BMC Psychol 2023; 11:224. [PMID: 37550697 PMCID: PMC10405510 DOI: 10.1186/s40359-023-01251-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/14/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Since March 2022, the COVID-19 epidemic has rebounded widely and frequently in China. Healthcare workers have faced grand challenges such as soaring COVID-19 patients, being busy with the nucleic acid screening of all the populations in the epidemic areas every day, and testing positive for COVID-19, all of which contributed to anxiety easily according to the Conservation of Resources theory. However, anxiety among healthcare workers is not only associated with personal health but also adversely affects the quality of health services. Therefore, it is crucial to search for suitable tools to monitor the anxiety related to COVID-19 among healthcare workers. The current study aimed to test the Coronavirus Anxiety Scale (CAS) in Chinese healthcare workers. METHODS The current study employed a cross-sectional design. The CAS was translated into Chinese. Then, according to Classical Test Theory (CTT) and Item Response Theory (IRT) models, the psychometric properties of the Chinese version were measured among 811 healthcare workers. RESULTS The split-half reliability was 0.855. The Cronbach's α coefficient was 0.895. The retest coefficient was 0.901 with 10 days as the retest interval. The content validity index was 0.920. In exploratory factor analysis, one common factor was extracted and explained 72.559% of the total variance. All item load values on the common factor ranged from 0.790 to 0.885, and the communality of each item ranged from 0.625 to 0.784. With confirmatory factor analysis, the single factor model showed an excellent goodness-of-fit, chi-square/degree of freedom (χ2/df) = 3.339, goodness of fit index (GFI) = 0.992, adjusted goodness of fit index (AGFI) = 0.975, root-mean-square error of approximation (RMSEA) = 0.054, root mean square residual (RMR) = 0.005, incremental fit index (IFI) = 0.967, Tucker-Lewis index (TLI) = 0.932, and comparative fit index (CFI) = 0.966. The multiple-group confirmatory factor analysis revealed the invariance measuring anxiety of COVID-19 was in similar ways across ages, hospital degrees, and professional titles. With convergent validity, the CAS was positively correlated with post-traumatic stress disorder (r = 0.619, P < 0.001), fear of COVID (r = 0.550, P < 0.001), and depression (r = 0.367, P < 0.001). According to IRT models, the results showed that all item discrimination parameters were higher than 1.70 and difficulty parameters ranged from 1.13 to 2.83. CONCLUSION The Chinese version of CAS has good psychometric properties in healthcare workers after China adjusted the COVID-19 management measures during the COVID-19 Omicron epidemic, and can be used for assessing the anxiety associated with COVID-19 in Chinese healthcare workers.
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Affiliation(s)
- Dongmei Zhang
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Congzhi Wang
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Ting Yuan
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Xiaoping Li
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Liu Yang
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Anle Huang
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Jing Li
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Mingming Liu
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Yunxiao Lei
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Lu Sun
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China
| | - Jing Zhang
- Nursing Department, the People's Hospital of Yingshang, 566 Ganluo Road, Chengbei New District, Yingshang County, Anhui Province, Fuyang, P.R. China.
| | - Lin Zhang
- School of Nursing, Wannan Medical College, 22 Wenchang West Road, Higher Education Park, Anhui Province, Wuhu City, P.R. China.
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50
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Zhang J, Zhu A, Mei M, Qu J, Huang Y, Shi Y, Xue M, Zhang J, Zhang R, Zhou B, Tan X, Zhao J, Wang Y. Repurposing CRISPR/Cas to Discover SARS-CoV-2 Detecting and Neutralizing Aptamers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300656. [PMID: 37204115 PMCID: PMC10401102 DOI: 10.1002/advs.202300656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/07/2023] [Indexed: 05/20/2023]
Abstract
RNA aptamers provide useful biological probes and therapeutic agents. New methodologies to screen RNA aptamers will be valuable by complementing the traditional Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Meanwhile, repurposing clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated systems (Cas) has expanded their utility far beyond their native nuclease function. Here, CRISmers, a CRISPR/Cas-based novel screening system for RNA aptamers based on binding to a chosen protein of interest in a cellular context, is presented. Using CRISmers, aptamers are identified specifically targeting the receptor binding domain (RBD) of the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two aptamer leads enable sensitive detection and potent neutralization of SARS-CoV-2 Delta and Omicron variants in vitro. Intranasal administration of one aptamer, further modified with 2'-fluoro pyrimidines (2'-F), 2'-O-methyl purines (2'-O), and conjugation with both cholesterol and polyethylene glycol of 40 kDa (PEG40K), achieves effective prophylactic and therapeutic antiviral activity against live Omicron BA.2 variants in vivo. The study concludes by demonstrating the robustness, consistency, and potential broad utility of CRISmers using two newly identified aptamers but switching CRISPR, selection marker, and host species.
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Affiliation(s)
- Ju Zhang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100005China
- College of Life Sciences and OceanographyShenzhen UniversityShenzhen518060China
| | - Airu Zhu
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510120China
| | - Miao Mei
- Tsinghua‐Peking Center for Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center for Biological StructureMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologySchool of Pharmaceutical SciencesCenter for infectious Disease ResearchSchool of MedicineTsinghua UniversityBeijing100084China
| | - Jing Qu
- Institute of Pathogenic OrganismsShenzhen Center for Disease Control and PreventionShenzhen518055China
| | - Yalan Huang
- Institute of Pathogenic OrganismsShenzhen Center for Disease Control and PreventionShenzhen518055China
| | - Yongshi Shi
- College of Life Sciences and OceanographyShenzhen UniversityShenzhen518060China
| | - Meiying Xue
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100005China
| | - Jingfang Zhang
- College of Life Sciences and OceanographyShenzhen UniversityShenzhen518060China
- School of Life SciencesBeijing University of Chinese MedicineBeijing100105China
| | - Renli Zhang
- Institute of Pathogenic OrganismsShenzhen Center for Disease Control and PreventionShenzhen518055China
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100005China
| | - Xu Tan
- Tsinghua‐Peking Center for Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center for Biological StructureMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologySchool of Pharmaceutical SciencesCenter for infectious Disease ResearchSchool of MedicineTsinghua UniversityBeijing100084China
| | - Jincun Zhao
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510120China
| | - Yu Wang
- College of Life Sciences and OceanographyShenzhen UniversityShenzhen518060China
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