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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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Dai B, Ji W, Zhu P, Han S, Chen Y, Jin Y. Update on Omicron variant and its threat to vulnerable populations. PUBLIC HEALTH IN PRACTICE 2024; 7:100494. [PMID: 38584806 PMCID: PMC10998192 DOI: 10.1016/j.puhip.2024.100494] [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: 05/19/2023] [Revised: 02/20/2024] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Objective To reduce the incidence of severe illness and fatalities, and promote the awareness of protection and precaution, increased vaccination, strengthen the physical fitness, frequent ventilation, and health education should be enhanced among vulnerable populations as essential measures for the future control of COVID-19. Study design Systematic review. Method The search was done using PubMed, EMBASE and Web of Science for studies without language restrictions, published up through March 2023, since their authoritative and comprehensive literature search database. Eighty articles were included. Extraction of articles and quality assessment of included reviews was performed independently by two authors using the AMSTAR 2 score. Results The articles in the final data set included research on epidemiological characteristics, pathogenicity, available vaccines, treatments and epidemiological features in special populations including the elders, pregnant women, kids, people with chronic diseases concerning Omicron. Conclusion Although less pathogenic potential is found in Omicron, highly mutated forms have enhanced the ability of immune evasion and resistance to existing vaccines compared with former variants. Severe complications and outcomes may occur in vulnerable populations. Infected pregnant women are more likely to give birth prematurely, and fatal implications in children infected with Omicron are hyperimmune response and severe neurological disorders. In immunocompromised patients, there is a greater reported mortality and complication compared to patients with normal immune systems. Therefore, maintain social distancing, wear masks, and receive vaccinations are effective long-term measures.
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Affiliation(s)
- Bowen Dai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Wangquan Ji
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Peiyu Zhu
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Shujie Han
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yu Chen
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yuefei Jin
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
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Wen Q, Guo Z, Zhang XH, Xu LP, Wang Y, Yan CH, Chen H, Chen YH, Han W, Wang FR, Sun YQ, Huang XJ, Mo XD. COVID-19 was associated with the complications after allogeneic hematopoietic stem cell transplantation. Sci Rep 2024; 14:11778. [PMID: 38782966 PMCID: PMC11116404 DOI: 10.1038/s41598-024-62731-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/21/2024] [Indexed: 05/25/2024] Open
Abstract
We aimed to identify the severity and duration of COVID-19 infection on complications after allo-HSCT. Enrolled 179 hospitalized patients with COVID-19 were categorized into long-term infection (> 18 days, n = 90) or short-term infection group (≤ 18 days, n = 89) according to the median duration of COVID-19. The severity of COVID-19 was categorized as asymptomatic infection, mild, moderate, severe, and critical illness according to guidelines of National Institutes of Health. Particularly, severe illness and critical illness were classified as serious infection. Asymptomatic infection, mild illness and moderate illness were classified as non-serious infection. The 150-day probabilities of poor graft function (PGF), cytomegalovirus (CMV) pneumonia and non-relapse mortality (NRM) were significantly higher in long-term infection group. The 150-day probabilities of CMV pneumonia and NRM after COVID-19 were higher in serious infection group. The 150-day probabilities of overall survival (OS) was significantly lower in long-term and serious infection group. In multivariable analysis, the severity of COVID-19 was associated with NRM and OS, and the duration of COVID-19 was associated with PGF. In summary, our data reported that the severity and duration of COVID-19 were associated with several complications and contribute to poor outcomes after allo-HSCT.
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Affiliation(s)
- Qi Wen
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Ze Guo
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Xiao-Hui Zhang
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Lan-Ping Xu
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Yu Wang
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Chen-Hua Yan
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Huan Chen
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Yu-Hong Chen
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Wei Han
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Feng-Rong Wang
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Yu-Qian Sun
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Xiao-Jun Huang
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, Beijing, 2019RU029, China
| | - Xiao-Dong Mo
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China.
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, Beijing, 2019RU029, China.
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4
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Otter CJ, Renner DM, Fausto A, Tan LH, Cohen NA, Weiss SR. Interferon signaling in the nasal epithelium distinguishes among lethal and common cold coronaviruses and mediates viral clearance. Proc Natl Acad Sci U S A 2024; 121:e2402540121. [PMID: 38758698 PMCID: PMC11127059 DOI: 10.1073/pnas.2402540121] [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: 02/05/2024] [Accepted: 03/27/2024] [Indexed: 05/19/2024] Open
Abstract
All respiratory viruses establish primary infections in the nasal epithelium, where efficient innate immune induction may prevent dissemination to the lower airway and thus minimize pathogenesis. Human coronaviruses (HCoVs) cause a range of pathologies, but the host and viral determinants of disease during common cold versus lethal HCoV infections are poorly understood. We model the initial site of infection using primary nasal epithelial cells cultured at an air-liquid interface (ALI). HCoV-229E, HCoV-NL63, and human rhinovirus-16 are common cold-associated viruses that exhibit unique features in this model: early induction of antiviral interferon (IFN) signaling, IFN-mediated viral clearance, and preferential replication at nasal airway temperature (33 °C) which confers muted host IFN responses. In contrast, lethal SARS-CoV-2 and MERS-CoV encode antagonist proteins that prevent IFN-mediated clearance in nasal cultures. Our study identifies features shared among common cold-associated viruses, highlighting nasal innate immune responses as predictive of infection outcomes and nasally directed IFNs as potential therapeutics.
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Affiliation(s)
- Clayton J. Otter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - David M. Renner
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Alejandra Fausto
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Li Hui Tan
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Noam A. Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Surgery, Corporal Michael J. Crescenz Department of Veterans Affairs Medical Center, Philadelphia, PA19104
- Monell Chemical Senses Center, Philadelphia, PA19104
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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5
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Takada K, Orba Y, Kida Y, Wu J, Ono C, Matsuura Y, Nakagawa S, Sawa H, Watanabe T. Genes involved in the limited spread of SARS-CoV-2 in the lower respiratory airways of hamsters may be associated with adaptive evolution. J Virol 2024; 98:e0178423. [PMID: 38624229 DOI: 10.1128/jvi.01784-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
Novel respiratory viruses can cause a pandemic and then evolve to coexist with humans. The Omicron strain of severe acute respiratory syndrome coronavirus 2 has spread worldwide since its emergence in late 2021, and its sub-lineages are now established in human society. Compared to previous strains, Omicron is markedly less invasive in the lungs and causes less severe disease. One reason for this is that humans are acquiring immunity through previous infection and vaccination, but the nature of the virus itself is also changing. Using our newly established low-volume inoculation system, which reflects natural human infection, we show that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain. Furthermore, by characterizing chimeric viruses with the Omicron gene in the Wuhan strain genetic background and vice versa, we found that viral genes downstream of ORF3a, but not the S gene, were responsible for the limited spread of the Omicron strain in the lower airways of the virus-infected hamsters. Moreover, molecular evolutionary analysis of SARS-CoV-2 revealed a positive selection of genes downstream of ORF3a (M and E genes). Our findings provide insight into the adaptive evolution of the virus in humans during the pandemic convergence phase.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread worldwide since its emergence in late 2021, and its sub-lineages are established in human society. Compared to previous strains, the Omicron strain is less invasive in the lower respiratory tract, including the lungs, and causes less severe disease; however, the mechanistic basis for its restricted replication in the lower airways is poorly understood. In this study, using a newly established low-volume inoculation system that reflects natural human infection, we demonstrated that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain and found that viral genes downstream of ORF3a are responsible for replication restriction in the lower respiratory tract of Omicron-infected hamsters. Furthermore, we detected a positive selection of genes downstream of ORF3a (especially the M and E genes) in SARS-CoV-2, suggesting that these genes may undergo adaptive changes in humans.
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Grants
- 16H06429, 16K21723, 16H06434, JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP16K21723, JP16H06432 MEXT | Japan Society for the Promotion of Science (JSPS)
- 22K15469, 21J01036 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20fk0108281, JP19fk0108113, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP23wm0125008, JP223fa627005 Japan Agency for Medical Research and Development (AMED)
- JP19fk018113, JP223fa627002h, 22gm1610010h0001 Japan Agency for Medical Research and Development (AMED)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
- JPMJCR20H6 MEXT | Japan Science and Technology Agency (JST)
- Takeda Science Foundation (TSF)
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Affiliation(s)
- Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yurie Kida
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hirofumi Sawa
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Virus Network, Baltimore, Maryland, USA
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
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6
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Di Maio VC, Scutari R, Forqué L, Colagrossi L, Coltella L, Ranno S, Linardos G, Gentile L, Galeno E, Vittucci AC, Pisani M, Cristaldi S, Villani A, Raponi M, Bernaschi P, Russo C, Perno CF. Presence and Significance of Multiple Respiratory Viral Infections in Children Admitted to a Tertiary Pediatric Hospital in Italy. Viruses 2024; 16:750. [PMID: 38793631 PMCID: PMC11126044 DOI: 10.3390/v16050750] [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: 04/23/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Viral co-infections are frequently observed among children, but whether specific viral interactions enhance or diminish the severity of respiratory disease is still controversial. This study aimed to investigate the type of viral mono- and co-infections by also evaluating viral correlations in 3525 respiratory samples from 3525 pediatric in/outpatients screened by the Allplex Respiratory Panel Assays and with a Severe Acute Respiratory Syndrome-COronaVirus 2 (SARS-CoV-2) test available. Overall, viral co-infections were detected in 37.8% of patients and were more frequently observed in specimens from children with lower respiratory tract infections compared to those with upper respiratory tract infections (47.1% vs. 36.0%, p = 0.003). SARS-CoV-2 and influenza A were more commonly detected in mono-infections, whereas human bocavirus showed the highest co-infection rate (87.8% in co-infection). After analyzing viral pairings using Spearman's correlation test, it was noted that SARS-CoV-2 was negatively associated with all other respiratory viruses, whereas a markedly significant positive correlation (p < 0.001) was observed for five viral pairings (involving adenovirus/human bocavirus/human enterovirus/metapneumoviruses/rhinovirus). The correlation between co-infection and clinical outcome may be linked to the type of virus(es) involved in the co-infection rather than simple co-presence. Further studies dedicated to this important point are needed, since it has obvious implications from a diagnostic and clinical point of view.
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Affiliation(s)
- Velia Chiara Di Maio
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Rossana Scutari
- Multimodal Laboratory Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Lorena Forqué
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Luna Colagrossi
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Luana Coltella
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Stefania Ranno
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Giulia Linardos
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Leonarda Gentile
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Eugenia Galeno
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Anna Chiara Vittucci
- Hospital University Pediatrics Clinical Area, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy (S.C.)
| | - Mara Pisani
- Hospital University Pediatrics Clinical Area, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy (S.C.)
| | - Sebastian Cristaldi
- Hospital University Pediatrics Clinical Area, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy (S.C.)
| | - Alberto Villani
- Hospital University Pediatrics Clinical Area, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy (S.C.)
| | - Massimiliano Raponi
- Medical Direction, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Paola Bernaschi
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Cristina Russo
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (V.C.D.M.)
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7
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Zhang L, Dopfer-Jablonka A, Nehlmeier I, Kempf A, Graichen L, Calderón Hampel N, Cossmann A, Stankov MV, Morillas Ramos G, Schulz SR, Jäck HM, Behrens GMN, Pöhlmann S, Hoffmann M. Virological Traits of the SARS-CoV-2 BA.2.87.1 Lineage. Vaccines (Basel) 2024; 12:487. [PMID: 38793739 PMCID: PMC11125805 DOI: 10.3390/vaccines12050487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/21/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Transmissibility and immune evasion of the recently emerged, highly mutated SARS-CoV-2 BA.2.87.1 are unknown. Here, we report that BA.2.87.1 efficiently enters human cells but is more sensitive to antibody-mediated neutralization than the currently dominating JN.1 variant. Acquisition of adaptive mutations might thus be needed for efficient spread in the population.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
| | - Amy Kempf
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Noemí Calderón Hampel
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
| | - Metodi V. Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
| | - Gema Morillas Ramos
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
| | - Sebastian R. Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany (H.-M.J.)
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany (H.-M.J.)
| | - Georg M. N. Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30625 Hannover, Germany
- Center for Individualized Infection Medicine (CiiM), 30625 Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
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8
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Zhao L, Wang C, Song J, Jiang P. Examining the potential risk factors for variable airflow limitation in patients recovering from SARS-CoV-2 Omicron variant infection: A case-control study. Am J Infect Control 2024; 52:541-545. [PMID: 38036179 DOI: 10.1016/j.ajic.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND The Omicron strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally. However, it remains uncertain whether variable airflow limitation (VAL) occurs during the recovery phase after contracting the Omicron variant. To address this question, we conducted a study to examine the occurrence of VAL in patients infected with the Omicron variant (BA.1) of SARS-CoV-2, and we also investigated the potential risk factors associated with this phenomenon. METHODS We summarized and analyzed data taken from the electronic health records of recovering patients who had contracted the Omicron variant. The information was obtained from the Shuixi Branch of our Hospital during the period from January 22 to February 24, 2022. We focused on examining the occurrence of VAL and identifying the associated risk factors among these patients. RESULTS In this case-control study, a total of 176 patients were enrolled. The occurrence of VAL was observed in 9.66% (17 individuals). Patients with VAL showed significantly elevated levels of the modified Borg dyspnea score, daytime cough score, night-time cough score, chest computed tomography severity score, and Treg ratio compared to those without VAL. Additionally, patients with VAL had a lower 6MWD value compared to those without it. Logistic regression analysis demonstrated that the modified Borg dyspnea score independently increased the risk of Omicron infection with VAL, with an odds ratio of 3.375, and a 95% confidence interval ranging from 1.537 to 7.408, with a P-value of .002. CONCLUSIONS There is a possibility of experiencing VAL in certain patients recovering from the SARS-CoV-2 Omicron variant infection. The modified Borg dyspnea score has been identified as a standalone risk factor for the occurrence of VAL in SARS-CoV-2 Omicron infection.
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Affiliation(s)
- Lihong Zhao
- Department of Respiratory and Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China
| | - Chunfang Wang
- Department of Respiratory and Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China
| | - Jinxin Song
- Department of Respiratory and Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China
| | - Ping Jiang
- Department of Respiratory and Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China.
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9
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Johannesen N, Tang-Andersen Martinello A, Meyer BB, Vestergaard ET, Andersen AL, Jensen TL. Substantial transmission of SARS-CoV-2 through casual contact in retail stores: Evidence from matched administrative microdata on card payments and testing. Proc Natl Acad Sci U S A 2024; 121:e2317589121. [PMID: 38630715 PMCID: PMC11047087 DOI: 10.1073/pnas.2317589121] [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: 10/10/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
This paper presents quasiexperimental evidence of Covid-19 transmission through casual contact between customers in retail stores. For a large sample of individuals in Denmark, we match card payment data, indicating exactly where and when each individual made purchases, with Covid-19 test data, indicating when each individual was tested and whether the test was positive. The resulting dataset identifies more than 100,000 instances where an infected individual made a purchase in a store and, in each instance, allows us to track the infection dynamics of other individuals who made purchases in the same store around the same time. We estimate transmissions by comparing the infection rate of exposed customers, who made a purchase within 5 min of an infected individual, and nonexposed customers, who made a purchase in the same store 16 to 30 min before. We find that exposure to an infected individual in a store increases the infection rate by around 0.12 percentage points (P < 0.001) between day 3 and day 7 after exposure. The estimates imply that transmissions in stores contributed around 0.04 to the reproduction number for the average infected individual and significantly more in the period where Omicron was the dominant variant.
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Affiliation(s)
- Niels Johannesen
- Saïd Business School, Oxford University, OxfordOX1 1HP, United Kingdom
- Department of Economics, University of Copenhagen, CopenhagenK 1353, Denmark
- Center for Economic Behavior and Inequality, University of Copenhagen, CopenhagenK 1353, Denmark
| | | | | | | | - Asger Lau Andersen
- Department of Economics, University of Copenhagen, CopenhagenK 1353, Denmark
- Center for Economic Behavior and Inequality, University of Copenhagen, CopenhagenK 1353, Denmark
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10
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Scheim DE, Parry PI, Rabbolini DJ, Aldous C, Yagisawa M, Clancy R, Borody TJ, Hoy WE. Back to the Basics of SARS-CoV-2 Biochemistry: Microvascular Occlusive Glycan Bindings Govern Its Morbidities and Inform Therapeutic Responses. Viruses 2024; 16:647. [PMID: 38675987 PMCID: PMC11054389 DOI: 10.3390/v16040647] [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: 03/14/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Consistent with the biochemistry of coronaviruses as well established over decades, SARS-CoV-2 makes its initial attachment to host cells through the binding of its spike protein (SP) to sialylated glycans (containing the monosaccharide sialic acid) on the cell surface. The virus can then slide over and enter via ACE2. SARS-CoV-2 SP attaches particularly tightly to the trillions of red blood cells (RBCs), platelets and endothelial cells in the human body, each cell very densely coated with sialic acid surface molecules but having no ACE2 or minimal ACE2. These interlaced attachments trigger the blood cell aggregation, microvascular occlusion and vascular damage that underlie the hypoxia, blood clotting and related morbidities of severe COVID-19. Notably, the two human betacoronaviruses that express a sialic acid-cleaving enzyme are benign, while the other three-SARS, SARS-CoV-2 and MERS-are virulent. RBC aggregation experimentally induced in several animal species using an injected polysaccharide caused most of the same morbidities of severe COVID-19. This glycan biochemistry is key to disentangling controversies that have arisen over the efficacy of certain generic COVID-19 treatment agents and the safety of SP-based COVID-19 vaccines. More broadly, disregard for the active physiological role of RBCs yields unreliable or erroneous reporting of pharmacokinetic parameters as routinely obtained for most drugs and other bioactive agents using detection in plasma, with whole-blood levels being up to 30-fold higher. Appreciation of the active role of RBCs can elucidate the microvascular underpinnings of other health conditions, including cardiovascular disease, and therapeutic opportunities to address them.
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Affiliation(s)
- David E. Scheim
- US Public Health Service, Commissioned Corps, Inactive Reserve, Blacksburg, VA 24060, USA
| | - Peter I. Parry
- Children’s Health Research Clinical Unit, Faculty of Medicine, The University of Queensland, South Brisbane, QLD 4101, Australia;
- Department of Psychiatry, Flinders University, Bedford Park, SA 5042, Australia
| | - David J. Rabbolini
- Kolling Institute, Faculty of Medicine and Health, The University of Sydney, St Leonards, NSW 2064, Australia
| | - Colleen Aldous
- College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa;
| | - Morimasa Yagisawa
- Satoshi Omura Memorial Research Institute, Kitasato University, Tokyo 108-8641, Japan
- Louis Pasteur Center for Medical Research, Kyoto 606-8225, Japan
| | - Robert Clancy
- Emeritus Professor, School of Medicine and Public Health, University of Newcastle, Newcastle, NE1 7RU, Australia
| | | | - Wendy E. Hoy
- Emeritus Professor of Medicine, University of Queensland, Herston, QLD 4029, Australia
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11
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Chávez-Vélez E, Álvarez-Nava F, Torres-Vinueza A, Balarezo-Díaz T, Pilataxi K, Acosta-López C, Peña IZ, Narváez K. Single nucleotide variants in the CCL2, OAS1 and DPP9 genes and their association with the severity of COVID-19 in an Ecuadorian population. Front Cell Infect Microbiol 2024; 14:1322882. [PMID: 38694517 PMCID: PMC11061356 DOI: 10.3389/fcimb.2024.1322882] [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: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 05/04/2024] Open
Abstract
COVID-19 has a broad clinical spectrum, ranging from asymptomatic-mild form to severe phenotype. The severity of COVID-19 is a complex trait influenced by various genetic and environmental factors. Ethnic differences have been observed in relation to COVID-19 severity during the pandemic. It is currently unknown whether genetic variations may contribute to the increased risk of severity observed in Latin-American individuals The aim of this study is to investigate the potential correlation between gene variants at CCL2, OAS1, and DPP9 genes and the severity of COVID-19 in a population from Quito, Ecuador. This observational case-control study was conducted at the Carrera de Biologia from the Universidad Central del Ecuador and the Hospital Quito Sur of the Instituto Ecuatoriano de Seguridad Social (Quito-SUR-IESS), Quito, Ecuador. Genotyping for gene variants at rs1024611 (A>G), rs10774671 (A>G), and rs10406145 (G>C) of CCL2, OAS1, and DPP9 genes was performed on 100 COVID-19 patients (43 with severe form and 57 asymptomatic-mild) using RFLP-PCR. The genotype distribution of all SNVs throughout the entire sample of 100 individuals showed Hardy Weinberg equilibrium (P=0.53, 0.35, and 0.4 for CCL2, OAS1, and DPP9, respectively). The HWE test did not find any statistically significant difference in genotype distribution between the study and control groups for any of the three SNVs. The multivariable logistic regression analysis showed that individuals with the GG of the CCL2 rs1024611 gene variant had an increased association with the severe COVID-19 phenotype in a recessive model (P = 0.0003, OR = 6.43, 95% CI 2.19-18.89) and for the OAS1 rs10774671 gene variant, the log-additive model showed a significant association with the severe phenotype of COVID-19 (P=0.0084, OR=3.85, 95% CI 1.33-11.12). Analysis of haplotype frequencies revealed that the coexistence of GAG at CCL2, OAS1, and DPP9 variants, respectively, in the same individual increased the presence of the severe COVID-19 phenotype (OR=2.273, 95% CI: 1.271-4.068, P=0.005305). The findings of the current study suggests that the ethnic background affects the allele and genotype frequencies of genes associated with the severity of COVID-19. The experience with COVID-19 has provided an opportunity to identify an ethnicity-based approach to recognize genetically high-risk individuals in different populations for emerging diseases.
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Affiliation(s)
- Erik Chávez-Vélez
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Francisco Álvarez-Nava
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Alisson Torres-Vinueza
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Thalía Balarezo-Díaz
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Kathya Pilataxi
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Camila Acosta-López
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Ivonne Z. Peña
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
| | - Katherin Narváez
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
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12
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Kawasuji H, Morinaga Y, Nagaoka K, Tani H, Yoshida Y, Yamada H, Takegoshi Y, Kaneda M, Murai Y, Kimoto K, Niimi H, Yamamoto Y. High interleukin-6 levels induced by COVID-19 pneumonia correlate with increased circulating follicular helper T cell frequency and strong neutralization antibody response in the acute phase of Omicron breakthrough infection. Front Immunol 2024; 15:1377014. [PMID: 38694512 PMCID: PMC11061453 DOI: 10.3389/fimmu.2024.1377014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
Background Acute immune responses to coronavirus disease 2019 (COVID-19) are influenced by variants, vaccination, and clinical severity. Thus, the outcome of these responses may differ between vaccinated and unvaccinated patients and those with and without COVID-19-related pneumonia. In this study, these differences during infection with the Omicron variant were investigated. Methods A total of 67 patients (including 47 vaccinated and 20 unvaccinated patients) who were hospitalized within 5 days after COVID-19 symptom onset were enrolled in this prospective observational study. Serum neutralizing activity was evaluated using a pseudotyped virus assay and serum cytokines and chemokines were measured. Circulating follicular helper T cell (cTfh) frequencies were evaluated using flow cytometry. Results Twenty-five patients developed COVID-19 pneumonia on hospitalization. Although the neutralizing activities against wild-type and Delta variants were higher in the vaccinated group, those against the Omicron variant as well as the frequency of developing pneumonia were comparable between the vaccinated and unvaccinated groups. IL-6 and CXCL10 levels were higher in patients with pneumonia than in those without it, regardless of their vaccination status. Neutralizing activity against the Omicron variant were higher in vaccinated patients with pneumonia than in those without it. Moreover, a distinctive correlation between neutralizing activity against Omicron, IL-6 levels, and cTfh proportions was observed only in vaccinated patients. Conclusions The present study demonstrates the existence of a characteristic relationship between neutralizing activity against Omicron, IL-6 levels, and cTfh proportions in Omicron breakthrough infection.
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Affiliation(s)
- Hitoshi Kawasuji
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yoshitomo Morinaga
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Kentaro Nagaoka
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Hideki Tani
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Yoshihiro Yoshida
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Hiroshi Yamada
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yusuke Takegoshi
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Makito Kaneda
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yushi Murai
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Kou Kimoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yoshihiro Yamamoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
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13
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Sim JK, Lee HS, Yang J, Gwack J, Kim BI, Cha JO, Min KH, Lee YS. Comparative Analysis of Clinical Outcomes Using Propensity Score Matching: Coronavirus Disease 2019 vs. Seasonal Influenza in Korea. J Korean Med Sci 2024; 39:e128. [PMID: 38622937 PMCID: PMC11018986 DOI: 10.3346/jkms.2024.39.e128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND The advent of the omicron variant and the formulation of diverse therapeutic strategies marked a new epoch in the realm of coronavirus disease 2019 (COVID-19). Studies have compared the clinical outcomes between COVID-19 and seasonal influenza, but such studies were conducted during the early stages of the pandemic when effective treatment strategies had not yet been developed, which limits the generalizability of the findings. Therefore, an updated evaluation of the comparative analysis of clinical outcomes between COVID-19 and seasonal influenza is requisite. METHODS This study used data from the severe acute respiratory infection surveillance system of South Korea. We extracted data for influenza patients who were infected between 2018 and 2019 and COVID-19 patients who were infected in 2021 (pre-omicron period) and 2022 (omicron period). Comparisons of outcomes were conducted among the pre-omicron, omicron, and influenza cohorts utilizing propensity score matching. The adjusted covariates in the propensity score matching included age, sex, smoking, and comorbidities. RESULTS The study incorporated 1,227 patients in the pre-omicron cohort, 1,948 patients in the omicron cohort, and 920 patients in the influenza cohort. Following propensity score matching, 491 patients were included in each respective group. Clinical presentations exhibited similarities between the pre-omicron and omicron cohorts; however, COVID-19 patients demonstrated a higher prevalence of dyspnea and pulmonary infiltrates compared to their influenza counterparts. Both COVID-19 groups exhibited higher in-hospital mortality and longer hospital length of stay than the influenza group. The omicron group showed no significant improvement in clinical outcomes compared to the pre-omicron group. CONCLUSION The omicron group did not demonstrate better clinical outcomes than the pre-omicron group, and exhibited significant disease severity compared to the influenza group. Considering the likely persistence of COVID-19 infections, it is imperative to sustain comprehensive studies and ongoing policy support for the virus to enhance the prognosis for individuals affected by COVID-19.
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Affiliation(s)
- Jae Kyeom Sim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Hye Sun Lee
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Korea
| | - Juyeon Yang
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Korea
| | - Jin Gwack
- Division of Infectious Disease Control, Bureau of Infectious Disease Policy, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - Bryan Inho Kim
- Division of Infectious Disease Control, Bureau of Infectious Disease Policy, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - Jeong-Ok Cha
- Division of Infectious Disease Control, Bureau of Infectious Disease Policy, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - Kyung Hoon Min
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Young Seok Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea.
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14
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Meyerowitz EA, Li Y. Review: The Landscape of Antiviral Therapy for COVID-19 in the Era of Widespread Population Immunity and Omicron-Lineage Viruses. Clin Infect Dis 2024; 78:908-917. [PMID: 37949817 DOI: 10.1093/cid/ciad685] [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: 09/11/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
The goals of coronavirus disease 2019 (COVID-19) antiviral therapy early in the pandemic were to prevent severe disease, hospitalization, and death. As these outcomes have become infrequent in the age of widespread population immunity, the objectives have shifted. For the general population, COVID-19-directed antiviral therapy should decrease symptom severity and duration and minimize infectiousness, and for immunocompromised individuals, antiviral therapy should reduce severe outcomes and persistent infection. The increased recognition of virologic rebound following ritonavir-boosted nirmatrelvir (NMV/r) and the lack of randomized controlled trial data showing benefit of antiviral therapy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection for standard-risk, vaccinated individuals remain major knowledge gaps. Here, we review data for selected antiviral agents and immunomodulators currently available or in late-stage clinical trials for use in outpatients. We do not review antibody products, convalescent plasma, systemic corticosteroids, IL-6 inhibitors, Janus kinase inhibitors, or agents that lack Food and Drug Administration approval or emergency use authorization or are not appropriate for outpatients.
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Affiliation(s)
- Eric A Meyerowitz
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Yijia Li
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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15
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Zhang X, Luo F, Zhang H, Guo H, Zhou J, Li T, Chen S, Song S, Shen M, Wu Y, Gao Y, Han X, Wang Y, Hu C, Zhao X, Guo H, Zhang D, Lu Y, Wang W, Wang K, Tang N, Jin T, Ding M, Luo S, Lin C, Lu T, Lu B, Tian Y, Yang C, Cheng G, Yang H, Jin A, Ji X, Gong R, Chiu S, Huang A. Prophylactic efficacy of an intranasal spray with 2 synergetic antibodies neutralizing Omicron. JCI Insight 2024; 9:e171034. [PMID: 38587080 PMCID: PMC11128199 DOI: 10.1172/jci.insight.171034] [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: 04/05/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDAs Omicron is prompted to replicate in the upper airway, neutralizing antibodies (NAbs) delivered through inhalation might inhibit early-stage infection in the respiratory tract. Thus, elucidating the prophylactic efficacy of NAbs via nasal spray addresses an important clinical need.METHODSThe applicable potential of a nasal spray cocktail containing 2 NAbs was characterized by testing its neutralizing potency, synergetic neutralizing mechanism, emergency protective and therapeutic efficacy in a hamster model, and pharmacokinetics/pharmacodynamic (PK/PD) in human nasal cavity.RESULTSThe 2 NAbs displayed broad neutralizing efficacy against Omicron, and they could structurally compensate each other in blocking the Spike-ACE2 interaction. When administrated through the intranasal mucosal route, this cocktail demonstrated profound efficacy in the emergency prevention in hamsters challenged with authentic Omicron BA.1. The investigator-initiated trial in healthy volunteers confirmed the safety and the PK/PD of the NAb cocktail delivered via nasal spray. Nasal samples from the participants receiving 4 administrations over a course of 16 hours demonstrated potent neutralization against Omicron BA.5 in an ex vivo pseudovirus neutralization assay.CONCLUSIONThese results demonstrate that the NAb cocktail nasal spray provides a good basis for clinical prophylactic efficacy against Omicron infections.TRIAL REGISTRATIONwww.chictr.org.cn, ChiCTR2200066525.FUNDINGThe National Science and Technology Major Project (2017ZX10202203), the National Key Research and Development Program of China (2018YFA0507100), Guangzhou National Laboratory (SRPG22-015), Lingang Laboratory (LG202101-01-07), Science and Technology Commission of Shanghai Municipality (YDZX20213100001556), and the Emergency Project from the Science & Technology Commission of Chongqing (cstc2021jscx-fyzxX0001).
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Affiliation(s)
- Xinghai Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Feiyang Luo
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Huajun Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Junhui Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Li
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Shaohong Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuyi Song
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Meiying Shen
- Department of Endocrine Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Wu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Xiaojian Han
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Yingming Wang
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Chao Hu
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | | | | | | | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | | | - Kai Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ni Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Tengchuan Jin
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | | | - Shuhui Luo
- Mindao Haoyue Co., Ltd., Chongqing, China
| | - Cuicui Lin
- Mindao Haoyue Co., Ltd., Chongqing, China
| | | | - Bingxia Lu
- Mindao Haoyue Co., Ltd., Chongqing, China
| | - Yang Tian
- Mindao Haoyue Co., Ltd., Chongqing, China
| | | | | | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Aishun Jin
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
- Institute of Life Sciences, and
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China
| | - Rui Gong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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16
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McMurry AJ, Zipursky AR, Geva A, Olson KL, Jones JR, Ignatov V, Miller TA, Mandl KD. Moving Biosurveillance Beyond Coded Data Using AI for Symptom Detection From Physician Notes: Retrospective Cohort Study. J Med Internet Res 2024; 26:e53367. [PMID: 38573752 PMCID: PMC11027052 DOI: 10.2196/53367] [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: 10/06/2023] [Revised: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Real-time surveillance of emerging infectious diseases necessitates a dynamically evolving, computable case definition, which frequently incorporates symptom-related criteria. For symptom detection, both population health monitoring platforms and research initiatives primarily depend on structured data extracted from electronic health records. OBJECTIVE This study sought to validate and test an artificial intelligence (AI)-based natural language processing (NLP) pipeline for detecting COVID-19 symptoms from physician notes in pediatric patients. We specifically study patients presenting to the emergency department (ED) who can be sentinel cases in an outbreak. METHODS Subjects in this retrospective cohort study are patients who are 21 years of age and younger, who presented to a pediatric ED at a large academic children's hospital between March 1, 2020, and May 31, 2022. The ED notes for all patients were processed with an NLP pipeline tuned to detect the mention of 11 COVID-19 symptoms based on Centers for Disease Control and Prevention (CDC) criteria. For a gold standard, 3 subject matter experts labeled 226 ED notes and had strong agreement (F1-score=0.986; positive predictive value [PPV]=0.972; and sensitivity=1.0). F1-score, PPV, and sensitivity were used to compare the performance of both NLP and the International Classification of Diseases, 10th Revision (ICD-10) coding to the gold standard chart review. As a formative use case, variations in symptom patterns were measured across SARS-CoV-2 variant eras. RESULTS There were 85,678 ED encounters during the study period, including 4% (n=3420) with patients with COVID-19. NLP was more accurate at identifying encounters with patients that had any of the COVID-19 symptoms (F1-score=0.796) than ICD-10 codes (F1-score =0.451). NLP accuracy was higher for positive symptoms (sensitivity=0.930) than ICD-10 (sensitivity=0.300). However, ICD-10 accuracy was higher for negative symptoms (specificity=0.994) than NLP (specificity=0.917). Congestion or runny nose showed the highest accuracy difference (NLP: F1-score=0.828 and ICD-10: F1-score=0.042). For encounters with patients with COVID-19, prevalence estimates of each NLP symptom differed across variant eras. Patients with COVID-19 were more likely to have each NLP symptom detected than patients without this disease. Effect sizes (odds ratios) varied across pandemic eras. CONCLUSIONS This study establishes the value of AI-based NLP as a highly effective tool for real-time COVID-19 symptom detection in pediatric patients, outperforming traditional ICD-10 methods. It also reveals the evolving nature of symptom prevalence across different virus variants, underscoring the need for dynamic, technology-driven approaches in infectious disease surveillance.
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Affiliation(s)
- Andrew J McMurry
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Amy R Zipursky
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
- Division of Pediatric Emergency Medicine, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Alon Geva
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
- Division of Critical Care Medicine, Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, MA, United States
- Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
| | - Karen L Olson
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - James R Jones
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
| | - Vladimir Ignatov
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
| | - Timothy A Miller
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
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17
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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18
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Gandikota C, Vaddadi K, Sivasami P, Huang C, Liang Y, Pushparaj S, Deng X, Channappanava R, Metcalf JP, Liu L. The use of human iPSC-derived alveolar organoids to explore SARS-CoV-2 variant infections and host responses. J Med Virol 2024; 96:e29579. [PMID: 38572923 DOI: 10.1002/jmv.29579] [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: 10/19/2023] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) primarily targets the respiratory system. Physiologically relevant human lung models are indispensable to investigate virus-induced host response and disease pathogenesis. In this study, we generated human induced pluripotent stem cell (iPSC)-derived alveolar organoids (AOs) using an established protocol that recapitulates the sequential steps of in vivo lung development. AOs express alveolar epithelial type II cell protein markers including pro-surfactant protein C and ATP binding cassette subfamily A member 3. Compared to primary human alveolar type II cells, AOs expressed higher mRNA levels of SARS-CoV-2 entry factors, angiotensin-converting enzyme 2 (ACE2), asialoglycoprotein receptor 1 (ASGR1) and basigin (CD147). Considering the localization of ACE2 on the apical side in AOs, we used three AO models, apical-in, sheared and apical-out for SARS-CoV-2 infection. All three models of AOs were robustly infected with the SARS-CoV-2 irrespective of ACE2 accessibility. Antibody blocking experiment revealed that ASGR1 was the main receptor for SARS-CoV2 entry from the basolateral in apical-in AOs. AOs supported the replication of SARS-CoV-2 variants WA1, Alpha, Beta, Delta, and Zeta and Omicron to a variable degree with WA1 being the highest and Omicron being the least. Transcriptomic profiling of infected AOs revealed the induction of inflammatory and interferon-related pathways with NF-κB signaling being the predominant host response. In summary, iPSC-derived AOs can serve as excellent human lung models to investigate infection of SARS-CoV-2 variants and host responses from both apical and basolateral sides.
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Affiliation(s)
- Chaitanya Gandikota
- Department of Physiological Sciences, The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Oklahoma State University, Stillwater, Oklahoma, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kishore Vaddadi
- Department of Physiological Sciences, The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Oklahoma State University, Stillwater, Oklahoma, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Pulavendran Sivasami
- Department of Physiological Sciences, The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Oklahoma State University, Stillwater, Oklahoma, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Chaoqun Huang
- Department of Physiological Sciences, The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Oklahoma State University, Stillwater, Oklahoma, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Yurong Liang
- Department of Physiological Sciences, The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Oklahoma State University, Stillwater, Oklahoma, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Samuel Pushparaj
- Department of Physiological Sciences, The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Oklahoma State University, Stillwater, Oklahoma, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Xufang Deng
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Rudragouda Channappanava
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jordan P Metcalf
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Pulmonary and Critical Care Division, Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Lin Liu
- Department of Physiological Sciences, The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Oklahoma State University, Stillwater, Oklahoma, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
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19
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Du P, Huang L, Fang Y, Zhao F, Li Q, Ma X, Li R, Chen Q, Shen H, Wang Q, Li H, Gao GF. Broad-spectrum Delta-BA.2 tandem-fused heterodimer mRNA vaccine delivered by lipopolyplex. PLoS Pathog 2024; 20:e1012116. [PMID: 38557908 PMCID: PMC11008869 DOI: 10.1371/journal.ppat.1012116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/11/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continues to mutate and generates new variants with increasingly severe immune escape, urging the upgrade of COVID-19 vaccines. Here, based on a similar dimeric RBD design as our previous ZF2001 vaccine, we developed a novel broad-spectrum COVID-19 mRNA vaccine, SWIM516, with chimeric Delta-BA.2 RBD dimer delivered by lipopolyplex (LPP). Unlike the popular lipid nanoparticle (LNP), this LPP-delivered mRNA expresses only in the injection site, which avoids potential toxicity to the liver. We demonstrated the broad-spectrum humoral and cellular immunogenicity of this vaccine to Delta and Omicron sub-variants in naïve mice and as booster shots. When challenged with Delta or Omicron live virus, vaccinated human angiotensin-converting enzyme (hACE2) transgenic mice and rhesus macaques were both protected, displaying significantly reduced viral loads and markedly relieved pathological damages. We believe the SWIM516 vaccine qualifies as a candidate for the next-generation broad-spectrum COVID-19 vaccine.
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Affiliation(s)
- Pei Du
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Lei Huang
- Stemirna Therapeutics, Shanghai, China
| | - Yi Fang
- Stemirna Therapeutics, Shanghai, China
| | | | | | - Xuehui Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ruiqi Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qian Chen
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | | | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Medical School, University of Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | | | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Medical School, University of Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
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20
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Fan S, Mo X, Zhang X, Xu L, Wang Y, Yan C, Chen H, Zhang Y, Cheng Y, Sun Y, Chen Y, Chen Y, Han W, Wang J, Wang F, Xu Z, Huang X. Clinical characteristics and outcomes of allogeneic hematopoietic stem cell transplantation recipients with coronavirus disease 2019 caused by the Omicron variant: a prospective, observational cohort study. Ann Hematol 2024; 103:1333-1344. [PMID: 38381172 DOI: 10.1007/s00277-024-05653-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
We aimed to describe the clinical characteristics, particularly the occurrence and risk factors of severe/critical illness, in allogeneic hematopoietic stem cell (allo-HSCT) recipients infected with coronavirus disease 2019 (COVID-19) caused by Omicron variant in an observational prospective study (n = 311). The median time from allo-HSCT to COVID-19 diagnosis was 8.5 months (range 0.8-106.1) months. Four patients (1.3%) were reported to be asymptomatic during Omicron variant infection, and 135 (43.4%) patients showed lower respiratory tract disease. Thirty-four (10.9%) patients were categorized into serious infection (severe illness n = 25; critical illness n = 9) and the median duration from COVID-19 diagnosis to serious infections was 6 days (range, 0-29) days. Thirteen (4.2%) and 6 (1.9%) patients required intensive care unit care and invasive mechanical ventilation, respectively. Receiving more than 1 type of immunosuppressive therapies at COVID-19 diagnosis was associated with severity and persistence of infection. Six patients (1.9%) died after diagnosis of COVID-19 infection. The 4-week probability of overall survival after COVID-19 diagnosis was 98.7%, which was 100% and 88.2% for non-serious and serious infection group (P < 0.001), respectively. Thus, we observed a relatively low serious infection and mortality rate in allo-HSCT recipients infected with COVID-19 caused by Omicron variant.
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Affiliation(s)
- Shuang Fan
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Xiaodong Mo
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, Beijing, 2019RU029, China
| | - Xiaohui Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - LanPing Xu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yu Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Chenhua Yan
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Huan Chen
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yuanyuan Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yifei Cheng
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yuqian Sun
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yuhong Chen
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yao Chen
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Wei Han
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Jingzhi Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Fengrong Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Zhengli Xu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Xiaojun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China.
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, Beijing, 2019RU029, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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21
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Zhang Q, Pavlinov I, Ye Y, Zheng W. Therapeutic development targeting host heparan sulfate proteoglycan in SARS-CoV-2 infection. Front Med (Lausanne) 2024; 11:1364657. [PMID: 38618194 PMCID: PMC11014733 DOI: 10.3389/fmed.2024.1364657] [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: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024] Open
Abstract
The global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an urgent need for effective therapeutic options. SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic that has resulted in significant morbidity and mortality worldwide. The virus is known to enter host cells by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, and emerging evidence suggests that heparan sulfate proteoglycans (HSPGs) play a crucial role in facilitating this process. HSPGs are abundant cell surface proteoglycan present in many tissues, including the lung, and have been shown to interact directly with the spike protein of SARS-CoV-2. This review aims to summarize the current understanding of the role of HSPGs in SARS-CoV-2 infection and the potential of developing new therapies targeting HSPGs.
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Affiliation(s)
- Qi Zhang
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Ivan Pavlinov
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Wei Zheng
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
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22
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Shawe-Taylor M, Greenwood D, Hobbs A, Dowgier G, Penn R, Sanderson T, Stevenson-Leggett P, Bazire J, Harvey R, Libri V, Kassiotis G, Gamblin S, Lewis NS, Williams B, Swanton C, Gandhi S, Carr EJ, Wu MY, Bauer DLV, Wall EC. Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign. Lancet 2024; 403:1133-1136. [PMID: 38484752 DOI: 10.1016/s0140-6736(24)00316-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Affiliation(s)
- Marianne Shawe-Taylor
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | | | | | | | | | | | | | | | - Ruth Harvey
- Worldwide Influenza Centre, London NW1 1AT, UK
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - George Kassiotis
- The Francis Crick Institute, London NW1 1AT, UK; Department of Infectious Disease, St Mary's Hospital, Imperial College London, London, UK
| | | | | | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Edward J Carr
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Mary Y Wu
- The Francis Crick Institute, London NW1 1AT, UK
| | - David L V Bauer
- The Francis Crick Institute, London NW1 1AT, UK; Genotype-to-Phenotype 2 Consortium (G2P2-UK), UK
| | - Emma C Wall
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK.
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23
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Li Y, Hu H, Liu J, Ma L, Wang X, Liu L, Liu Q, Ren L, Li J, Deng F, Hu Z, Zhou Y, Wang M. Crucial role played by CK8 + cells in mediating alveolar injury remodeling for patients with COVID-19. Virol Sin 2024:S1995-820X(24)00033-6. [PMID: 38521412 DOI: 10.1016/j.virs.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 03/25/2024] Open
Abstract
The high risk of SARS-CoV-2 infection and reinfection and the occurrence of post-acute pulmonary sequelae have highlighted the importance of understanding the mechanism underlying lung repair after injury. To address this concern, comparative and systematic analyses of SARS-CoV-2 infection in COVID-19 patients and animals were conducted. In the lungs of nine patients who died of COVID-19 and one recovered from COVID-19 but died of unrelated disease in early 2020, damage-related transient progenitor (DATP) cells expressing CK8 marker proliferated significantly. These CK8+ DATP cells were derived from bronchial CK5+ basal cells. However, they showed different cell fate toward differentiation into type I alveolar cells in the deceased and convalescent patients, respectively. By using a self-limiting hamster infection model mimicking the dynamic process of lung injury remodeling in mild COVID-19 patients, the accumulation and regression of CK8+ cell marker were found to be closely associated with the disease course. Finally, we examined the autopsied lungs of two patients who died of infection by the recent Omicron variant and found that they only exhibited mild pathological injury with no CK8+ cell proliferation. These results indicate a clear pulmonary cell remodeling route and suggest that CK8+ DATP cells play a primary role in mediating alveolar remodeling, highlighting their potential applications as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Yufeng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hengrui Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jia Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Longda Ma
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Xi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Liang Liu
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Qian Liu
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Liang Ren
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Jiang Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yiwu Zhou
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430010, China.
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
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24
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Amblard F, LeCher JC, De R, Zhou S, Liu P, Goh SL, Tao S, Patel D, Downs-Bowen J, Zandi K, Zhang H, Chaudhry G, McBrayer T, Muczynski M, Al-Homoudi A, Engel J, Lan S, Sarafianos SG, Kovari LC, Schinazi RF. Synthesis and biological evaluation of novel peptidomimetic inhibitors of the coronavirus 3C-like protease. Eur J Med Chem 2024; 268:116263. [PMID: 38432056 DOI: 10.1016/j.ejmech.2024.116263] [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: 12/13/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and related variants, are responsible for the devastating coronavirus disease 2019 (COVID-19) pandemic. The SARS-CoV-2 main protease (Mpro) plays a central role in the replication of the virus and represents an attractive drug target. Herein, we report the discovery of novel SARS-CoV-2 Mpro covalent inhibitors, including highly effective compound NIP-22c which displays high potency against several key variants and clinically relevant nirmatrelvir Mpro E166V mutants.
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Affiliation(s)
- Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
| | - Julia C LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shaoman Zhou
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Peng Liu
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Dharmeshkumar Patel
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Jessica Downs-Bowen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Huanchun Zhang
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Gitika Chaudhry
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Tamara McBrayer
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Michael Muczynski
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Abdullah Al-Homoudi
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Joseph Engel
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Shuiyun Lan
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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25
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Wang Z, Hu S, Popowski KD, Liu S, Zhu D, Mei X, Li J, Hu Y, Dinh PUC, Wang X, Cheng K. Inhalation of ACE2-expressing lung exosomes provides prophylactic protection against SARS-CoV-2. Nat Commun 2024; 15:2236. [PMID: 38472181 DOI: 10.1038/s41467-024-45628-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/24/2024] [Indexed: 03/14/2024] Open
Abstract
Continued emergence of SARS-CoV-2 variants of concern that are capable of escaping vaccine-induced immunity highlights the urgency of developing new COVID-19 therapeutics. An essential mechanism for SARS-CoV-2 infection begins with the viral spike protein binding to the human ACE2. Consequently, inhibiting this interaction becomes a highly promising therapeutic strategy against COVID-19. Herein, we demonstrate that ACE2-expressing human lung spheroid cells (LSC)-derived exosomes (LSC-Exo) could function as a prophylactic agent to bind and neutralize SARS-CoV-2, protecting the host against SARS-CoV-2 infection. Inhalation of LSC-Exo facilitates its deposition and biodistribution throughout the whole lung in a female mouse model. We show that LSC-Exo blocks the interaction of SARS-CoV-2 with host cells in vitro and in vivo by neutralizing the virus. LSC-Exo treatment protects hamsters from SARS-CoV-2-induced disease and reduced viral loads. Furthermore, LSC-Exo intercepts the entry of multiple SARS-CoV-2 variant pseudoviruses in female mice and shows comparable or equal potency against the wild-type strain, demonstrating that LSC-Exo may act as a broad-spectrum protectant against existing and emerging virus variants.
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Affiliation(s)
- Zhenzhen Wang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, P.R. China.
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA.
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University, Raleigh, NC, 27606, USA.
| | - Shiqi Hu
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA
| | - Kristen D Popowski
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University, Raleigh, NC, 27606, USA
| | - Shuo Liu
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA
| | - Dashuai Zhu
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA
| | - Xuan Mei
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University, Raleigh, NC, 27606, USA
| | - Junlang Li
- Xsome Biotech Inc., Raleigh, North Carolina, 27607, USA
| | - Yilan Hu
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA
| | - Phuong-Uyen C Dinh
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University, Raleigh, NC, 27606, USA
| | - Xiaojie Wang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, 325035, P.R. China.
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, P.R. China.
| | - Ke Cheng
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA.
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26
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Xu F, Bai Y, Xie F, Liu D, Wang Z, Wang S. Postoperative morbidity and mortality of patients with COVID-19 undergoing cardiovascular surgery: an inverse propensity-weighted study : Postoperative outcomes of patients undergoing cardiovascular surgery during the COVID-19 pandemic. BMC Anesthesiol 2024; 24:98. [PMID: 38459441 PMCID: PMC10924331 DOI: 10.1186/s12871-024-02445-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND To evaluate the postoperative morbidity and mortality of patients undergoing cardiovascular surgery during the 2022 nationwide Omicron variant infection wave in China. METHODS This retrospective cohort study included 403 patients who underwent cardiovascular surgery for the first time during the 2022 wave of the pandemic within 1 month. Among them, 328 patients were preoperatively diagnosed with COVID-19 Omicron variant infection during the pandemic, and 75 patients were negative. The association between Omicron variant exposure and postoperative prognosis was explored by comparing patients with and without COVID-19 exposure. The primary outcome was in-hospital death after cardiovascular surgery. The secondary outcomes were major postoperative morbidity, including myocardial infarction (MI), acute kidney injury (AKI), postoperative mechanical ventilation hours, ICU stay hours, and postoperative length of stay. The data were analyzed using inverse probability of treatment weighting (IPTW) to minimize bias. RESULTS We identified 403 patients who underwent cardiovascular surgery, 328 (81.39%) had Omicron variant infections. In total, 10 patients died in the hospital. Omicron variant infection was associated with a much greater risk of death during cardiovascular surgery after adjustment for IPTW (2.8% vs. 1.3%, adjusted OR 2.185, 95%CI = 1.193 to 10.251, P = 0.041). For major postoperative morbidity, there were no significant differences in terms of myocardial infarction between the two groups (adjusted OR = 0.861, 95%CI = 0.444 to 1.657, P = 0.653), acute kidney injury (adjusted OR = 1.157, 95%CI = 0.287 to 5.155, P = 0.820), postoperative mechanical ventilation hours (B -0.375, 95%CI=-8.438 to 7.808, P = 0.939), ICU stay hours (B 2.452, 95%CI=-13.269 to 8.419, P = 0.660) or postoperative stay (B -1.118, 95%CI=-2.237 to 1.154, P = 0.259) between the two groups. CONCLUSION Perioperative COVID-19 infection was associated with an increased risk of in-hospital death among patients who underwent cardiovascular surgery during the Omicron variant wave of the pandemic.
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Affiliation(s)
- Fei Xu
- Department of Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yunbo Bai
- Department of Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Fang Xie
- Department of Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Daqi Liu
- Department of Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Zhaoqi Wang
- Department of Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Sheng Wang
- Department of Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
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27
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Tang S, Lin G, Wu X, Chen Z. SARS-CoV-2 infection increases airway bleeding risk in patients after tracheostomies. Virol J 2024; 21:61. [PMID: 38454485 PMCID: PMC10921690 DOI: 10.1186/s12985-024-02320-2] [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: 12/20/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Airway bleeding events are a rare incident in SARS-CoV-2-infected patients after tracheostomies. We aimed to explore the correlation between airway bleeding and SARS-CoV-2 infection and evaluate the consistency of SARS-CoV-2 RNA test results in the upper and lower airway samples from patients after tracheostomies. METHODS Forty-four patients after temporary or permanent tracheostomy were divided into a positive group (29 patients) and a negative group (15 patients) based on the SARS-CoV-2 RNA test results of their oropharyngeal swabs. The oropharyngeal and tracheal swabs of the positive group were re-collected for SARS-CoV-2 RNA detection. Demographic and clinical characteristics and airway bleeding events were recorded for all enrolled patients. RESULTS Airway bleeding was reported in eleven patients of the positive group (11/29), with seven displaying bloody sputum or hemoptysis, and four featuring massive sputum crust formation in the trachea that resulted in dyspnea, and only one patient in the negative group (1/15), with a significant difference in the airway bleeding rate (37.9% vs. 6.7%, p < 0.05). The SARS-CoV-2 RNA test results showed a statistical difference in cycle threshold (Ct) values between oropharyngeal swabs and tracheal swabs (p < 0.05). CONCLUSIONS After tracheostomies, patients are more susceptible to airway bleeding if they are infected with SARS-CoV-2. The findings signify that in addition to droplet transmission through tracheostoma, SARS-CoV-2 may infect the oropharynx by airborne and close contact transmission, and that given the higher viral load and longer infection time in the trachea, tracheal swabs are more reliable for SARS-CoV-2 detection in these patients.
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Affiliation(s)
- Shupin Tang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Otorhinolaryngology Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Fujian Institute of Otorhinolaryngology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Gongbiao Lin
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Otorhinolaryngology Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Institute of Otorhinolaryngology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
| | - Xiaobo Wu
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Otorhinolaryngology Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Fujian Institute of Otorhinolaryngology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Zhihong Chen
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Otorhinolaryngology Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Fujian Institute of Otorhinolaryngology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
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28
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Miyashita N, Nakamori Y, Ogata M, Fukuda N, Yamura A, Ito T. Aspiration pneumonia was the most frequent cause of death in older patients with SARS-CoV-2 omicron-related pneumonia in Japan. J Am Geriatr Soc 2024. [PMID: 38450705 DOI: 10.1111/jgs.18852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
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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Fang X, Shi F, Liu F, Wei Y, Li J, Wu J, Wang T, Lu J, Shao C, Bian Y. Tracheal computed tomography radiomics model for prediction of the Omicron variant of severe acute respiratory syndrome coronavirus 2. RADIOLOGIE (HEIDELBERG, GERMANY) 2024:10.1007/s00117-024-01275-3. [PMID: 38446170 DOI: 10.1007/s00117-024-01275-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/11/2024] [Indexed: 03/07/2024]
Abstract
OBJECTIVES The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, fast-spreading, and insidious. Most patients present with normal findings on lung computed tomography (CT). The current study aimed to develop and validate a tracheal CT radiomics model to predict Omicron variant infection. MATERIALS AND METHODS In this retrospective study, a radiomics model was developed based on a training set consisting of 157 patients with an Omicron variant infection and 239 healthy controls between 1 January and 30 April 2022. A set of morphological expansions, with dilations of 1, 3, 5, 7, and 9 voxels, was applied to the trachea, and radiomic features were extracted from different dilation voxels of the trachea. Logistic regression (LR), support vector machines (SVM), and random forests (RF) were developed and evaluated; the models were validated on 67 patients with the Omicron variant and on 103 healthy controls between 1 May and 30 July 2022. RESULTS Logistic regression with 12 radiomic features extracted from the tracheal wall with dilation of 5 voxels achieved the highest classification performance compared with the other models. The LR model achieved an area under the curve of 0.993 (95% confidence interval [CI]: 0.987-0.998) in the training set and 0.989 (95% CI: 0.979-0.999) in the validation set. Sensitivity, specificity, and accuracy of the model for the training set were 0.994, 0.946, and 0.965, respectively, whereas those for the validation set were 0.970, 0.952, and 0.959, respectively. CONCLUSION The tracheal CT radiomics model reliably identified the Omicron variant of SARS-CoV‑2, and may help in clinical decision-making in future, especially in cases of normal lung CT findings.
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Affiliation(s)
- Xu Fang
- Department of Radiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, 200433, Shanghai, China
| | - Feng Shi
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Fang Liu
- Department of Radiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, 200433, Shanghai, China
| | - Ying Wei
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Jing Li
- Department of Radiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, 200433, Shanghai, China
| | - Jiaojiao Wu
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Tiegong Wang
- Department of Radiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, 200433, Shanghai, China
| | - Jianping Lu
- Department of Radiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, 200433, Shanghai, China
| | - Chengwei Shao
- Department of Radiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, 200433, Shanghai, China.
| | - Yun Bian
- Department of Radiology, Changhai Hospital, Naval Medical University, 168 Changhai Road, 200433, Shanghai, China.
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30
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Li Y, Jiang X, Qiu Y, Gao F, Xin H, Li D, Qin Y, Li Z. Latent and incubation periods of Delta, BA.1, and BA.2 variant cases and associated factors: a cross-sectional study in China. BMC Infect Dis 2024; 24:294. [PMID: 38448822 PMCID: PMC10916204 DOI: 10.1186/s12879-024-09158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The latent and incubation periods characterize the transmission of infectious viruses and are the basis for the development of outbreak prevention and control strategies. However, systematic studies on the latent period and associated factors with the incubation period for SAS-CoV-2 variants are still lacking. We inferred the two durations of Delta, BA.1, and BA.2 cases and analyzed the associated factors. METHODS The Delta, BA.1, and BA.2 (and its lineages BA.2.2 and BA.2.76) cases with clear transmission chains and infectors from 10 local SAS-CoV-2 epidemics in China were enrolled. The latent and incubation periods were fitted by the Gamma distribution, and associated factors were analyzed using the accelerated failure time model. RESULTS The mean latent period for 672 Delta, 208 BA.1, and 677 BA.2 cases was 4.40 (95%CI: 4.24 ~ 4.63), 2.50 (95%CI: 2.27 ~ 2.76), and 2.58 (95%CI: 2.48 ~ 2.69) days, respectively, with 85.65% (95%CI: 83.40 ~ 87.77%), 97.80% (95%CI: 96.35 ~ 98.89%), and 98.87% (95%CI: 98.40 ~ 99.27%) of them starting to shed viruses within 7 days after exposure. In 405 Delta, 75 BA.1, and 345 BA.2 symptomatic cases, the mean latent period was 0.76, 1.07, and 0.79 days shorter than the mean incubation period [5.04 (95%CI: 4.83 ~ 5.33), 3.42 (95%CI: 3.00 ~ 3.89), and 3.39 (95%CI: 3.24 ~ 3.55) days], respectively. No significant difference was observed in the two durations between BA.1 and BA.2 cases. After controlling for the sex, clinical severity, vaccination history, number of infectors, the length of exposure window and shedding window, the latent period [Delta: exp(β) = 0.81, 95%CI: 0.66 ~ 0.98, p = 0.034; Omicron: exp(β) = 0.82, 95%CI: 0.71 ~ 0.94, p = 0.004] and incubation period [Delta: exp(β) = 0.69, 95%CI: 0.55 ~ 0.86, p < 0.001; Omicron: exp(β) = 0.83, 95%CI: 0.72 ~ 0.96, p = 0.013] were significantly shorter in 18 ~ 49 years but did not change significantly in ≥ 50 years compared with 0 ~ 17 years. CONCLUSION Pre-symptomatic transmission can occur in Delta, BA.1, and BA.2 cases. The latent and incubation periods between BA.1 and BA.2 were similar but shorter compared with Delta. Age may be associated with the latent and incubation periods of SARS-CoV-2.
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Affiliation(s)
- Yu Li
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xinli Jiang
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yan Qiu
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Feng Gao
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hualei Xin
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- School of Population Medicine and Public Health, Chinese Academy of Medical Science (CAMS), Peking Union Medical College (PUMC), No. 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Dan Li
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ying Qin
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhongjie Li
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- School of Population Medicine and Public Health, Chinese Academy of Medical Science (CAMS), Peking Union Medical College (PUMC), No. 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China.
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Zhang Y, Li Q, Xiang JL, Li XH, Li J. Comparison of Computed Tomography and Clinical Features Between Patients Infected with the SARS-CoV-2 Omicron Variant and the Original Strain. Infect Drug Resist 2024; 17:807-818. [PMID: 38476766 PMCID: PMC10929164 DOI: 10.2147/idr.s448713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Purpose To investigate potential differences in clinical and computed tomography (CT) features between patients with the SARS-CoV-2 Omicron variant and the original strain. Patients and Methods This retrospective study included 69 hospitalized patients infected with Omicron variant from November to December 2022, and 96 hospitalized patients infected with the original strain from February to March 2020 in Chongqing, China. The clinical features, CT manifestations, degrees of lung involvement in different stages on CT, and imaging changes after the reverse-transcription polymerase chain reaction (RT-PCR) results turned negative were compared between the two groups. Results For clinical features, patients with Omicron were predominantly old people and females, without manifestation of any clinical symptoms, who had low serum levels of C-reactive protein and procalcitonin. Shorter interval from symptoms onset to initial CT scan was observed in Omicron patients compared to patients with the original strain (all P < 0.05). For CT features, patients with Omicron were more likely to present with round-like opacities and tree-in-bud pattern (all P < 0.05), but less likely to exhibit a diffuse distribution, patchy and linear opacities, as well as vascular enlargement pattern (all P < 0.05). The Omicron group was more susceptible to exhibiting lower CT involvement scores in each stage (all P < 0.05) and imaging progression after the RT-PCR results turned negative (P < 0.001). Conclusion Patients infected with the Omicron variant exhibited less severe changes on chest CT compared to those infected with the original strain. Furthermore, imaging progression under low viral load conditions was more common in patients with Omicron than in those with the original strain.
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Affiliation(s)
- Yue Zhang
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Qi Li
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Jiang-Lin Xiang
- Department of Infectious Disease, Chongqing University Three Gorges Hospital, Chongqing, 404000, People’s Republic of China
| | - Xing-Hua Li
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Jing Li
- Medical Department, Liangjiang New Area Renhe Community Health Service Center, Chongqing, 401147, People’s Republic of China
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Kimpel J, Rössler A, Bante D, Borena W, von Laer D, Zehetner C, Rauchegger T, Seiwald S, Falkensammer B. Detection of infectious SARS-CoV-2 in ocular samples is linked to viral load in the nasopharynx. Front Cell Infect Microbiol 2024; 14:1332157. [PMID: 38500504 PMCID: PMC10946250 DOI: 10.3389/fcimb.2024.1332157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/05/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction SARS-CoV-2 is known to infect respiratory tissue cells. However, less is known about infection of ocular tissue and potential infectivity of lacrimal fluid. With this study, we want to compare viral loads in eye and nasopharyngeal swabs and analyze these for infectious virus. Methods Between May 2020 and April 2021 ocular and nasopharyngeal swabs were collected from 28 SARS-CoV-2 infected patients treated on the corona virus disease 2019 (COVID-19)-ward of the University Hospital of Innsbruck, Austria. Samples with PCR detectable SARS-CoV-2 were analyzed via whole genome sequencing and an attempt was made to isolate infectious virus. Results At the time point of sample collection, 22 individuals were still PCR positive in nasopharyngeal samples and in 6 of these patients one or both ocular samples were additionally positive. CT-values in eyes were generally higher compared to corresponding nasopharyngeal samples and we observed a tendency for lower CT-values, i.e. increased viral load, in nasopharyngeal swabs of individuals with at least one infected eye, compared to those where ocular samples were PCR negative. Ocular and nasopharyngeal sequences from the same patient were assigned to the same variant, either the D614G or the Alpha variant. Infectious virus was successfully isolated from 9 nasopharyngeal swabs, however only from one of the seven PCR positive ocular samples. Conclusion We could detect SARS-CoV-2 in eyes of some of the infected patients albeit at lower levels compared to nasopharyngeal swabs. However, our results also indicate that lacrimal fluid might be infectious in patients with high viral load.
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Affiliation(s)
- Janine Kimpel
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Annika Rössler
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wegene Borena
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Claus Zehetner
- Department of Ophthalmology, Medical University of Innsbruck, Innsbruck, Austria
| | - Teresa Rauchegger
- Department of Ophthalmology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefanie Seiwald
- Department of Internal Medicine III, Medical University of Innsbruck, Innsbruck, Austria
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Di Modugno F, Di Carlo A, Spada S, Palermo B, D'Ambrosio L, D'Andrea D, Morello G, Belmonte B, Sperduti I, Balzano V, Gallo E, Melchionna R, Panetta M, Campo G, De Nicola F, Goeman F, Antoniani B, Carpano S, Frigè G, Warren S, Gallina F, Lambrechts D, Xiong J, Vincent BG, Wheeler N, Bortone DS, Cappuzzo F, Facciolo F, Tripodo C, Visca P, Nisticò P. Tumoral and stromal hMENA isoforms impact tertiary lymphoid structure localization in lung cancer and predict immune checkpoint blockade response in patients with cancer. EBioMedicine 2024; 101:105003. [PMID: 38340557 PMCID: PMC10869748 DOI: 10.1016/j.ebiom.2024.105003] [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: 07/27/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Tertiary Lymphoid Structures (TLS) correlate with positive outcomes in patients with NSCLC and the efficacy of immune checkpoint blockade (ICB) in cancer. The actin regulatory protein hMENA undergoes tissue-specific splicing, producing the epithelial hMENA11a linked to favorable prognosis in early NSCLC, and the mesenchymal hMENAΔv6 found in invasive cancer cells and pro-tumoral cancer-associated fibroblasts (CAFs). This study investigates how hMENA isoforms in tumor cells and CAFs relate to TLS presence, localization and impact on patient outcomes and ICB response. METHODS Methods involved RNA-SEQ on NSCLC cells with depleted hMENA isoforms. A retrospective observational study assessed tissues from surgically treated N0 patients with NSCLC, using immunohistochemistry for tumoral and stromal hMENA isoforms, fibronectin, and TLS presence. ICB-treated patient tumors were analyzed using Nanostring nCounter and GeoMx spatial transcriptomics. Multiparametric flow cytometry characterized B cells and tissue-resident memory T cells (TRM). Survival and ICB response were estimated in the cohort and validated using bioinformatics pipelines in different datasets. FINDINGS Findings indicate that hMENA11a in NSCLC cells upregulates the TLS regulator LTβR, decreases fibronectin, and favors CXCL13 production by TRM. Conversely, hMENAΔv6 in CAFs inhibits LTβR-related NF-kB pathway, reduces CXCL13 secretion, and promotes fibronectin production. These patterns are validated in N0 NSCLC tumors, where hMENA11ahigh expression, CAF hMENAΔv6low, and stromal fibronectinlow are associated with intratumoral TLS, linked to memory B cells and predictive of longer survival. The hMENA isoform pattern, fibronectin, and LTβR expression broadly predict ICB response in tumors where TLS indicates an anti-tumor immune response. INTERPRETATION This study uncovers hMENA alternative splicing as an unexplored contributor to TLS-related Tumor Immune Microenvironment (TIME) and a promising biomarker for clinical outcomes and likely ICB responsiveness in N0 patients with NSCLC. FUNDING This work is supported by AIRC (IG 19822), ACC (RCR-2019-23669120), CAL.HUB.RIA Ministero Salute PNRR-POS T4, "Ricerca Corrente" granted by the Italian Ministry of Health.
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Affiliation(s)
- Francesca Di Modugno
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
| | - Anna Di Carlo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Sheila Spada
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Belinda Palermo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Lorenzo D'Ambrosio
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Daniel D'Andrea
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, New Hall Block - Room 171, Clifton Campus - NG11 8NS, Nottingham, United Kingdom
| | - Gaia Morello
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Beatrice Belmonte
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Isabella Sperduti
- Biostatistics and Scientific Direction, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Vittoria Balzano
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Enzo Gallo
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Roberta Melchionna
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Mariangela Panetta
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Giulia Campo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Francesca De Nicola
- SAFU Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Frauke Goeman
- SAFU Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Barbara Antoniani
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Silvia Carpano
- Second Division of Medical Oncology, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, Milan, Italy
| | - Sarah Warren
- NanoString Technologies Inc., 530 Fairview Ave N, Seattle, WA, 98109, USA
| | - Filippo Gallina
- Thoracic-Surgery Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Diether Lambrechts
- Center for Cancer Biology, Herestraat 49 box 912, VIB, 3000, Leuven, Belgium
| | - Jieyi Xiong
- Center for Cancer Biology, Herestraat 49 box 912, VIB, 3000, Leuven, Belgium
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Nathan Wheeler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Federico Cappuzzo
- Second Division of Medical Oncology, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Francesco Facciolo
- Thoracic-Surgery Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Paolo Visca
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Paola Nisticò
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
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Sindu D, Razia D, Bay C, Padiyar J, Grief K, Buddhdev B, Arjuna A, Abdelrazek H, Mohamed H, McAnally K, Omar A, Walia R, Schaheen L, Tokman S. Evolving impact of the COVID-19 pandemic on lung transplant recipients: A single-center experience. J Heart Lung Transplant 2024; 43:442-452. [PMID: 37852512 DOI: 10.1016/j.healun.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/19/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Lung transplant recipients (LTRs) are at increased risk of morbidity and mortality from coronavirus disease 2019 (COVID-19); however, the disease course has changed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants have mutated. We compared COVID-19-related clinical outcomes in LTRs at different stages of the pandemic. We also identified risk factors for developing severe COVID-19 independent of the dominant SARS-CoV-2 variant. METHODS This single-center, retrospective cohort study of LTRs with COVID-19 used Cox regression analyses and bootstrapping to identify factors affecting COVID-19 severity. RESULTS Between March 2020 and August 2022, 195 LTRs were diagnosed with COVID-19, almost half (89 [45.6%]) during the Omicron period. A total of 113 (58.5%) LTRs were hospitalized and 47 (24.1%) died. Age >65 years increased the risk of hospitalization and death. Although infection with the Omicron variant was associated with a lower risk of hospitalization, the median length of hospital stay (10 days, [interquartile range, 5-19]) was similar between the variants. Intensive care unit (ICU) admission and death were more common with the Delta variant but comparable between the original, Alpha, and Omicron variants. Remdesivir and molnupiravir reduced the risk of hospitalization, and monoclonal antibody therapy reduced the risk of ICU admission, intubation, and death. Vaccination and pre-exposure prophylaxis (PrEP) with tixagevimab-cilgavimab did not significantly reduce COVID-19-related ICU admission, intubation, or mortality among LTRs. CONCLUSIONS LTRs with COVID-19 continue to have high hospitalization rates and prolonged hospital stays, despite the reduced virulence of the Omicron variant. More effective PrEP and therapeutic interventions for COVID-19 among vulnerable patient groups are needed.
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Affiliation(s)
- Devika Sindu
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona
| | - Deepika Razia
- Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Curt Bay
- Department of Interdisciplinary Health Sciences, A. T. Still University, Phoenix, Arizona
| | - Josna Padiyar
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Katherine Grief
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona
| | - Bhuvin Buddhdev
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Ashwini Arjuna
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Hesham Abdelrazek
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Hesham Mohamed
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Kendra McAnally
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Ashraf Omar
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Rajat Walia
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Lara Schaheen
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Surgery, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona
| | - Sofya Tokman
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; Department of Medicine, Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, Arizona.
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van der Zwet W, Klomp-Berens E, Demandt A, Dingemans J, van der Veer B, van Alphen L, Dirks J, Savelkoul P. Analysis of two sequential SARS-CoV-2 outbreaks on a haematology-oncology ward and the role of infection prevention. Infect Prev Pract 2024; 6:100335. [PMID: 38292209 PMCID: PMC10826166 DOI: 10.1016/j.infpip.2023.100335] [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: 10/18/2023] [Accepted: 12/04/2023] [Indexed: 02/01/2024] Open
Abstract
Two SARS-CoV-2 nosocomial outbreaks occurred on the haematology ward of our hospital. Patients on the ward were at high risk for severe infection because of their immunocompromised status. Whole Genome Sequencing proved transmission of a particular SARS-CoV-2 variant in each outbreak. The first outbreak (20 patients/31 healthcare workers (HCW)) occurred in November 2020 and was caused by a variant belonging to lineage B.1.221. At that time, there were still uncertainties on mode of transmission of SARS-CoV-2, and vaccines nor therapy were available. Despite HCW wearing II-R masks in all patient contacts and FFP-2 masks during aerosol generating procedures (AGP), the outbreak continued. Therefore, extra measures were introduced. Firstly, regular PCR-screening of asymptomatic patients and HCW; positive patients were isolated and positive HCW were excluded from work as a rule and they were only allowed to resume their work if a follow-up PCR CT-value was ≥30 and were asymptomatic or having only mild symptoms. Secondly, the use of FFP-2 masks was expanded to some long-lasting, close-contact, non-AGPs. After implementing these measures, the incidence of new cases declined gradually. Thirty-seven percent of patients died due to COVID-19. The second outbreak (10 patients/2 HCW) was caused by the highly transmissible omicron BA.1 variant and occurred in February 2022, where transmission occurred on shared rooms despite the extra infection control measures. It was controlled much faster, and the clinical impact was low as the majority of patients was vaccinated; no patients died and symptoms were relatively mild in both patients and HCW.
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Affiliation(s)
- W.C. van der Zwet
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - E.A. Klomp-Berens
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - A.M.P. Demandt
- Division of Hematology, Department of Internal Medicine, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - J. Dingemans
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - B.M.J.W. van der Veer
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - L.B. van Alphen
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - J.A.M.C. Dirks
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - P.H.M. Savelkoul
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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Inokuchi S, Shimamoto K. Persistent Risk of Developing Autoimmune Diseases Associated With COVID-19: An Observational Study Using an Electronic Medical Record Database in Japan. J Clin Rheumatol 2024; 30:65-72. [PMID: 38190730 DOI: 10.1097/rhu.0000000000002054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
OBJECTIVE This study aimed to investigate the risk of developing autoimmune diseases associated with coronavirus disease 2019 (COVID-19) in Japan, including long-term risks and risks specific to different variants of concern. METHODS This observational study used an electronic medical record database in Japan. The COVID-19 group is composed of patients diagnosed with COVID-19, whereas the non-COVID-19 group had data sampled from the database. The outcomes of interest encompassed several autoimmune diseases, including rheumatoid arthritis, systemic sclerosis, and immunoglobulin G4-related disease, as well as a composite of these diseases (any autoimmune disease). We examined the relative risk of autoimmune diseases using standardized mortality ratio weighting and the Cox proportional hazards model. Subgroup analyses based on epidemic variants were performed. In addition, short- and long-term risks were investigated using piecewise constant hazard models. RESULTS A total of 90,855 COVID-19 and 459,827 non-COVID-19 patients were included between January 16, 2020, and December 31, 2022. The relative risk of any autoimmune disease was 2.32 (95% confidence interval, 2.08-2.60). All the investigated outcomes showed a significant risk associated with COVID-19. Several autoimmune diseases exhibit a risk associated with COVID-19 in the short to long term, and the long-term risk is substantial for systemic sclerosis and immunoglobulin G4-related disease. The variant-specific risk varied across outcomes. CONCLUSIONS COVID-19 is associated with an increased risk of developing autoimmune diseases in the Japanese population, and this effect persists for a long time. This study provides insights into the association between viral infections and autoimmunity.
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Affiliation(s)
- Shoichiro Inokuchi
- From the Research and Analytics Department, Real World Data Co, Ltd, Kyoto, Japan
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Chiyyeadu A, Asgedom G, Bruhn M, Rocha C, Schlegel TU, Neumann T, Galla M, Vollmer Barbosa P, Hoffmann M, Ehrhardt K, Ha TC, Morgan M, Schoeder CT, Pöhlmann S, Kalinke U, Schambach A. A tetravalent bispecific antibody outperforms the combination of its parental antibodies and neutralizes diverse SARS-CoV-2 variants. Clin Immunol 2024; 260:109902. [PMID: 38218210 DOI: 10.1016/j.clim.2024.109902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The devastating impact of COVID-19 on global health shows the need to increase our pandemic preparedness. Recombinant therapeutic antibodies were successfully used to treat and protect at-risk patients from COVID-19. However, the currently circulating Omicron subvariants of SARS-CoV-2 are largely resistant to therapeutic antibodies, and novel approaches to generate broadly neutralizing antibodies are urgently needed. Here, we describe a tetravalent bispecific antibody, A7A9 TVB, which actively neutralized many SARS-CoV-2 variants of concern, including early Omicron subvariants. Interestingly, A7A9 TVB neutralized more variants at lower concentration as compared to the combination of its parental monoclonal antibodies, A7K and A9L. A7A9 also reduced the viral load of authentic Omicron BA.1 virus in infected pseudostratified primary human nasal epithelial cells. Overall, A7A9 displayed the characteristics of a potent broadly neutralizing antibody, which may be suitable for prophylactic and therapeutic applications in the clinics, thus highlighting the usefulness of an effective antibody-designing approach.
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Affiliation(s)
- Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Girmay Asgedom
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany
| | - Cheila Rocha
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Tom U Schlegel
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Thomas Neumann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Katrin Ehrhardt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Teng-Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Clara T Schoeder
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Stefan Pöhlmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States of America.
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Sočan M, Mrzel M, Prosenc K, Korva M, Avšič-Županc T, Poljak M, Lunar MM, Zupanič T. Comparing COVID-19 severity in patients hospitalized for community-associated Delta, BA.1 and BA.4/5 variant infection. Front Public Health 2024; 12:1294261. [PMID: 38450129 PMCID: PMC10915065 DOI: 10.3389/fpubh.2024.1294261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Background Despite decreasing COVID-19 disease severity during the Omicron waves, a proportion of patients still require hospitalization and intensive care. Objective To compare demographic characteristics, comorbidities, vaccination status, and previous infections in patients hospitalized for community-associated COVID-19 (CAC) in predominantly Delta, Omicron BA.1 and BA.4/5 SARS-CoV-2 waves. Methods Data were extracted from three national databases-the National COVID-19 Database, National Vaccination Registry and National Registry of Hospitalizations. Results Among the hospitalized CAC patients analyzed in this study, 5,512 were infected with Delta, 1,120 with Omicron BA.1, and 1,143 with the Omicron BA.4/5 variant. The age and sex structure changed from Delta to BA.4/5, with the proportion of women (9.5% increase), children and adolescents (10.4% increase), and octa- and nonagenarians increasing significantly (24.5% increase). Significantly more patients had comorbidities (measured by the Charlson Comorbidity Index), 30.3% in Delta and 43% in BA.4/5 period. The need for non-invasive ventilatory support (NiVS), ICU admission, mechanical ventilation (MV), and in-hospital mortality (IHM) decreased from Delta to Omicron BA.4/5 period for 12.6, 13.5, 11.5, and 6.3%, respectively. Multivariate analysis revealed significantly lower odds for ICU admission (OR 0.68, CI 0.54-0.84, p < 0.001) and IHM (OR 0.74, CI 0.58-0.93, p = 0.011) during the Delta period in patients who had been fully vaccinated or boosted with a COVID-19 vaccine within the previous 6 months. In the BA.1 variant period, patients who had less than 6 months elapsed between the last vaccine dose and SARS-CoV-2 positivity had lower odds for MV (OR 0.38, CI 0.18-0.72, p = 0.005) and IHM (OR 0.56, CI 0.37- 0.83, p = 0.005), but not for NIVS or ICU admission. Conclusion The likelihood of developing severe CAC in hospitalized patients was higher in those with the Delta and Omicron BA.1 variant compared to BA.4/5.
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Affiliation(s)
- Maja Sočan
- National Institute of Public Health, Ljubljana, Slovenia
| | - Maja Mrzel
- National Institute of Public Health, Ljubljana, Slovenia
| | - Katarina Prosenc
- National Institute of Health, Environment and Food, Ljubljana, Slovenia
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja M. Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tina Zupanič
- National Institute of Public Health, Ljubljana, Slovenia
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Griggs EP, Mitchell PK, Lazariu V, Gaglani M, McEvoy C, Klein NP, Valvi NR, Irving SA, Kojima N, Stenehjem E, Crane B, Rao S, Grannis SJ, Embi PJ, Kharbanda AB, Ong TC, Natarajan K, Dascomb K, Naleway AL, Bassett E, DeSilva MB, Dickerson M, Konatham D, Fireman B, Allen KS, Barron MA, Beaton M, Arndorfer J, Vazquez-Benitez G, Garg S, Murthy K, Goddard K, Dixon BE, Han J, Grisel N, Raiyani C, Lewis N, Fadel WF, Stockwell MS, Mamawala M, Hansen J, Zerbo O, Patel P, Link-Gelles R, Adams K, Tenforde MW. Clinical Epidemiology and Risk Factors for Critical Outcomes Among Vaccinated and Unvaccinated Adults Hospitalized With COVID-19-VISION Network, 10 States, June 2021-March 2023. Clin Infect Dis 2024; 78:338-348. [PMID: 37633258 DOI: 10.1093/cid/ciad505] [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: 07/31/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND The epidemiology of coronavirus disease 2019 (COVID-19) continues to develop with emerging variants, expanding population-level immunity, and advances in clinical care. We describe changes in the clinical epidemiology of COVID-19 hospitalizations and risk factors for critical outcomes over time. METHODS We included adults aged ≥18 years from 10 states hospitalized with COVID-19 June 2021-March 2023. We evaluated changes in demographics, clinical characteristics, and critical outcomes (intensive care unit admission and/or death) and evaluated critical outcomes risk factors (risk ratios [RRs]), stratified by COVID-19 vaccination status. RESULTS A total of 60 488 COVID-19-associated hospitalizations were included in the analysis. Among those hospitalized, median age increased from 60 to 75 years, proportion vaccinated increased from 18.2% to 70.1%, and critical outcomes declined from 24.8% to 19.4% (all P < .001) between the Delta (June-December, 2021) and post-BA.4/BA.5 (September 2022-March 2023) periods. Hospitalization events with critical outcomes had a higher proportion of ≥4 categories of medical condition categories assessed (32.8%) compared to all hospitalizations (23.0%). Critical outcome risk factors were similar for unvaccinated and vaccinated populations; presence of ≥4 medical condition categories was most strongly associated with risk of critical outcomes regardless of vaccine status (unvaccinated: adjusted RR, 2.27 [95% confidence interval {CI}, 2.14-2.41]; vaccinated: adjusted RR, 1.73 [95% CI, 1.56-1.92]) across periods. CONCLUSIONS The proportion of adults hospitalized with COVID-19 who experienced critical outcomes decreased with time, and median patient age increased with time. Multimorbidity was most strongly associated with critical outcomes.
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Affiliation(s)
- Eric P Griggs
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Victoria Lazariu
- Department of Clinical Research, Westat, Inc, Rockville, Maryland, USA
| | - Manjusha Gaglani
- Section of Pediatric Infectious Diseases, Department of Pediatrics, Baylor Scott & White Health, Temple, Texas, USA
- Department of Medical Education, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Charlene McEvoy
- Department of Research, HealthPartners Institute, Minneapolis, Minnesota, USA
| | - Nicola P Klein
- Kaiser Permanente Vaccine Study Center, Division of Research, Kaiser Permanente Northern California, Oakland, USA
| | - Nimish R Valvi
- Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, Indiana, USA
| | - Stephanie A Irving
- Department of Science Programs, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Noah Kojima
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Edward Stenehjem
- Division of Infectious Diseases and Clinical Epidemiology, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Bradley Crane
- Department of Science Programs, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Suchitra Rao
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Shaun J Grannis
- Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, Indiana, USA
- Department of Family Medicine, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Peter J Embi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Anupam B Kharbanda
- Department of Emergency Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Toan C Ong
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
- Medical Informatics Services, New York-Presbyterian Hospital, New York, New York, USA
| | - Kristin Dascomb
- Division of Infectious Diseases and Clinical Epidemiology, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Allison L Naleway
- Department of Science Programs, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Elizabeth Bassett
- Department of Clinical Research, Westat, Inc, Rockville, Maryland, USA
| | - Malini B DeSilva
- Department of Research, HealthPartners Institute, Minneapolis, Minnesota, USA
| | - Monica Dickerson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Deepika Konatham
- Department of Research Analytics and Development, Baylor Scott & White Research Institute, Baylor Scott & White Health, Temple, Texas, USA
| | - Bruce Fireman
- Kaiser Permanente Vaccine Study Center, Division of Research, Kaiser Permanente Northern California, Oakland, USA
| | - Katie S Allen
- Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, Indiana, USA
- Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana, USA
| | - Michelle A Barron
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Maura Beaton
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
| | - Julie Arndorfer
- Division of Infectious Diseases and Clinical Epidemiology, Intermountain Healthcare, Salt Lake City, Utah, USA
| | | | - Shikha Garg
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kempapura Murthy
- Department of Research Analytics and Development, Baylor Scott & White Research Institute, Baylor Scott & White Health, Temple, Texas, USA
| | - Kristin Goddard
- Kaiser Permanente Vaccine Study Center, Division of Research, Kaiser Permanente Northern California, Oakland, USA
| | - Brian E Dixon
- Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, Indiana, USA
- Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana, USA
| | - Jungmi Han
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
| | - Nancy Grisel
- Division of Infectious Diseases and Clinical Epidemiology, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Chandni Raiyani
- Department of Research Analytics and Development, Baylor Scott & White Research Institute, Baylor Scott & White Health, Temple, Texas, USA
| | - Ned Lewis
- Kaiser Permanente Vaccine Study Center, Division of Research, Kaiser Permanente Northern California, Oakland, USA
| | - William F Fadel
- Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, Indiana, USA
- Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana, USA
| | - Melissa S Stockwell
- Division of Child & Adolescent Health, Department of Pediatrics, New York-Presbyterian Hospital, New York, New York, USA
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Population and Family Health, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Mufaddal Mamawala
- Department of Research Analytics and Development, Baylor Scott & White Research Institute, Baylor Scott & White Health, Temple, Texas, USA
| | - John Hansen
- Kaiser Permanente Vaccine Study Center, Division of Research, Kaiser Permanente Northern California, Oakland, USA
| | - Ousseny Zerbo
- Kaiser Permanente Vaccine Study Center, Division of Research, Kaiser Permanente Northern California, Oakland, USA
| | - Palak Patel
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ruth Link-Gelles
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katherine Adams
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark W Tenforde
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Wang CY, Kuo BS, Lee YH, Ho YH, Pan YH, Yang YT, Chang HC, Fu LF, Peng WJ. UB-612 pan-SARS-CoV-2 T cell immunity-promoting vaccine protects against COVID-19 moderate-severe disease. iScience 2024; 27:108887. [PMID: 38318376 PMCID: PMC10839960 DOI: 10.1016/j.isci.2024.108887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/08/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
UB-612 pan-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine targets the monomeric Spike S1-receptor binding domain (RBD) subunit protein along with five sequence-conserved T cell epitopes found on Spike S2 and non-Spike M and N proteins. UB-612 vaccination safely induces potent, broad, and long-lasting immunity against SARS-CoV-2. A phase-2 trial-extended observational study during the Omicron BA.2-/BA.5-dominated outbreak was conducted to investigate UB-612's protective effect against COVID-19 hospitalization and intensive care unit (ICU) admission (H-ICU). Additionally, memory viral-neutralizing titer and T cell immunity behind disease protection were explored. No cases of H-ICU were reported beyond 14 months post-second dose or beyond 10 months post-booster (third dose). The positive outcome correlates with strong cytotoxic CD8 T cell immunity, in line with the results of an ongoing phase-3 heterologous booster trial showing that UB-612 can enhance anti-BA.5 seroconversion rate and viral-neutralizing titer for mRNA, adeno-vectored, and virus-inactivated vaccine platforms. The UB-612 multitope vaccine may serve as an effective primer and booster for those at risk of SARS-CoV-2 infection.
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Sun J, Zhang H, Yang Z. A retrospective analysis of children with mild and asymptomatic Omicron infections under 14: A single-center study. Medicine (Baltimore) 2024; 103:e37149. [PMID: 38363889 PMCID: PMC10869072 DOI: 10.1097/md.0000000000037149] [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: 10/12/2023] [Accepted: 01/11/2024] [Indexed: 02/18/2024] Open
Abstract
Omicron BA.5 subvariant has been proven to be more transmissible than other Omicron subvariants. But the studies on the spread of the Omicron BA.5 subvariant in children are still limited. This study aimed to analyze the clinical features of children infected with Omicron BA.5.2 variant in the mobile cabin hospital and the influence factors of the infections. Children with mild and asymptomatic Omicron infections under 14 years old who were admitted to the mobile cabin hospital from October 30 to December 7, 2022 were retrospectively collected. A total of 741 children, 424 boys (57.2%) and 317 girls (42.8%) were enrolled, including 145 asymptomatic cases (22.7%) and 493 (77.3%) mild cases. Upper respiratory tract infection was the dominant manifestation. Fever was the most common presenting symptom (80.7%), followed by cough (52.5%). The average time to symptom disappearance was 3.76 days, and the average negative conversion time of nucleic acid was 12.3 days. Univariate analysis showed that the negative conversion time of nucleic acid differed significantly across the age groups. The multivariate analysis showed that the older the age, the longer the negative conversion time of nucleic acid. Among those with the negative conversion time of nucleic acid longer than 12 days, age was positively correlated to the negative conversion time of nucleic acid, while the number of vaccine doses received was negatively correlated to the negative conversion time of nucleic acid. Omicron infection occurred in children of any age group, with good prospect for recovery. Age and number of vaccine doses received were risk factors influencing the negative conversion time of nucleic acid.
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Affiliation(s)
- Jing Sun
- Department of Pediatrics, Lanzhou Chengguan District People’s Hospital, Lanzhou City, China
| | - Haiyan Zhang
- Department of Pediatrics, Lanzhou Chengguan District People’s Hospital, Lanzhou City, China
| | - Zhen Yang
- Department of Pediatrics, Lanzhou Maternal and Child Health Care Hospital, Lanzhou City, China
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Lan PD, Nissley DA, O'Brien EP, Nguyen TT, Li MS. Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2. J Chem Phys 2024; 160:055101. [PMID: 38310477 DOI: 10.1063/5.0188053] [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: 11/18/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
The binding of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein to the host cell receptor angiotensin-converting enzyme 2 (ACE2) is the first step in human viral infection. Therefore, understanding the mechanism of interaction between RBD and ACE2 at the molecular level is critical for the prevention of COVID-19, as more variants of concern, such as Omicron, appear. Recently, atomic force microscopy has been applied to characterize the free energy landscape of the RBD-ACE2 complex, including estimation of the distance between the transition state and the bound state, xu. Here, using a coarse-grained model and replica-exchange umbrella sampling, we studied the free energy landscape of both the wild type and Omicron subvariants BA.1 and XBB.1.5 interacting with ACE2. In agreement with experiment, we find that the wild type and Omicron subvariants have similar xu values, but Omicron binds ACE2 more strongly than the wild type, having a lower dissociation constant KD.
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Affiliation(s)
- Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Daniel A Nissley
- Department of Statistics, University of Oxford, Oxford Protein Bioinformatics Group, Oxford OX1 2JD, United Kingdom
| | - Edward P O'Brien
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
- Institute for Computational and Data Sciences, Penn State University, University Park, Pennsylvania 16802, USA
| | - Toan T Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems and Department of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University - Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 11400, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
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Li G, Wu J, Huang Y, Wang Q, Xing T, Ou T. Risk factors for SARS-CoV-2 pneumonia among renal transplant recipients in Beijing Omicron wave. Microbiol Spectr 2024; 12:e0300523. [PMID: 38230924 PMCID: PMC10846129 DOI: 10.1128/spectrum.03005-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024] Open
Abstract
The novel coronavirus disease-19 had become an unprecedented global health emergency, quickly expanding worldwide. Omicron (B.1.1.529), as a novel variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was initially identified in South Africa and Botswana. Renal transplant recipients (RTRs) are a special group and are more vulnerable to viral pneumonia. Thus, this study aimed to assess the incidence and risk factors of SARS-CoV-2 pneumonia that occurred in RTRs with Omicron infection. This single-center case-control study enrolled the RTRs who were diagnosed with SARS-CoV-2 infection by the SARS-CoV-2 nucleic acid test, which were divided into two groups according to the imaging features of SARS-CoV-2 pneumonia. The parameters were collected by questionnaires and analyzed using Statistical Product and Service Solutions. A total of 313 RTRs completed the questionnaires, and 131 were enrolled in this study with a mean age of 42.66 years. The incidence of SARS-CoV-2 pneumonia among the enrolled participants was 76.3%. The first symptoms included fever (89.3%), cough (93.1%), and expectoration (81.7%). From the comparison, the parameters such as age, gender, body mass index, lymphocyte count, and the percent of neutrophils and the basic serum creatinine before SARS-CoV-2 infection were significantly different between the two groups (P < 0.05). In multivariate analysis, age and the basic serum creatinine were independent risk factors for developing SARS-CoV-2 pneumonia (P < 0.05). Older RTRs with a high level of serum creatinine before SARS-CoV-2 infection were more at risk of developing SARS-CoV-2 pneumonia. More randomized controlled studies are needed.IMPORTANCEThis study aimed to assess the incidence and the risk factors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia that occurred in renal transplant recipients (RTRs) with Omicron infection. In conclusion, older RTRs with a high level of serum creatinine before SARS-CoV-2 infection were more at risk of developing SARS-CoV-2 pneumonia and should be timely treated, in case of severe pneumonia.
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Affiliation(s)
- Guangping Li
- Department of Urology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Jiangtao Wu
- Department of Urology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Ying Huang
- Department of Urology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Qi Wang
- Department of Urology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Tianying Xing
- Department of Urology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Tongwen Ou
- Department of Urology, Xuanwu Hospital Capital Medical University, Beijing, China
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Xu T, Chen Y, Zhan W, Chung KF, Qiu Z, Huang K, Chen R, Xie J, Wang G, Zhang M, Wang X, Yao H, Liao X, Zhang Y, Zhang G, Zhang W, Sun D, Zhu J, Jiang S, Feng J, Zhao J, Sun G, Huang H, Zhang J, Wang L, Wu F, Li S, Xu P, Chi C, Chen P, Jiang M, He W, Huang L, Luo W, Li S, Zhong N, Lai K. Profiles of Cough and Associated Risk Factors in Nonhospitalized Individuals With SARS-CoV-2 Omicron Variant Infection: Cross-Sectional Online Survey in China. JMIR Public Health Surveill 2024; 10:e47453. [PMID: 38315527 PMCID: PMC10877488 DOI: 10.2196/47453] [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: 03/21/2023] [Revised: 07/19/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Cough is a common symptom during and after COVID-19 infection; however, few studies have described the cough profiles of COVID-19. OBJECTIVE The aim of this study was to investigate the prevalence, severity, and associated risk factors of severe and persistent cough in individuals with COVID-19 during the latest wave of the Omicron variant in China. METHODS In this nationwide cross-sectional study, we collected information of the characteristics of cough from individuals with infection of the SARS-CoV-2 Omicron variant using an online questionnaire sent between December 31, 2022, and January 11, 2023. RESULTS There were 11,718 (n=7978, 68.1% female) nonhospitalized responders, with a median age of 37 (IQR 30-47) years who responded at a median of 16 (IQR 12-20) days from infection onset to the time of the survey. Cough was the most common symptom, occurring in 91.7% of participants, followed by fever, fatigue, and nasal congestion (68.8%-87.4%). The median cough visual analog scale (VAS) score was 70 (IQR 50-80) mm. Being female (odds ratio [OR] 1.31, 95% CI 1.20-1.43), having a COVID-19 vaccination history (OR 1.71, 95% CI 1.37-2.12), current smoking (OR 0.48, 95% CI 0.41-0.58), chronic cough (OR 2.04, 95% CI 1.69-2.45), coronary heart disease (OR 1.71, 95% CI 1.17-2.52), asthma (OR 1.22, 95% CI 1.02-1.46), and gastroesophageal reflux disease (GERD) (OR 1.21, 95% CI 1.01-1.45) were independent factors for severe cough (VAS>70, 37.4%). Among all respondents, 35.0% indicated having a productive cough, which was associated with risk factors of being female (OR 1.44, 95% CI 1.31-1.57), having asthma (OR 1.84, 95% CI 1.52-2.22), chronic cough (OR 1.44, 95% CI 1.19-1.74), and GERD (OR 1.22, 95% CI 1.01-1.47). Persistent cough (>3 weeks) occurred in 13.0% of individuals, which was associated with the risk factors of having diabetes (OR 2.24, 95% CI 1.30-3.85), asthma (OR 1.70, 95% CI 1.11-2.62), and chronic cough (OR 1.97, 95% CI 1.32-2.94). CONCLUSIONS Cough is the most common symptom in nonhospitalized individuals with Omicron SARS-CoV-2 variant infection. Being female, having asthma, chronic cough, GERD, coronary heart disease, diabetes, and a COVID-19 vaccination history emerged as independent factors associated with severe cough, productive cough, and persistent cough.
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Affiliation(s)
- Tingting Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuehan Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenzhi Zhan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kian Fan Chung
- Department of Respiratory Medicine, Royal Brompton and Harefield Hospital, London, United Kingdom
- Experimental Studies Unit, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Zhongmin Qiu
- Department of Pulmonary and Critical Care Medicine, School of Medicine, Tongji Hospital, Tongji University, Shanghai, China
| | - Kewu Huang
- Department of Pulmonary and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ruchong Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiaxing Xie
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Gang Wang
- West China School of Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Min Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Xuefen Wang
- Department of Respiratory Medicine, The First Affliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongmei Yao
- Department of Respiratory Medicine, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Xiuqing Liao
- Department of Respiratory Medicine, Fuling Center Hospital of Chongqing, Chongqing, China
| | - Yunhui Zhang
- The First People's Hospital of Yunnan Province, Kunming, China
| | - Guojun Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dejun Sun
- Department of Pulmonary and Critical Care Medicine, the Inner Mongolia Autonomous Region People's Hospital, Hohhot, China
| | - Jia Zhu
- Department of Respiratory Medicine, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Shujuan Jiang
- Department of Pulmonary Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Juntao Feng
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Jianping Zhao
- Department of Respiratory Medicine, Tongji Hospital, Tongji Medical College of Hua Zhong University of Science and Technology, Wuhan, China
| | - Gengyun Sun
- Department of Respiratory Medicine, The First Affiliated Hospital of Medical University of Anhui, Hefei, China
| | - Huaqiong Huang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jianyong Zhang
- The Second Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Lingwei Wang
- Shenzhen People's Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Feng Wu
- Department of Pulmonary and Critical Care Medicine, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, China
| | - Suyun Li
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Pusheng Xu
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunhua Chi
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing, China
| | - Ping Chen
- General Hospital of Northern Theater Command, Shenyang, China
| | - Mei Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wen He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lianrong Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Luo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shiyue Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kefang Lai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Qu P, Xu K, Faraone JN, Goodarzi N, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Gumina RJ, Liu SL. Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants. Cell 2024; 187:585-595.e6. [PMID: 38194968 PMCID: PMC10872432 DOI: 10.1016/j.cell.2023.12.026] [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: 09/11/2023] [Revised: 11/11/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose-vaccinated and bivalent-vaccinated healthcare workers, XBB.1.5-wave-infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially different conformational stability of BA.2.86 spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Negin Goodarzi
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph S Bednash
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Jeffrey C Horowitz
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Rama K Mallampalli
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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47
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Zhang L, Kempf A, Nehlmeier I, Cossmann A, Richter A, Bdeir N, Graichen L, Moldenhauer AS, Dopfer-Jablonka A, Stankov MV, Simon-Loriere E, Schulz SR, Jäck HM, Čičin-Šain L, Behrens GMN, Drosten C, Hoffmann M, Pöhlmann S. SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency. Cell 2024; 187:596-608.e17. [PMID: 38194966 DOI: 10.1016/j.cell.2023.12.025] [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: 09/11/2023] [Revised: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
BA.2.86, a recently identified descendant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage, contains ∼35 mutations in the spike (S) protein and spreads in multiple countries. Here, we investigated whether the virus exhibits altered biological traits, focusing on S protein-driven viral entry. Employing pseudotyped particles, we show that BA.2.86, unlike other Omicron sublineages, enters Calu-3 lung cells with high efficiency and in a serine- but not cysteine-protease-dependent manner. Robust lung cell infection was confirmed with authentic BA.2.86, but the virus exhibited low specific infectivity. Further, BA.2.86 was highly resistant against all therapeutic antibodies tested, efficiently evading neutralization by antibodies induced by non-adapted vaccines. In contrast, BA.2.86 and the currently circulating EG.5.1 sublineage were appreciably neutralized by antibodies induced by the XBB.1.5-adapted vaccine. Collectively, BA.2.86 has regained a trait characteristic of early SARS-CoV-2 lineages, robust lung cell entry, and evades neutralizing antibodies. However, BA.2.86 exhibits low specific infectivity, which might limit transmissibility.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Najat Bdeir
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | | | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, 75015 Paris, France; National Reference Center for Viruses of respiratory Infections, Institut Pasteur, 75015 Paris, France
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
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48
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Wang YN, Zhou LY, Huang YH, Jiang M, Dai C. The incidence and predisposing factors for irritable bowel syndrome following COVID-19: a systematic review and meta-analysis. Eur J Gastroenterol Hepatol 2024; 36:168-176. [PMID: 38047738 DOI: 10.1097/meg.0000000000002688] [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] [Indexed: 12/05/2023]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a common functional gastrointestinal (GI) disorder. Several studies have analyzed the long-term GI symptoms and IBS following coronavirus disease 2019 (COVID-19). The purpose of this study is to evaluate the incidence and predisposing factors for IBS following COVID-19 by a systematic review and meta-analysis. METHODS Electronic databases were searched to identify relevant studies. Primary outcomes were the pooled incidence rate of IBS following COVID-19 and the pooled relative risk (RR) for IBS in the COVID-19 group compared to the non-COVID-19 group. Secondary outcomes were the pooled RR and the standardized mean difference (SMD) for predisposing factors in the IBS group compared to the non-IBS group. Heterogeneity was evaluated using Cochran's Q test and I2 statistics. RESULTS Ten studies were included in this study. The pooled incidence rate of IBS in COVID-19 patients was 12%. The pooled incidence rate of IBS-D, IBS-C and IBS-M was 5%, 2% and 1%. The pooled incidence rate of IBS in 6 and 12 months was 10% and 3%. The pooled RR for IBS in COVID-19 patients was 1.23 [95% confidence interval (CI) = 0.50-3.01] compared to non-COVID-19 patients. The pooled RR or SMD for mild, moderate, and severe disease activity, procalcitonin (PCT), depression or anxiety in IBS patients following COVID-19 was 0.94 (95% CI = 0.74-1.21), 1.19 (95% CI = 0.65-2.21), 1.30 (95% CI = 0.63-2.66), 6.73 (95% CI = 6.08-7.38) and 3.21 (95% CI = 1.79-5.75). CONCLUSION The incidence of IBS following COVID-19 was 12%. But it was not higher than the general population. We also found some predisposing factors for IBS including depression or anxiety, PCT.
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Affiliation(s)
- Yi-Nuo Wang
- Department of Gastroenterology, First Hospital of China Medical University, Shenyang, China
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49
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Liu P, Xing Z, Peng X, Zhang M, Shu C, Wang C, Li R, Tang L, Wei H, Ran X, Qiu S, Gao N, Yeo YH, Liu X, Ji F. Machine learning versus multivariate logistic regression for predicting severe COVID-19 in hospitalized children with Omicron variant infection. J Med Virol 2024; 96:e29447. [PMID: 38305064 DOI: 10.1002/jmv.29447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 01/02/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024]
Abstract
With the emergence of the Omicron variant, the number of pediatric Coronavirus Disease 2019 (COVID-19) cases requiring hospitalization and developing severe or critical illness has significantly increased. Machine learning and multivariate logistic regression analysis were used to predict risk factors and develop prognostic models for severe COVID-19 in hospitalized children with the Omicron variant in this study. Of the 544 hospitalized children including 243 and 301 in the mild and severe groups, respectively. Fever (92.3%) was the most common symptom, followed by cough (79.4%), convulsions (36.8%), and vomiting (23.2%). The multivariate logistic regression analysis showed that age (1-3 years old, odds ratio (OR): 3.193, 95% confidence interval (CI): 1.778-5.733], comorbidity (OR: 1.993, 95% CI:1.154-3.443), cough (OR: 0.409, 95% CI:0.236-0.709), and baseline neutrophil-to-lymphocyte ratio (OR: 1.108, 95% CI: 1.023-1.200), lactate dehydrogenase (OR: 1.993, 95% CI: 1.154-3.443), blood urea nitrogen (OR: 1.002, 95% CI: 1.000-1.003) and total bilirubin (OR: 1.178, 95% CI: 1.005-3.381) were independent risk factors for severe COVID-19. The area under the curve (AUC) of the prediction models constructed by multivariate logistic regression analysis and machine learning (RandomForest + TomekLinks) were 0.7770 and 0.8590, respectively. The top 10 most important variables of random forest variables were selected to build a prediction model, with an AUC of 0.8210. Compared with multivariate logistic regression, machine learning models could more accurately predict severe COVID-19 in children with Omicron variant infection.
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Affiliation(s)
- Pan Liu
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Zixuan Xing
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaokang Peng
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Mengyi Zhang
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, China
| | - Chang Shu
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Ce Wang
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Ruina Li
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Li Tang
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Huijing Wei
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Xiaoshan Ran
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Sikai Qiu
- Department of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Ning Gao
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yee Hui Yeo
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Xiaoguai Liu
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Fanpu Ji
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Shaanxi Provincial Clinical Medical Research Center of Infectious Diseases, Xi'an, China
- Key Laboratory of Surgical Critical Care and Life Support (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
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50
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Erabi G, Faridzadeh A, Parvin A, Deravi N, Rahmanian M, Fathi M, Aleebrahim‐Dehkordi E, Rezaei N. SARS-CoV-2 Omicron (BA.4, BA.5) variant: Lessons learned from a new variant during the COVID-19 pandemic. Health Sci Rep 2024; 7:e1873. [PMID: 38332930 PMCID: PMC10851086 DOI: 10.1002/hsr2.1873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 01/05/2024] [Accepted: 01/21/2024] [Indexed: 02/10/2024] Open
Abstract
Background and Aim In late 2021, the world faced the rapid spread of the SARS-CoV-2 Omicron variant, which quickly became the variant of concern. In April 2022, two new lineages of Omicron (BA.4/BA.5) emerged from Africa, where they caused the fifth wave of infection. Method We searched PubMed, Google Scholar, and Scopus online databases up to December 2023 for founding relevant studies. Results BA.4 and BA.5 subgroups, with changes in the spike protein, have a greater ability to escape from the immune system, which was possible with the help of L452R and F486V mutations. Epidemiologically, these evolving subtypes show similarities to seasonal influenza but with higher mortality rates. The symptoms of these subgroups are different from the previous types in the form of upper respiratory symptoms. Antiviral treatments, the use of antibodies such as bebtelovimab, and the development of vaccines are promising. Conclusion Consequently, we must continue to be vigilant in our joint surveillance efforts against COVID-19 in diagnosis and treatment.
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Affiliation(s)
- Gisou Erabi
- Student Research CommitteeUrmia University of Medical SciencesUrmiaIran
| | - Arezoo Faridzadeh
- Department of Immunology and AllergyMashhad University of Medical SciencesMashhadIran
- Immunology Research CenterMashhad University of Medical SciencesMashhadIran
| | - Ali Parvin
- Student Research CommitteeUrmia University of Medical SciencesUrmiaIran
| | - Niloofar Deravi
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Mohammad Rahmanian
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Mobina Fathi
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Elahe Aleebrahim‐Dehkordi
- Medical Plants Research Center, Basic Health Sciences instituteShahrekord University of Medical SciencesShahrekordIran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical CenterTehran University of Medical SciencesTehranIran
- Department of Immunology, School of MedicineTehran University of Medical SciencesTehranIran
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA)Universal Scientific Education and Research Network (USERN)TehranIran
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