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Yang YL, Wang B, Li W, Cai HL, Qian QY, Qin Y, Shi FS, Bosch BJ, Huang YW. Functional dissection of the spike glycoprotein S1 subunit and identification of cellular cofactors for regulation of swine acute diarrhea syndrome coronavirus entry. J Virol 2024; 98:e0013924. [PMID: 38501663 PMCID: PMC11019839 DOI: 10.1128/jvi.00139-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/02/2024] [Indexed: 03/20/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel porcine enteric coronavirus, and the broad interspecies infection of SADS-CoV poses a potential threat to human health. This study provides experimental evidence to dissect the roles of distinct domains within the SADS-CoV spike S1 subunit in cellular entry. Specifically, we expressed the S1 and its subdomains, S1A and S1B. Cell binding and invasion inhibition assays revealed a preference for the S1B subdomain in binding to the receptors on the cell surface, and this unknown receptor is not utilized by the porcine epidemic diarrhea virus. Nanoparticle display demonstrated hemagglutination of erythrocytes from pigs, humans, and mice, linking the S1A subdomain to the binding of sialic acid (Sia) involved in virus attachment. We successfully rescued GFP-labeled SADS-CoV (rSADS-GFP) from a recombinant cDNA clone to track viral infection. Antisera raised against S1, S1A, or S1B contained highly potent neutralizing antibodies, with anti-S1B showing better efficiency in neutralizing rSADS-GFP infection compared to anti-S1A. Furthermore, depletion of heparan sulfate (HS) by heparinase treatment or pre-incubation of rSADS-GFP with HS or constituent monosaccharides could inhibit SADS-CoV entry. Finally, we demonstrated that active furin cleavage of S glycoprotein and the presence of type II transmembrane serine protease (TMPRSS2) are essential for SADS-CoV infection. These combined observations suggest that the wide cell tropism of SADS-CoV may be related to the distribution of Sia or HS on the cell surface, whereas the S1B contains the main protein receptor binding site. Specific host proteases also play important roles in facilitating SADS-CoV entry.IMPORTANCESwine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel pathogen infecting piglet, and its unique genetic evolution characteristics and broad species tropism suggest the potential for cross-species transmission. The virus enters cells through its spike (S) glycoprotein. In this study, we identify the receptor binding domain on the C-terminal part of the S1 subunit (S1B) of SADS-CoV, whereas the sugar-binding domain located at the S1 N-terminal part of S1 (S1A). Sialic acid, heparan sulfate, and specific host proteases play essential roles in viral attachment and entry. The dissection of SADS-CoV S1 subunit's functional domains and identification of cellular entry cofactors will help to explore the receptors used by SADS-CoV, which may contribute to exploring the mechanisms behind cross-species transmission and host tropism.
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Affiliation(s)
- Yong-Le Yang
- Xianghu Laboratory, Hangzhou, China
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Bin Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Wentao Li
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Qian-Yu Qian
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yu Qin
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Fang-Shu Shi
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Yao-Wei Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
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Tanneti NS, Patel AK, Tan LH, Marques AD, Perera RAPM, Sherrill-Mix S, Kelly BJ, Renner DM, Collman RG, Rodino K, Lee C, Bushman FD, Cohen NA, Weiss SR. Comparison of SARS-CoV-2 variants of concern in primary human nasal cultures demonstrates Delta as most cytopathic and Omicron as fastest replicating. mBio 2024; 15:e0312923. [PMID: 38477472 PMCID: PMC11005367 DOI: 10.1128/mbio.03129-23] [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: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The SARS-CoV-2 pandemic was marked with emerging viral variants, some of which were designated as variants of concern (VOCs) due to selection and rapid circulation in the human population. Here, we elucidate functional features of each VOC linked to variations in replication rate. Patient-derived primary nasal cultures grown at air-liquid interface were used to model upper respiratory infection and compared to cell lines derived from human lung epithelia. All VOCs replicated to higher titers than the ancestral virus, suggesting a selection for replication efficiency. In primary nasal cultures, Omicron replicated to the highest titers at early time points, followed by Delta, paralleling comparative studies of population sampling. All SARS-CoV-2 viruses entered the cell primarily via a transmembrane serine protease 2 (TMPRSS2)-dependent pathway, and Omicron was more likely to use an endosomal route of entry. All VOCs activated and overcame dsRNA-induced cellular responses, including interferon (IFN) signaling, oligoadenylate ribonuclease L degradation, and protein kinase R activation. Among the VOCs, Omicron infection induced expression of the most IFN and IFN-stimulated genes. Infections in nasal cultures resulted in cellular damage, including a compromise of cell barrier integrity and loss of nasal cilia and ciliary beating function, especially during Delta infection. Overall, Omicron was optimized for replication in the upper respiratory tract and least favorable in the lower respiratory cell line, and Delta was the most cytopathic for both upper and lower respiratory cells. Our findings highlight the functional differences among VOCs at the cellular level and imply distinct mechanisms of pathogenesis in infected individuals. IMPORTANCE Comparative analysis of infections by SARS-CoV-2 ancestral virus and variants of concern, including Alpha, Beta, Delta, and Omicron, indicated that variants were selected for efficiency in replication. In infections of patient-derived primary nasal cultures grown at air-liquid interface to model upper respiratory infection, Omicron reached the highest titers at early time points, a finding that was confirmed by parallel population sampling studies. While all infections overcame dsRNA-mediated host responses, infections with Omicron induced the strongest interferon and interferon-stimulated gene response. In both primary nasal cultures and lower respiratory cell line, infections by Delta were most damaging to the cells as indicated by syncytia formation, loss of cell barrier integrity, and nasal ciliary function.
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Affiliation(s)
- Nikhila S. Tanneti
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Anant K. Patel
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Li Hui Tan
- Department of Otorhinolaryngology- Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew D. Marques
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ranawaka A. P. M. Perera
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David M. Renner
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle Rodino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carole Lee
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Noam A. Cohen
- Department of Otorhinolaryngology- Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Corporal Michael J. Crescenz VA Medical Center, Surgical Services, Philadelphia, Pennsylvania, USA
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, USA
| | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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3
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Scovino AM, Dahab EC, Diniz-Lima I, de Senna Silveira E, Barroso SPC, Cardoso KM, Nico D, Makhoul GJ, da Silva-Junior EB, Freire-de-Lima CG, Freire-de-Lima L, da Fonseca LM, Valente N, Nacife V, Machado A, Araújo M, Vieira GF, Pauvolid-Corrêa A, Siqueira M, Morrot A. A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants. Microorganisms 2024; 12:720. [PMID: 38674664 PMCID: PMC11052025 DOI: 10.3390/microorganisms12040720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/16/2023] [Accepted: 11/28/2023] [Indexed: 04/28/2024] Open
Abstract
The SARS-CoV-2 P.1 variant, responsible for an outbreak in Manaus, Brazil, is distinguished by 12 amino acid differences in the S protein, potentially increasing its ACE-2 affinity and immune evasion capability. We investigated the innate immune response of this variant compared to the original B.1 strain, particularly concerning cytokine production. Blood samples from three severe COVID-19 patients were analyzed post-infection with both strains. Results showed no significant difference in cytokine production of mononuclear cells and neutrophils for either variant. While B.1 had higher cytopathogenicity, neither showed viral replication in mononuclear cells. Structural analyses of the S protein highlighted physicochemical variations, which might be linked to the differences in infectivity between the strains. Our studies point to the increased infectivity of P.1 could stem from altered immunogenicity and receptor-binding affinity.
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Affiliation(s)
- Aline Miranda Scovino
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
| | - Elizabeth Chen Dahab
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
| | - Israel Diniz-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Etiele de Senna Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil; (E.d.S.S.)
| | - Shana Priscila Coutinho Barroso
- Laboratório de Biologia Molecular, Instituto de Pesquisa Biomédica, Hospital Naval Marcílio Dias, Marinha do Brazil, Rio de Janeiro 20725-090, Brazil; (S.P.C.B.); (K.M.C.)
- Biomanguinhos, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, Brazil
| | - Karina Martins Cardoso
- Laboratório de Biologia Molecular, Instituto de Pesquisa Biomédica, Hospital Naval Marcílio Dias, Marinha do Brazil, Rio de Janeiro 20725-090, Brazil; (S.P.C.B.); (K.M.C.)
| | - Dirlei Nico
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
| | - Gustavo José Makhoul
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Elias Barbosa da Silva-Junior
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Celio Geraldo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Leonardo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Leonardo Marques da Fonseca
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
- Curso de Medicina, Universidade Castelo Branco (UCB), Rio de Janeiro 21710-255, Brazil
| | - Natalia Valente
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Valeria Nacife
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Ana Machado
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Mia Araújo
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Gustavo Fioravanti Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil; (E.d.S.S.)
- PPGSDH—Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas 92010-000, Brazil
| | - Alex Pauvolid-Corrêa
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
- Laboratório de Virologia Veterinária de Viçosa, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Marilda Siqueira
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Alexandre Morrot
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
- Escola de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
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Xia Q, Yang Y, Wang F, Huang Z, Qiu W, Mao A. Case fatality rates of COVID-19 during epidemic periods of variants of concern: A meta-analysis by continents. Int J Infect Dis 2024; 141:106950. [PMID: 38309460 DOI: 10.1016/j.ijid.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/25/2024] [Indexed: 02/05/2024] Open
Abstract
OBJECTIVES To calculate the case fatality rates (CFR) of COVID-19 during epidemic periods of different variants of concern (VOC) by continents. METHODS We systematically searched five authoritative databases (Web of Science, PubMed, Embase, Cochrane Library, and MedRxiv) for epidemiological studies on the CFR of COVID-19 published between January 1, 2020, and March 31, 2023. After identifying the epidemic trends of variants, we used a random-effects model to calculate the pooled CFRs during periods of different VOCs. This meta-analysis was conducted following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and registered with PROSPERO (CRD42023431572). RESULTS There were variations in the CFRs among different variants of COVID-19 (Alpha: 2.62%, Beta: 4.19%, Gamma: 3.60%, Delta: 2.01%, Omicron: 0.70%), and disparities in CFRs also existed among continents. On the whole, the CFRs of COVID-19 in Europe and Oceania were slightly lower than in other continents. There was a statistically significant association between the variant, HDI value, age distribution, coverage of full vaccination of cases, and the CFR. CONCLUSIONS The CFRs of COVID-19 varied across the epidemic periods of different VOCs, and disparities existed among continents. The CFR value reflected combined effects of various factors within a certain context. Caution should be exercised when comparing CFRs due to disparities in testing capabilities and age distribution among countries, etc.
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Affiliation(s)
- Qianhang Xia
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China
| | - Yujie Yang
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China
| | - Fengling Wang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong China
| | - Zhongyue Huang
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China
| | - Wuqi Qiu
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China
| | - Ayan Mao
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China.
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Lee KS, Han C, Min HS, Lee J, Youn SH, Kim Y, Moon JY, Lee YS, Kim SJ, Sung HK. Impact of the early phase of the COVID-19 pandemic on emergency department-to-intensive care unit admissions in Korea: an interrupted time-series analysis. BMC Emerg Med 2024; 24:51. [PMID: 38561666 PMCID: PMC10985913 DOI: 10.1186/s12873-024-00968-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic resulted in significant disruptions to critical care systems globally. However, research on the impact of the COVID-19 pandemic on intensive care unit (ICU) admissions via the emergency department (ED) is limited. Therefore, this study evaluated the changes in the number of ED-to-ICU admissions and clinical outcomes in the periods before and during the pandemic. METHODS We identified all adult patients admitted to the ICU through level 1 or 2 EDs in Korea between February 2018 and January 2021. February 2020 was considered the onset point of the COVID-19 pandemic. The monthly changes in the number of ED-to-ICU admissions and the in-hospital mortality rates before and during the COVID-19 pandemic were evaluated using interrupted time-series analysis. RESULTS Among the 555,793 adult ED-to-ICU admissions, the number of ED-to-ICU admissions during the pandemic decreased compared to that before the pandemic (step change, 0.916; 95% confidence interval [CI] 0.869-0.966], although the trend did not attain statistical significance (slope change, 0.997; 95% CI 0.991-1.003). The proportion of patients who arrived by emergency medical services, those transferred from other hospitals, and those with injuries declined significantly among the number of ED-to-ICU admissions during the pandemic. The proportion of in-hospital deaths significantly increased during the pandemic (step change, 1.054; 95% CI 1.003-1.108); however, the trend did not attain statistical significance (slope change, 1.001; 95% CI 0.996-1.007). Mortality rates in patients with an ED length of stay of ≥ 6 h until admission to the ICU rose abruptly following the onset of the pandemic (step change, 1.169; 95% CI 1.021-1.339). CONCLUSIONS The COVID-19 pandemic significantly affected ED-to-ICU admission and in-hospital mortality rates in Korea. This study's findings have important implications for healthcare providers and policymakers planning the management of future outbreaks of infectious diseases. Strategies are needed to address the challenges posed by pandemics and improve the outcomes in critically ill patients.
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Affiliation(s)
- Kyung-Shin Lee
- Public Health Research Institute, National Medical Center, 245 Eulgi-ro, Jung-gu, 04564, Seoul, Korea
| | - Changwoo Han
- Department of Preventive Medicine, Chungnam National University College of Medicine, Daejeon, Korea
| | - Hye Sook Min
- Public Health Research Institute, National Medical Center, 245 Eulgi-ro, Jung-gu, 04564, Seoul, Korea
| | - Jeehye Lee
- Department of Preventive Medicine, Konkuk University College of Medicine, Chungju-si, Korea
| | - Seok Hwa Youn
- Department of Trauma Surgery, National Medical Center, Seoul, Korea
| | - Younghwan Kim
- Department of Trauma Surgery, National Medical Center, Seoul, Korea
| | - Jae Young Moon
- Department of Pulmonary and Critical Care Medicine, Chungnam National University Sejong Hospital, Sejong, Korea
| | - Young Seok Lee
- Division of Pulmonology, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Su Jin Kim
- Department of Emergency Medicine, Korea University Anam Hospital, Seoul, Korea
| | - Ho Kyung Sung
- Public Health Research Institute, National Medical Center, 245 Eulgi-ro, Jung-gu, 04564, Seoul, Korea.
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA.
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Vulturar DM, Moacă LȘ, Neag MA, Mitre AO, Alexescu TG, Gherman D, Făgărășan I, Chețan IM, Gherman CD, Melinte OE, Trofor AC, Todea DA. Delta Variant in the COVID-19 Pandemic: A Comparative Study on Clinical Outcomes Based on Vaccination Status. J Pers Med 2024; 14:358. [PMID: 38672984 PMCID: PMC11050903 DOI: 10.3390/jpm14040358] [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: 02/26/2024] [Revised: 03/17/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND As the global battle against the COVID-19 pandemic endures, the spread of the Delta variant has introduced nuanced challenges, prompting a nuanced examination. MATERIALS AND METHODS We performed a multilevel logistic regression analysis encompassing 197 patients, comprising 44 vaccinated individuals (V group) and 153 unvaccinated counterparts (UV). These patients, afflicted with the Delta variant of SARS-CoV-2, were hospitalized between October 2021 and February 2022 at the COVID-19 department of a University Centre in Cluj-Napoca, Romania. We compared patient characteristics, CT lung involvement, Padua score, oxygen saturation (O2 saturation), ventilation requirements, dynamics of arterial blood gas (ABG) parameters, ICU admission rates, and mortality rates between the two groups. RESULTS The UV group exhibited a statistically significant (p < 0.05) proclivity toward developing a more severe form of infection, marked by elevated rates of lung involvement, oxygen requirement, ICU admission, and mortality. CONCLUSION Our findings underscore the substantial efficacy of the vaccine in diminishing the incidence of severe disease, lowering the rates of ICU admissions, and mitigating mortality among hospitalized patients.
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Affiliation(s)
- Damiana-Maria Vulturar
- Department of Pneumology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400332 Cluj-Napoca, Romania; (D.-M.V.); (I.F.); (I.M.C.); (D.-A.T.)
| | - Liviu-Ștefan Moacă
- Department of Pneumology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400332 Cluj-Napoca, Romania; (D.-M.V.); (I.F.); (I.M.C.); (D.-A.T.)
| | - Maria Adriana Neag
- Department of Pharmacology, Toxicology and Clinical Pharmacology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
| | - Andrei-Otto Mitre
- Department of Pathophysiology, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
| | - Teodora-Gabriela Alexescu
- 4th Department Internal Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400015 Cluj-Napoca, Romania;
| | - Diana Gherman
- Department of Radiology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400347 Cluj-Napoca, Romania;
| | - Iulia Făgărășan
- Department of Pneumology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400332 Cluj-Napoca, Romania; (D.-M.V.); (I.F.); (I.M.C.); (D.-A.T.)
| | - Ioana Maria Chețan
- Department of Pneumology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400332 Cluj-Napoca, Romania; (D.-M.V.); (I.F.); (I.M.C.); (D.-A.T.)
| | - Claudia Diana Gherman
- Department of Surgery-Practical Abilities,“Iuliu Hatieganu” University of Medicine and Pharmacy, Marinescu Street, No. 23, 400337 Cluj-Napoca, Romania;
| | - Oana-Elena Melinte
- Discipline of Pneumology, III-rd Medical Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (O.-E.M.); (A.C.T.)
| | - Antigona Carmen Trofor
- Discipline of Pneumology, III-rd Medical Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (O.-E.M.); (A.C.T.)
| | - Doina-Adina Todea
- Department of Pneumology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400332 Cluj-Napoca, Romania; (D.-M.V.); (I.F.); (I.M.C.); (D.-A.T.)
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7
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Md Nadzri MN, Md Zamri ASS, Singh S, Sumarni MG, Lai CH, Tan CV, Aris T, Mohd Ibrahim H, Gill BS, Mohd Ghazali N, Md Iderus NH, Lim MC, Ahmad LCRQ, Kamarudin MK, Ahmad NAR, Tee KK, Zulkifli AA. Description of the COVID-19 epidemiology in Malaysia. Front Public Health 2024; 12:1289622. [PMID: 38544725 PMCID: PMC10968133 DOI: 10.3389/fpubh.2024.1289622] [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: 09/06/2023] [Accepted: 02/26/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction Since the COVID-19 pandemic began, it has spread rapidly across the world and has resulted in recurrent outbreaks. This study aims to describe the COVID-19 epidemiology in terms of COVID-19 cases, deaths, ICU admissions, ventilator requirements, testing, incidence rate, death rate, case fatality rate (CFR) and test positivity rate for each outbreak from the beginning of the pandemic in 2020 till endemicity of COVID-19 in 2022 in Malaysia. Methods Data was sourced from the GitHub repository and the Ministry of Health's official COVID-19 website. The study period was from the beginning of the outbreak in Malaysia, which began during Epidemiological Week (Ep Wk) 4 in 2020, to the last Ep Wk 18 in 2022. Data were aggregated by Ep Wk and analyzed in terms of COVID-19 cases, deaths, ICU admissions, ventilator requirements, testing, incidence rate, death rate, case fatality rate (CFR) and test positivity rate by years (2020 and 2022) and for each outbreak of COVID-19. Results A total of 4,456,736 cases, 35,579 deaths and 58,906,954 COVID-19 tests were reported for the period from 2020 to 2022. The COVID-19 incidence rate, death rate, CFR and test positivity rate were reported at 1.085 and 0.009 per 1,000 populations, 0.80 and 7.57%, respectively, for the period from 2020 to 2022. Higher cases, deaths, testing, incidence/death rate, CFR and test positivity rates were reported in 2021 and during the Delta outbreak. This is evident by the highest number of COVID-19 cases, ICU admissions, ventilatory requirements and deaths observed during the Delta outbreak. Conclusion The Delta outbreak was the most severe compared to other outbreaks in Malaysia's study period. In addition, this study provides evidence that outbreaks of COVID-19, which are caused by highly virulent and transmissible variants, tend to be more severe and devastating if these outbreaks are not controlled early on. Therefore, close monitoring of key epidemiological indicators, as reported in this study, is essential in the control and management of future COVID-19 outbreaks in Malaysia.
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Affiliation(s)
- Mohamad Nadzmi Md Nadzri
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Ahmed Syahmi Syafiq Md Zamri
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Sarbhan Singh
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Mohd Ghazali Sumarni
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Chee Herng Lai
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Cia Vei Tan
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Tahir Aris
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | | | - Balvinder Singh Gill
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Nur’Ain Mohd Ghazali
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Nuur Hafizah Md Iderus
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Mei Cheng Lim
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Lonny Chen Rong Qi Ahmad
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Mohd Kamarulariffin Kamarudin
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Nur Ar Rabiah Ahmad
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Asrul Anuar Zulkifli
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
- International Medical School, Management and Science University, Shah Alam, Selangor, Malaysia
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8
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Zhang H, Zhao Y, Li W, Chai Y, Gu X. Difference in mortality risk predicted by leukocyte and lymphocyte levels in COVID-19 patients infected with the Wild-type, Delta, and Omicron strains. Medicine (Baltimore) 2024; 103:e37516. [PMID: 38457534 PMCID: PMC10919463 DOI: 10.1097/md.0000000000037516] [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: 08/01/2023] [Revised: 01/01/2024] [Accepted: 02/15/2024] [Indexed: 03/10/2024] Open
Abstract
This study aimed to investigate the changing trends, level differences, and prognostic performance of the leukocyte and lymphocyte levels of patients infected with the Wild strains, Delta strains and Omicron strains to provide a reference for prognostic assessment. In the current study, we conducted a retrospective cross-sectional study to evaluate the changing trends, level differences, and prognostic performance of leukocyte and lymphocyte of different strains at admission and discharge may already exist in patients with coronavirus disease-2019 (COVID-19) infected with the Wild type, Delta, and Omicron strains. A retrospective cross-sectional study was conducted. We recruited and screened the 243 cases infected with the Wild-type strains in Wuhan, the 629 cases infected with the Delta and 116 cases infected strains with the Omicron strains in Xi'an. The leukocyte and lymphocyte levels were compared the cohort of Wild-type infection with the cohort of Delta and the Omicron. The changes in the levels of leukocytes and lymphocytes exhibit a completely opposite trend in patients with COVID-19 infected with the different strains. The lymphocyte level at admission and discharge in patients with COVID-19 infected with Omicron strains (area under curve [AUC] receiver operating characteristic curve [ROC] 72.8-90.2%, 82.8-97.2%) presented better performance compared patients with COVID-19 infected with Wild type strains (AUC ROC 60.9-80.7%, 82.3-97.2%) and Delta strains (AUC ROC 56.1-84.7%, 40.3-93.3%). Kaplan-Meier curves showed that the leukocyte levels above newly established cutoff values and the lymphocyte levels below newly established cutoff values had a significantly higher risk of in-hospital mortality in COVID-19 patients with Wild-type and Omicron strains (P < .01). The levels of leukocyte and lymphocyte at admission and discharge in patients with COVID-19 infected with the Wild type, Delta, and Omicron strains may be differences among strains, which indicates different death risks. Our research may help clinicians identify patients with a poor prognosis for severe acute respiratory syndrome coronavirus 2 infection.
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Affiliation(s)
- Hongjun Zhang
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
- Infectious Disease Department, Wuhan Huoshenshan Hospital, Wuhan, Hubei, PR China
| | - Yanjun Zhao
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
| | - Wenjie Li
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
| | - Yaqin Chai
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
| | - Xing Gu
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
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9
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Çakmak R, Bektaş M. Individualized High Dose Intravenous Anakinra Treatment in Cancer Patients with COVID-19 Associated Cytokine Storm: A Retrospective Controlled Study. INFECTIOUS DISEASES & CLINICAL MICROBIOLOGY 2024; 6:32-43. [PMID: 38633444 PMCID: PMC11019726 DOI: 10.36519/idcm.2024.287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/14/2024] [Indexed: 04/19/2024]
Abstract
Objective Patients with COVID-19 accompanying cancer have been reported to have higher morbidity and mortality. In this study, we aimed to evaluate the high-dose high intravenous anakinra treatment response and outcome in patients with COVID-19-associated cytokine storm accompanying cancer. Materials and Methods This retrospective observational study was carried out at a tertiary referral center between September 01, 2021, and February 01, 2022, in Turkey. The study population consisted of two groups: patients receiving high-dose intravenous anakinra and patients treated with standard care. Results Data from 146 patients in the anakinra group and 114 patients in the control group were analyzed. Malignancy frequency was 11% (n=16) in the anakinra group and 7% (n=8) in the control group. In survival analysis, a significantly lower survival rate was observed in patients with malignancy than those without in the control group (log-rank: p=0.002) and patients with malignancy in the control group compared to the anakinra group (log-rank: p=0.013). However, it did not differ between patients with and without malignancy in the anakinra group (log-rank: p=0.9). Conclusion In the control group, mortality was higher in patients with malignancy compared to those without malignancy, but not in the anakinra group. Also, mortality was higher in patients receiving SoC compared to anakinra. Intravenous high-dose anakinra treatment is safe and effective in patients with COVID-19 accompanying cancer.
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Affiliation(s)
- Ramazan Çakmak
- Department of Internal Medicine, Division of Endocrinology and Metabolism, İstinye University School of Medicine, İstanbul, Türkiye
| | - Murat Bektaş
- Department of Internal Medicine, Division of Rheumatology, Aksaray Training and Research Hospital, Aksaray, Türkiye
- Department of Internal Medicine, Division of Rheumatology, İstanbul Aydın University School of Medicine, İstanbul, Türkiye
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10
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Reeves EL, Neelam V, Carlson JM, Olsen EO, Fox CJ, Woodworth KR, Nestoridi E, Mobley E, Montero Castro S, Dzimira P, Sokale A, Sizemore L, Hall AJ, Ellington S, Cohn A, Gilboa SM, Tong VT. Pregnancy and infant outcomes following SARS-CoV-2 infection in pregnancy during delta variant predominance - Surveillance for Emerging Threats to Pregnant People and Infants. Am J Obstet Gynecol MFM 2024; 6:101265. [PMID: 38135220 DOI: 10.1016/j.ajogmf.2023.101265] [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: 09/29/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND SARS-CoV-2 infection in pregnancy is associated with an increased risk of adverse birth outcomes such as preterm birth, stillbirth, and maternal and infant complications. Previous research suggests an increased risk of severe COVID-19 illness and stillbirth in pregnant people during delta variant predominance in 2021; however, those studies did not assess timing of infection during pregnancy, and few of them described COVID-19 vaccination status. OBJECTIVE Using a large population-based cohort, this study compared pregnancy and infant outcomes and described demographic and clinical characteristics of pregnant people with SARS-CoV-2 infection prior to and during the delta variant period. STUDY DESIGN This retrospective cohort analysis included persons with confirmed SARS-CoV-2 infection in pregnancy from 6 US jurisdictions reporting to the Surveillance for Emerging Threats to Pregnant People and Infants Network. Data were collected through case reports of polymerase chain reaction-positive pregnant persons and linkages to birth certificates, fetal death records, and immunization records. We described clinical characteristics and compared frequency of spontaneous abortion (<20 weeks of gestation), stillbirth (≥20 weeks), preterm birth (<37 weeks), small for gestational age, and term infant neonatal intensive care unit admission between the time periods of pre-delta and delta variant predominance. Study time periods were determined by when variants constituted more than 50% of sequences isolated according to regional SARS-CoV-2 genomic surveillance data, with time periods defined for pre-delta (March 3, 2020-June 25, 2021) and Delta (June 26, 2021-December 25, 2021). Adjusted prevalence ratios were estimated for each outcome measure using Poisson regression and were adjusted for continuous maternal age, race and ethnicity, and insurance status at delivery. RESULTS Among 57,563 pregnancy outcomes, 57,188 (99.3%) were liveborn infants, 65 (0.1%) were spontaneous abortions, and 310 (0.5%) were stillbirths. Most pregnant persons were unvaccinated at the time of SARS-CoV-2 infection, with a higher proportion in pre-delta (99.4%) than in the delta period (78.4%). Of those with infections during delta and who were previously vaccinated, the timing from last vaccination to infection was a median of 183 days. Compared to pre-delta, infections during delta were associated with a higher frequency of stillbirths (0.7% vs 0.4%; adjusted prevalence ratio, 1.55; 95% confidence interval, 1.14-2.09) and preterm births (12.8% vs 11.9%; adjusted prevalence ratio, 1.14; 95% confidence interval, 1.07-1.20). The delta period was associated with a lower frequency of neonatal intensive care unit admission (adjusted prevalence ratio, 0.74; 95% confidence interval, 0.67-0.82) than in the pre-delta period. During the delta period, infection during the third trimester was associated with a higher frequency of preterm birth (adjusted prevalence ratio, 1.41; 95% confidence interval, 1.28-1.56) and neonatal intensive care unit admission (adjusted prevalence ratio, 1.21; 95% confidence interval, 1.01-1.45) compared to the first and second trimester combined. CONCLUSION In this US-based cohort of persons with SARS-CoV-2 infection in pregnancy, the majority were unvaccinated, and frequencies of stillbirth and preterm birth were higher during the delta variant predominance period than in the pre-delta period. During the delta period, frequency of preterm birth and neonatal intensive care unit admission was higher among infections occurring in the third trimester vs those earlier in pregnancy. These findings demonstrate population-level increases of adverse fetal and infant outcomes, specifically in the presence of a COVID-19 variant with more severe presentation.
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Affiliation(s)
- Emily L Reeves
- Eagle Global Scientific, LLC, Atlanta, GA (Ms Reeves, Dr Carlson, and Ms Fox).
| | - Varsha Neelam
- Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA (Ms Neelam; Drs Olsen, Woodworth, Cohn, and Gilboa; and Ms Tong)
| | - Jeffrey M Carlson
- Eagle Global Scientific, LLC, Atlanta, GA (Ms Reeves, Dr Carlson, and Ms Fox)
| | - Emily O Olsen
- Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA (Ms Neelam; Drs Olsen, Woodworth, Cohn, and Gilboa; and Ms Tong)
| | - Charise J Fox
- Eagle Global Scientific, LLC, Atlanta, GA (Ms Reeves, Dr Carlson, and Ms Fox)
| | - Kate R Woodworth
- Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA (Ms Neelam; Drs Olsen, Woodworth, Cohn, and Gilboa; and Ms Tong)
| | - Eirini Nestoridi
- Massachusetts Department of Public Health, Boston, MA (Dr Nestoridi)
| | - Evan Mobley
- Missouri Department of Health and Senior Services, Jefferson City, MO (Mr Mobley)
| | | | - Paula Dzimira
- Pennsylvania Department of Health, Pittsburgh, PA (Ms Dzimira)
| | - Ayomide Sokale
- Philadelphia Department of Public Health, Philadelphia, PA (Ms Sokale)
| | | | - Aron J Hall
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA (Dr Hall)
| | - Sascha Ellington
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA (Dr Ellington)
| | - Amanda Cohn
- Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA (Ms Neelam; Drs Olsen, Woodworth, Cohn, and Gilboa; and Ms Tong)
| | - Suzanne M Gilboa
- Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA (Ms Neelam; Drs Olsen, Woodworth, Cohn, and Gilboa; and Ms Tong)
| | - Van T Tong
- Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA (Ms Neelam; Drs Olsen, Woodworth, Cohn, and Gilboa; and Ms Tong)
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11
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Vică ML, Dobreanu M, Curocichin G, Matei HV, Bâlici Ș, Vușcan ME, Chiorean AD, Nicula GZ, Pavel Mironescu DC, Leucuța DC, Teodoru CA, Siserman CV. The Influence of HLA Polymorphisms on the Severity of COVID-19 in the Romanian Population. Int J Mol Sci 2024; 25:1326. [PMID: 38279325 PMCID: PMC10816224 DOI: 10.3390/ijms25021326] [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: 12/12/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
In this study, we aimed to investigate whether specific HLA alleles found in patients from Romania and the Republic of Moldova were associated with the severity of COVID-19 infection and its associated mortality. We analyzed the HLA alleles at the -A, -B, -C, -DRB1, and -DQB1 loci in a cohort of 130 individuals with severe and extremely severe forms of COVID-19, including 44 individuals who died. We compared these findings to a control group consisting of individuals who had either not been diagnosed with COVID-19 or had experienced mild forms of the disease. Using multivariate logistic regression models, we discovered that the B*27 and B*50 alleles were associated with an increased susceptibility to developing a severe form of COVID-19. The A*33 and C*15 alleles showed potential for offering protection against the disease. Furthermore, we identified two protective alleles (A*03 and DQB1*02) against the development of extremely severe forms of COVID-19. By utilizing score statistics, we established a statistically significant association between haplotypes and disease severity (p = 0.021). In summary, this study provides evidence that HLA genotype plays a role in influencing the clinical outcome of COVID-19 infection.
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Affiliation(s)
- Mihaela Laura Vică
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Minodora Dobreanu
- Emergency Clinical County Hospital, 540136 Târgu Mureș, Romania;
- Department of Laboratory Medicine, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology, 540142 Târgu Mureș, Romania
- Center for Advanced Medical and Pharmaceutical Research, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology, 540142 Târgu Mureș, Romania
| | - Ghenadie Curocichin
- Department of Family Medicine, “Nicolae Testemițanu” State University of Medicine and Pharmacy, MD-2004 Chișinău, Moldova;
| | - Horea Vladi Matei
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Ștefana Bâlici
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
| | - Mihaela Elvira Vușcan
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Alin Dan Chiorean
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Emergency Clinical Hospital for Children, 400370 Cluj-Napoca, Romania
| | - Gheorghe Zsolt Nicula
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
| | - Daniela Cristina Pavel Mironescu
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Daniel Corneliu Leucuța
- Department of Medical Informatics and Biostatistics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
| | - Cosmin Adrian Teodoru
- Clinical Surgical Department, Faculty of Medicine, “Lucian Blaga” University of Sibiu, 550169 Sibiu, Romania;
| | - Costel Vasile Siserman
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
- Department of Legal Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
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12
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Carroll TD, Wong T, Morris MK, Di Germanio C, Ma ZM, Stone M, Ball E, Fritts L, Rustagi A, Simmons G, Busch M, Miller CJ. Vaccine-Boosted CCP Decreases Virus Replication and Hastens Resolution of Infection Despite Transiently Enhancing Disease in SARS-CoV-2-Infected Hamsters. J Infect Dis 2024:jiad568. [PMID: 38213276 DOI: 10.1093/infdis/jiad568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024] Open
Abstract
Definitive data demonstrating the utility of coronavirus disease 2019 (COVID-19) convalescent plasma (CCP) for treating immunocompromised patients remains elusive. To better understand the mechanism of action of CCP, we studied viral replication and disease progression in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected hamsters treated with CCP obtained from recovered COVID-19 patients that were also vaccinated with an mRNA vaccine, hereafter referred to as Vaxplas. Vaxplas transiently enhanced disease severity and lung pathology in hamsters treated near peak viral replication due to immune complex and activated complement deposition in pulmonary endothelium, and recruitment of M1 proinflammatory macrophages into the lung parenchyma. However, aside from one report, transient enhanced disease has not been reported in CCP recipient patients, and the transient enhanced disease in Vaxplas hamsters may have been due to mismatched species IgG-FcR interactions, infusion timing, or other experimental factors. Despite transient disease enhancement, Vaxplas dramatically reduced virus replication in lungs and improved infection outcome in SARS-CoV-2-infected hamsters.
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Affiliation(s)
- Timothy D Carroll
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
- California National Primate Research Center, University of California Davis, Davis, California, USA
| | - Talia Wong
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Mary Kate Morris
- Division of Viral and Rickettsial Diseases, California Department of Public Health, Richmond, California, USA
| | | | - Zhong-Min Ma
- California National Primate Research Center, University of California Davis, Davis, California, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, California, USA
| | - Erin Ball
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Linda Fritts
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
- California National Primate Research Center, University of California Davis, Davis, California, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Graham Simmons
- Vitalant Research Institute, San Francisco, California, USA
| | - Michael Busch
- Vitalant Research Institute, San Francisco, California, USA
| | - Christopher J Miller
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
- California National Primate Research Center, University of California Davis, Davis, California, USA
- Division of Infectious Diseases, Department of Internal Medicine, School of Medicine, University of California Davis, Sacramento, California, USA
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13
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Messchendorp AL, Sanders JSF, Abrahams AC, Bemelman FJ, Bouwmans P, van den Dorpel RMA, Hilbrands LB, Imhof C, Reinders MEJ, Rispens T, Steenhuis M, ten Dam MAGJ, Vart P, de Vries APJ, Hemmelder MH, Gansevoort RT. Incidence and Severity of COVID-19 in Relation to Anti-Receptor-Binding Domain IgG Antibody Level after COVID-19 Vaccination in Kidney Transplant Recipients. Viruses 2024; 16:114. [PMID: 38257814 PMCID: PMC10820724 DOI: 10.3390/v16010114] [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: 11/02/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Kidney transplant recipients (KTRs) elicit an impaired immune response after COVID-19 vaccination; however, the exact clinical impact remains unclear. We therefore analyse the relationship between antibody levels after vaccination and the risk of COVID-19 in a large cohort of KTRs. All KTRs living in the Netherlands were invited to send a blood sample 28 days after their second COVID-19 vaccination for measurement of their IgG antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein (anti-RBD IgG). Information on COVID-19 was collected from the moment the blood sample was obtained until 6 months thereafter. Multivariable Cox and logistic regression analyses were performed to analyse which factors affected the occurrence and severity (i.e., hospitalization and/or death) of COVID-19. In total, 12,159 KTRs were approached, of whom 2885 were included in the analyses. Among those, 1578 (54.7%) became seropositive (i.e., anti-RBD IgG level >50 BAU/mL). Seropositivity was associated with a lower risk for COVID-19, also after adjusting for multiple confounders, including socio-economic status and adherence to COVID-19 restrictions (HR 0.37 (0.19-0.47), p = 0.005). When studied on a continuous scale, we observed a log-linear relationship between antibody level and the risk for COVID-19 (HR 0.52 (0.31-0.89), p = 0.02). Similar results were found for COVID-19 severity. In conclusion, antibody level after COVID-19 vaccination is associated in a log-linear manner with the occurrence and severity of COVID-19 in KTRs. This implies that if future vaccinations are indicated, the aim should be to reach for as high an antibody level as possible and not only seropositivity to protect this vulnerable patient group from disease.
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Affiliation(s)
- A. Lianne Messchendorp
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Jan-Stephan F. Sanders
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Alferso C. Abrahams
- Department of Nephrology and Hypertension, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Frederike J. Bemelman
- Division of Nephrology, Department of Internal Medicine, Amsterdam University Medical Center, Location Amsterdam Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Pim Bouwmans
- Department of Internal Medicine, Division of Nephrology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
- CARIM School for Cardiovascular Disease, University of Maastricht, 6211 LK Maastricht, The Netherlands
| | | | - Luuk B. Hilbrands
- Department of Nephrology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Céline Imhof
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Marlies E. J. Reinders
- Erasmus MC Transplant Institute, Nephrology and Transplantation, Department of Internal Medicine, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Theo Rispens
- Department of Immunopathology, Sanquin Research, 1006 AD Amsterdam, The Netherlands
- Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, 1012 WP Amsterdam, The Netherlands
| | - Maurice Steenhuis
- Department of Immunopathology, Sanquin Research, 1006 AD Amsterdam, The Netherlands
- Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, 1012 WP Amsterdam, The Netherlands
| | - Marc A. G. J. ten Dam
- Department of Internal Medicine, Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Priya Vart
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Aiko P. J. de Vries
- Leiden University Medical Center, Department of Nephrology and Leiden Transplant Center, 2333 ZA Leiden, The Netherlands
| | - Marc H. Hemmelder
- Department of Internal Medicine, Division of Nephrology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Ron T. Gansevoort
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
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14
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Harte JV, Coleman-Vaughan C, Crowley MP, Mykytiv V. It's in the blood: a review of the hematological system in SARS-CoV-2-associated COVID-19. Crit Rev Clin Lab Sci 2023; 60:595-624. [PMID: 37439130 DOI: 10.1080/10408363.2023.2232010] [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: 04/10/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an unprecedented global healthcare crisis. While SARS-CoV-2-associated COVID-19 affects primarily the respiratory system, patients with COVID-19 frequently develop extrapulmonary manifestations. Notably, changes in the hematological system, including lymphocytopenia, neutrophilia and significant abnormalities of hemostatic markers, were observed early in the pandemic. Hematological manifestations have since been recognized as important parameters in the pathophysiology of SARS-CoV-2 and in the management of patients with COVID-19. In this narrative review, we summarize the state-of-the-art regarding the hematological and hemostatic abnormalities observed in patients with SARS-CoV-2-associated COVID-19, as well as the current understanding of the hematological system in the pathophysiology of acute and chronic SARS-CoV-2-associated COVID-19.
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Affiliation(s)
- James V Harte
- Department of Haematology, Cork University Hospital, Wilton, Cork, Ireland
- School of Biochemistry & Cell Biology, University College Cork, Cork, Ireland
| | | | - Maeve P Crowley
- Department of Haematology, Cork University Hospital, Wilton, Cork, Ireland
- Irish Network for Venous Thromboembolism Research (INViTE), Ireland
| | - Vitaliy Mykytiv
- Department of Haematology, Cork University Hospital, Wilton, Cork, Ireland
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15
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Liu X, Zhang P, Chen M, Zhou H, Yue T, Xu M, Cai T, Huang J, Yue X, Li G, Zhou Z. Epidemiological and clinical features of COVID-19 inpatients in Changsha, China: A retrospective study from 2020 to 2022. Heliyon 2023; 9:e22873. [PMID: 38125480 PMCID: PMC10731055 DOI: 10.1016/j.heliyon.2023.e22873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Objectives The spread of SARS-Cov-2 remains a global concern along with the emergence of variants. This study aims to characterize the epidemiological and clinical features of hospitalized patients who were dragonized with five different variants of SARS-CoV-2 during the past 3 years. Methods This retrospective study recruited 432 COVID-19 patients who were hospitalized in the First Hospital of Changsha from January 2020 to August 2022. Clinical records on clinical symptoms, laboratory profiles, and chest CT images was collected. The epidemiological and clinical features were compared between COVID-19 patients infected with either the wild-type, Omicron variant or pre- Omicron variants (e.g., Alpha, Beta, Delta). Results A total of 432 laboratory-confirmed COVID-19 inpatients were dialogized during three waves, including 247 cases during the wild-type transmission period, 65 cases during the transmission period of pre-Omicron variants, and 119 cases during the transmission period of Omicron variants. The proportion of moderately or severely ill inpatients showed a gradual decline from the wild-type transmission period to the Omicron transmission period. The common symptoms of inpatients infected with SARS-CoV-2 wildtype strains included fever (67.61 %), cough (57.89 %), fatigue (33.60 %), and shortness of breath (12.15 %). In contrast, patients infected with other variants mostly showed upper respiratory symptoms. Based on chest CT images, a lower degree of acute pulmonary infection was observed among inpatients infected with the Omicron variants than those infected with the wild-type strain (31.09 % vs 93.12 %, p-value<0.01). Conclusions Compared with the wild-type strain, SARS-CoV-2 variants of concern, especially the Omicron variant, mostly caused a lower degree of acute pulmonary infection, indicating the reduced disease severity and mortality among hospitalized COVID-19 patients.
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Affiliation(s)
- Xiaofang Liu
- Department of Medical Administration, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha) Changsha 410000, China
| | - Pan Zhang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Meiping Chen
- Department of Infectious Diseases, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, China
| | - Haibo Zhou
- Department of Respiratory and Critical Care Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, China
| | - Tingting Yue
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ming Xu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ting Cai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Juan Huang
- Department of Pediatrics, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University(The First Hospital of Changsha), Changsha, 410000, China
| | - Xiaoyang Yue
- Department of General Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University(The First Hospital of Changsha), Changsha, 410000, China
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zhiguo Zhou
- Department of Respiratory and Critical Care Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, China
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16
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Ma Y, Zhang P, Hou M. Association of hypernatremia with mortality in patients with COVID-19: A systematic review and meta-analysis. Immun Inflamm Dis 2023; 11:e1109. [PMID: 38156387 PMCID: PMC10714304 DOI: 10.1002/iid3.1109] [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: 09/01/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic worldwide has caused varying degrees of severity of lung damage in patients, with acute respiratory distress and death in severe cases. However, this is not directly caused by the virus itself, but by the production of inflammasome by monocytes in the body, leading to a systemic inflammatory response, which results in a very poor clinical prognosis for patients with COVID-19. OBJECTIVE The purpose of this meta-analysis was to look at the relationship between hypernatremia and mortality in COVID-19 patients. METHODS We searched the PubMed, Web of Science, Embase, and Cochrane databases for articles published from the inception of the database until August 27, 2022. Three researchers reviewed the literature, retrieved data, and assessed the quality of the literature, respectively. A meta-analysis was performed using State 17 software to assess the value of the effect of hypernatremia on mortality in patients with new coronavirus pneumonia. RESULTS A total of nine publications was finally included in this study, including a total of 11,801 patients with COVID-19, including 1278 in the hypernatremia group and 10,523 in the normonatremia group. Meta-analysis showed that hypernatremia was associated with mortality in patients with COVID-19 [OR = 4.15, 95% CI (2.95-5.84), p = .002, I² = 66.7%] with a sensitivity of 0.36 [0.26, 0.48] and a specificity of 0.88 [0.83, 0.91]. The posterior probability of mortality was 42% in patients with COVID-19 hypernatremia and 15% in patients who did not have COVID-19 hypernatremia. CONCLUSION According to available data, hypernatremia is associated with death in patients with COVID-19.
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Affiliation(s)
- Yongzhi Ma
- Qinghai University Affiliated HospitalXiningChina
| | | | - Ming Hou
- Qinghai University Affiliated HospitalXiningChina
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17
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Wada N, Li Y, Gagne S, Hino T, Valtchinov VI, Gay E, Nishino M, Hammer MM, Madore B, Guttmann CRG, Ishigami K, Hunninghake GM, Levy BD, Kaye KM, Christiani DC, Hatabu H. Incidence and severity of pulmonary embolism in COVID-19 infection: Ancestral, Alpha, Delta, and Omicron variants. Medicine (Baltimore) 2023; 102:e36417. [PMID: 38050198 PMCID: PMC10695578 DOI: 10.1097/md.0000000000036417] [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: 08/09/2023] [Accepted: 11/10/2023] [Indexed: 12/06/2023] Open
Abstract
Little information is available regarding incidence and severity of pulmonary embolism (PE) across the periods of ancestral strain, Alpha, Delta, and Omicron variants. The aim of this study is to investigate the incidence and severity of PE over the dominant periods of ancestral strain and Alpha, Delta, and Omicron variants. We hypothesized that the incidence and the severity by proximity of PE in patients with the newer variants and vaccination would be decreased compared with those in ancestral and earlier variants. Patients with COVID-19 diagnosis between March 2020 and February 2022 and computed tomography pulmonary angiogram performed within a 6-week window around the diagnosis (-2 to +4 weeks) were studied retrospectively. The primary endpoints were the associations of the incidence and location of PE with the ancestral strain and each variant. Of the 720 coronavirus disease 2019 patients with computed tomography pulmonary angiogram (58.6 ± 17.2 years; 374 females), PE was diagnosed among 42/358 (12%) during the ancestral strain period, 5/60 (8%) during the Alpha variant period, 16/152 (11%) during the Delta variant period, and 13/150 (9%) during the Omicron variant period. The most proximal PE (ancestral strain vs variants) was located in the main/lobar arteries (31% vs 6%-40%), in the segmental arteries (52% vs 60%-75%), and in the subsegmental arteries (17% vs 0%-19%). There was no significant difference in both the incidence and location of PE across the periods, confirmed by multivariable logistic regression models. In summary, the incidence and severity of PE did not significantly differ across the periods of ancestral strain and Alpha, Delta, and Omicron variants.
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Affiliation(s)
- Noriaki Wada
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Yi Li
- Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Staci Gagne
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Takuya Hino
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
| | - Vladimir I. Valtchinov
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Elizabeth Gay
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Mizuki Nishino
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Mark M. Hammer
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Bruno Madore
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Charles R. G. Guttmann
- Center for Neurological Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Kousei Ishigami
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
| | - Gary M. Hunninghake
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Bruce D. Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Kenneth M. Kaye
- Division of Infectious Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - David C. Christiani
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA
| | - Hiroto Hatabu
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
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Ma Y, Lei M, Chen H, Huang P, Sun J, Sun Q, Hu Y, Shi J. Susceptibility of bovine to SARS-CoV-2 variants of concern: insights from ACE2, AXL, and NRP1 receptors. Virol J 2023; 20:276. [PMID: 38012648 PMCID: PMC10680262 DOI: 10.1186/s12985-023-02222-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
The possibilities of cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between humans and important livestock species are not yet known. Herein, we used the structural and genetic alignment and surface potential analysis of the amino acid (aa) in angiotensin-converting enzyme 2 (ACE2), tyrosine kinase receptor UFO (AXL), and neuropilin 1 (NRP1) in different species with substantial public health importance. The residues interfacing with the N-terminal domain (NTD) or receptor-binding domain (RBD) of S were aligned to screen the critical aa sites that determined the susceptibility of the SARS-CoV-2 to the host. We found that AXL and NRP1 proteins might be used as the receptors of SARS-CoV-2 in bovines. However, ACE2 protein may not be considered to be involved in the cross-species transmission of SARS-CoV-2 VOCs in cattle because the key residues of the ACE2-S-binding interface were different from those in known susceptible species. This study indicated that emerging SARS-CoV-2 variants potentially expand species tropism to bovines through AXL and NRP1 proteins.
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Affiliation(s)
- Ying Ma
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China
| | - Mengyue Lei
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China
| | - Hongli Chen
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China
- Kunming Medical University, Kunming, Yunnan Province, China
| | - Pu Huang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China
| | - Jing Sun
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China.
| | - Qiangming Sun
- National Kunming High-Level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China.
| | - Yunzhang Hu
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China.
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China.
- National Kunming High-Level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan Province, China.
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Lopes-Ribeiro Á, Oliveira PDM, Retes H, Barbosa-Stancioli EF, da Fonseca FG, Tsuji M, Coelho-dos-Reis JGA. Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8 + T cells. Front Immunol 2023; 14:1229712. [PMID: 38022506 PMCID: PMC10656734 DOI: 10.3389/fimmu.2023.1229712] [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: 05/26/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction and methods In this present work, coronavirus subfamilies and SARS-CoV-2 Variants of Concern (VOCs) were investigated for the presence of MHC-I immunodominant viral peptides using in silico and in vitro tools. Results In our results, HLA-A*02 haplotype showed the highest number of immunodominant epitopes but with the lowest combined prediction score. Furthermore, a decrease in combined prediction score was observed for HLA-A*02-restricted epitopes when the original strain was compared to the VOCs, indicating that the mutations on the VOCs are promoting escape from HLA-A2-mediated antigen presentation, which characterizes a immune evasion process. Additionally, epitope signature analysis revealed major immunogenic peptide loss for structural (S) and non-structural (ORF8) proteins of VOCs in comparison to the Wuhan sequence. Discussion These results may indicate that the antiviral CD8+ T-cell responses generated by original strains could not be sufficient for clearance of variants in either newly or reinfection with SARS-CoV-2. In contrast, N epitopes remain the most conserved and reactive peptides across SARS-CoV-2 VOCs. Overall, our data could contribute to the rational design and development of new vaccinal platforms to induce a broad cellular CD8+ T cell antiviral response, aiming at controlling viral transmission of future SARS-CoV-2 variants.
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Affiliation(s)
- Ágata Lopes-Ribeiro
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Patrícia de Melo Oliveira
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henrique Morais Retes
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edel Figueiredo Barbosa-Stancioli
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Centro de Tecnologia (CT) Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Moriya Tsuji
- Aaron Diamond AIDS Research Center, Irving Medical School, Columbia University, New York, NY, United States
| | - Jordana Grazziela Alves Coelho-dos-Reis
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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20
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Dai K, Foerster S, Vora NM, Blaney K, Keeley C, Hendricks L, Varma JK, Long T, Shaman J, Pei S. Community transmission of SARS-CoV-2 during the Delta wave in New York City. BMC Infect Dis 2023; 23:753. [PMID: 37915079 PMCID: PMC10621074 DOI: 10.1186/s12879-023-08735-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Understanding community transmission of SARS-CoV-2 variants of concern (VOCs) is critical for disease control in the post pandemic era. The Delta variant (B.1.617.2) emerged in late 2020 and became the dominant VOC globally in the summer of 2021. While the epidemiological features of the Delta variant have been extensively studied, how those characteristics shaped community transmission in urban settings remains poorly understood. METHODS Using high-resolution contact tracing data and testing records, we analyze the transmission of SARS-CoV-2 during the Delta wave within New York City (NYC) from May 2021 to October 2021. We reconstruct transmission networks at the individual level and across 177 ZIP code areas, examine network structure and spatial spread patterns, and use statistical analysis to estimate the effects of factors associated with COVID-19 spread. RESULTS We find considerable individual variations in reported contacts and secondary infections, consistent with the pre-Delta period. Compared with earlier waves, Delta-period has more frequent long-range transmission events across ZIP codes. Using socioeconomic, mobility and COVID-19 surveillance data at the ZIP code level, we find that a larger number of cumulative cases in a ZIP code area is associated with reduced within- and cross-ZIP code transmission and the number of visitors to each ZIP code is positively associated with the number of non-household infections identified through contact tracing and testing. CONCLUSIONS The Delta variant produced greater long-range spatial transmission across NYC ZIP code areas, likely caused by its increased transmissibility and elevated human mobility during the study period. Our findings highlight the potential role of population immunity in reducing transmission of VOCs. Quantifying variability of immunity is critical for identifying subpopulations susceptible to future VOCs. In addition, non-pharmaceutical interventions limiting human mobility likely reduced SARS-CoV-2 spread over successive pandemic waves and should be encouraged for reducing transmission of future VOCs.
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Affiliation(s)
- Katherine Dai
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th St, New York, NY, 10032, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Steffen Foerster
- New York City Department of Health and Mental Hygiene (DOHMH), Long Island City, NY, 11001, USA
| | - Neil M Vora
- New York City Department of Health and Mental Hygiene (DOHMH), Long Island City, NY, 11001, USA
| | - Kathleen Blaney
- New York City Department of Health and Mental Hygiene (DOHMH), Long Island City, NY, 11001, USA
| | - Chris Keeley
- New York City Department of Health and Mental Hygiene (DOHMH), Long Island City, NY, 11001, USA
| | - Lisa Hendricks
- New York City Department of Health and Mental Hygiene (DOHMH), Long Island City, NY, 11001, USA
| | - Jay K Varma
- Department of Population Health Sciences, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Theodore Long
- NYC Health + Hospitals, New York, NY, USA
- Department of Population Health, New York University, New York, NY, 10016, USA
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th St, New York, NY, 10032, USA
- Columbia Climate School, Columbia University, New York, NY, 10025, USA
| | - Sen Pei
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th St, New York, NY, 10032, USA.
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21
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Pitsillou E, Yu Y, Beh RC, Liang JJ, Hung A, Karagiannis TC. Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity. Clin Exp Med 2023; 23:3277-3298. [PMID: 37615803 DOI: 10.1007/s10238-023-01168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Yiping Yu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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22
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Brehm TT, Heyer A, Woo MS, Fischer M, van der Meirschen M, Wichmann D, Jarczak D, Roedl K, Schmiedel S, Addo MM, Lütgehetmann M, Christner M, Huber S, Lohse AW, Kluge S, Schulze Zur Wiesch J. Comparative analysis of characteristics and outcomes in hospitalized COVID-19 patients infected with different SARS-CoV-2 variants between January 2020 and April 2022 - A retrospective single-center cohort study. J Infect Public Health 2023; 16:1806-1812. [PMID: 37741015 DOI: 10.1016/j.jiph.2023.08.010] [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: 02/15/2023] [Revised: 03/31/2023] [Accepted: 08/14/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, the roll-out of vaccines and therapeutic agents, as well as the emergence of novel SARS-CoV-2 variants, have shown significant effects on disease severity. METHODS Patients hospitalized at our center between January 2020 and April 2022 were attributed to subgroups depending on which SARS-CoV-2 variant was predominantly circulating in Germany: (i) Wild-type: January 1, 2020, to March 7, 2021, (ii) Alpha variant: August 3, 2021, to June 27, 2021, (iii) Delta variant: June 28, 2021, to December 26, 2021, and (iv) Omicron variant: December 27, 2021, to April 30, 2022. RESULTS Between January 2020 and April 2022, 1500 patients with SARS-CoV-2 infections were admitted to the University Medical Center Hamburg-Eppendorf. The rate of patients who were admitted to the intensive care unit (ICU) decreased from 31.2% (n = 223) in the wild-type group, 28.5% (n = 72) in the Alpha variant group, 18.8% (n = 67) in the Delta variant group, and 13.4% (n = 135) in the Omicron variant group. Also, in-hospital mortality decreased from 20.6% (n = 111) in the wild-type group, 17.5% (n = 30) in the Alpha variant group, 16.8% (n = 33) in the Delta variant group, and 6.6% (n = 39) in the Omicron variant group. The median duration of hospitalization was similar in all subgroups and ranged between 11 and 15 days throughout the pandemic. CONCLUSIONS In-hospital mortality and rate of ICU admission among hospitalized COVID-19 patients steadily decreased throughout the pandemic. However, the practically unchanged duration of hospitalization demonstrates the persistent burden of COVID-19 on the healthcare system.
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Affiliation(s)
- Thomas Theo Brehm
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Andreas Heyer
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marcel S Woo
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Neuroimmunology and Multiple Sclerosis (INIMS), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marlene Fischer
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marc van der Meirschen
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Dominic Wichmann
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Dominik Jarczak
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Kevin Roedl
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Stefan Schmiedel
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Marylyn M Addo
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; Institute for Infection Research and Vaccine Development (IIRVD), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Martin Christner
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Samuel Huber
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Ansgar W Lohse
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Stefan Kluge
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Julian Schulze Zur Wiesch
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany.
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23
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Alisoltani A, Simons LM, Agnes MFR, Heald-Sargent TA, Muller WJ, Kociolek LK, Hultquist JF, Lorenzo-Redondo R, Ozer EA. Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient. Virol J 2023; 20:246. [PMID: 37891657 PMCID: PMC10604949 DOI: 10.1186/s12985-023-02186-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Persistent SARS-CoV-2 infection in immunocompromised hosts is thought to contribute to viral evolution by facilitating long-term natural selection and viral recombination in cases of viral co-infection or superinfection. However, there are limited data on the longitudinal intra-host population dynamics of SARS-CoV-2 co-infection/superinfection, especially in pediatric populations. Here, we report a case of Delta-Omicron superinfection in a hospitalized, immunocompromised pediatric patient. METHODS We conducted Illumina whole genome sequencing (WGS) for longitudinal specimens to investigate intra-host dynamics of SARS-CoV-2 strains. Topoisomerase PCR cloning of Spike open-reading frame and Sanger sequencing of samples was performed for four specimens to validate the findings. Analysis of publicly available SARS-CoV-2 sequence data was performed to investigate the co-circulation and persistence of SARS-CoV-2 variants. RESULTS Results of WGS indicate the patient was initially infected with the SARS-CoV-2 Delta variant before developing a SARS-CoV-2 Omicron variant superinfection, which became predominant. Shortly thereafter, viral loads decreased below the level of detection before resurgence of the original Delta variant with no residual trace of Omicron. After 54 days of persistent infection, the patient tested negative for SARS-CoV-2 but ultimately succumbed to a COVID-19-related death. Despite protracted treatment with remdesivir, no antiviral resistance mutations emerged. These results indicate a unique case of persistent SARS-CoV-2 infection with the Delta variant interposed by a transient superinfection with the Omicron variant. Analysis of publicly available sequence data suggests the persistence and ongoing evolution of Delta subvariants despite the global predominance of Omicron, potentially indicative of continued transmission in an unknown population or niche. CONCLUSION A better understanding of SARS-CoV-2 intra-host population dynamics, persistence, and evolution during co-infections and/or superinfections will be required to continue optimizing patient care and to better predict the emergence of new variants of concern.
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Affiliation(s)
- Arghavan Alisoltani
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Maria Francesca Reyes Agnes
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | | | - William J Muller
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Larry K Kociolek
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
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24
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Singh MK, Anjali A, Singh BK, Cattani C. Impact of general incidence function on three-strain SEIAR model. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:19710-19731. [PMID: 38052621 DOI: 10.3934/mbe.2023873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
We investigate the behavior of a complex three-strain model with a generalized incidence rate. The incidence rate is an essential aspect of the model as it determines the number of new infections emerging. The mathematical model comprises thirteen nonlinear ordinary differential equations with susceptible, exposed, symptomatic, asymptomatic and recovered compartments. The model is well-posed and verified through existence, positivity and boundedness. Eight equilibria comprise a disease-free equilibria and seven endemic equilibrium points following the existence of three strains. The basic reproduction numbers $ \mathfrak{R}_{01} $, $ \mathfrak{R}_{02} $ and $ \mathfrak{R}_{03} $ represent the dominance of strain 1, strain 2 and strain 3 in the environment for new strain emergence. The model establishes local stability at a disease-free equilibrium point. Numerical simulations endorse the impact of general incidence rates, including bi-linear, saturated, Beddington DeAngelis, non-monotone and Crowley Martin incidence rates.
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Affiliation(s)
- Manoj Kumar Singh
- Faculty of Mathematics & Computing, Department of Mathematics & Statistics, Banasthali Vidyapith, Rajasthan 304022, India
| | - Anjali Anjali
- Faculty of Mathematics & Computing, Department of Mathematics & Statistics, Banasthali Vidyapith, Rajasthan 304022, India
| | - Brajesh K Singh
- Department of Mathematics, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Carlo Cattani
- Department of Mathematics and Informatics, Azerbaijan University, J. Hajibeyli str., AZ1007, Baku
- Azerbaijan Engineering School, DEIM, University of Tuscia, P.le dellUniversità, Viterbo 01100, Italy
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25
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Liu LT, Chiou SS, Chen PC, Chen CH, Lin PC, Tsai CY, Chuang WL, Hwang SJ, Chong IW, Tsai JJ. Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan. Sci Rep 2023; 13:16583. [PMID: 37789031 PMCID: PMC10547678 DOI: 10.1038/s41598-023-43357-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first detected in October 2021, possessed many mutations compared to previous variants. We aimed to identify and analyze SARS-CoV-2 Omicron subvariants among coronavirus disease 2019 (COVID-19) patients between January 2022 and September 2022 in Taiwan. The results revealed that BA.2.3.7, featuring K97E and G1251V in the spike protein compared with BA.2, emerged in March 2022 and persistently dominated between April 2022 and August 2022, resulting in the largest COVID-19 outbreak since 2020. The accumulation of amino acid (AA) variations, mainly AA substitution, in the spike protein was accompanied by increasing severity in Omicron-related COVID-19 between April 2022 and January 2023. Older patients were more likely to have severe COVID-19, and comorbidity was a risk factor for COVID-19-related mortality. The accumulated case fatality rate (CFR) dropped drastically after Omicron variants, mainly BA.2.3.7, entered Taiwan after April 2022, and the CFR was 0.16% in Taiwan, which was lower than that worldwide (0.31%) between April 2021 and January 2023. The relatively low CFR in Omicron-related COVID-19 patients can be attributed to adjustments to public health policies, promotion of vaccination programs, effective antiviral drugs, and the lower severity of the Omicron variant.
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Affiliation(s)
- Li-Teh Liu
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan City, Taiwan
| | - Shyh-Shin Chiou
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Po-Chih Chen
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Chun-Hong Chen
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Ping-Chang Lin
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Ching-Yi Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Wan-Long Chuang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Shang-Jyh Hwang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Inn-Wen Chong
- Department of Internal Medicine and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Department of Pulmonary Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan.
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan.
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, No. 100, Tzyou 1st Road, Kaohsiung City, 80756, Taiwan.
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26
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Srivastava PK, Klomhaus AM, Tehrani DM, Fonarow GC, Ziaeian B, Desai PS, Rafique A, de Lemos J, Parikh RV, Yang EH. Impact of Age and Variant Time Period on Clinical Presentation and Outcomes of Hospitalized Coronavirus Disease 2019 Patients. Mayo Clin Proc Innov Qual Outcomes 2023; 7:411-429. [PMID: 37731677 PMCID: PMC10507578 DOI: 10.1016/j.mayocpiqo.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023] Open
Abstract
Objective To evaluate the impact of age and COVID-19 variant time period on morbidity and mortality among those hospitalized with COVID-19. Patients and Methods Patients from the American Heart Association's Get With The Guidelines COVID-19 cardiovascular disease registry (January 20, 2020-February 14, 2022) were divided into groups based on whether they presented during periods of wild type/alpha, delta, or omicron predominance. They were further subdivided by age (young: 18-40 years; older: more than 40 years), and characteristics and outcomes were compared. Results The cohort consisted of 45,421 hospitalized COVID-19 patients (wild type/alpha period: 41,426, delta period: 3349, and omicron period: 646). Among young patients (18-40 years), presentation during delta was associated with increased odds of severe COVID-19 (OR, 1.6; 95% CI, 1.3-2.1), major adverse cardiovascular events (MACE) (OR, 1.8; 95% CI, 1.3-2.5), and in-hospital mortality (OR, 2.2; 95% CI, 1.5-3.3) when compared with presentation during wild type/alpha. Among older patients (more than 40 years), presentation during delta was associated with increased odds of severe COVID-19 (OR, 1.2; 95% CI, 1.1-1.3), MACE (OR, 1.5; 95% CI, 1.4-1.7), and in-hospital mortality (OR, 1.4; 95% CI, 1.3-1.6) when compared with wild type/alpha. Among older patients (more than 40 years), presentation during omicron associated with decreased odds of severe COVID-19 (OR, 0.7; 95% CI, 0.5-0.9) and in-hospital mortality (OR, 0.6; 95% CI, 0.5-0.9) when compared with wild type/alpha. Conclusion Among hospitalized adults with COVID-19, presentation during a time of delta predominance was associated with increased odds of severe COVID-19, MACE, and in-hospital mortality compared with presentation during wild type/alpha. Among older patients (aged more than 40 years), presentation during omicron was associated with decreased odds of severe COVID-19 and in-hospital mortality compared with wild type/alpha.
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Affiliation(s)
- Pratyaksh K. Srivastava
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - David M. Tehrani
- Division of Cardiology, Ronald Reagan UCLA Medical Center, Los Angeles, CA
| | - Gregg C. Fonarow
- Ahmanson-UCLA Cardiomyopathy Center, Ronald Reagan UCLA Medical Center, Los Angeles, CA
| | - Boback Ziaeian
- Division of Cardiology, West Los Angeles Medical Center, Los Angeles, CA
| | - Pooja S. Desai
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Asim Rafique
- Division of Cardiology, Santa Monica UCLA Medical Center, Los Angeles, CA
| | - James de Lemos
- Division of Cardiology, UT Southwestern Medical Center, Dallas, TX
| | - Rushi V. Parikh
- Division of Cardiology, Ronald Reagan UCLA Medical Center, Los Angeles, CA
| | - Eric H. Yang
- Division of Cardiology, Ronald Reagan UCLA Medical Center, Los Angeles, CA
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27
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Jank M, Oechsle AL, Armann J, Behrends U, Berner R, Chao CM, Diffloth N, Doenhardt M, Hansen G, Hufnagel M, Lander F, Liese JG, Muntau AC, Niehues T, von Both U, Verjans E, Weil K, von Kries R, Schroten H. Comparing SARS-CoV-2 variants among children and adolescents in Germany: relative risk of COVID-19-related hospitalization, ICU admission and mortality. Infection 2023; 51:1357-1367. [PMID: 36787015 PMCID: PMC9925936 DOI: 10.1007/s15010-023-01996-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
PURPOSE SARS-CoV-2 infections cause COVID-19 and have a wide spectrum of morbidity. Severe disease courses among children are rare. To date, data on the variability of morbidity in relation to variant of concern (VOC) in children has been sparse and inconclusive. We compare the clinical severity of SARS-CoV-2 infection among children and adolescents in Germany during the Wildtype and Alpha combined, Delta and Omicron phases of the COVID-19 pandemic. METHODS Comparing risk of COVID-19-related hospitalization, intensive care unit (ICU) admission and death due to COVID-19 in children and adolescents, we used: (1) a multi-center seroprevalence study (SARS-CoV-2-KIDS study); (2) a nationwide registry of pediatric patients hospitalized with SARS-CoV-2 infections; and (3) compulsory national reporting for RT-PCR-confirmed SARS-CoV-2 infections in Germany. RESULTS During the Delta predominant phase, risk of COVID-19-related hospitalization among all SARS-CoV-2 seropositive children was 3.35, ICU admission 1.19 and fatality 0.09 per 10,000; hence about halved for hospitalization and ICU admission and unchanged for deaths as compared to the Wildtype- and Alpha-dominant period. The relative risk for COVID-19-related hospitalization and ICU admission compared to the alpha period decreased during Delta [0.60 (95% CI 0.54; 0.67) and 0.51 (95% CI 0.42; 0.61)] and Omicron [0.27 (95% CI 0.24; 0.30) and 0.06 (95% CI 0.05; 0.08)] period except for the < 5-year-olds. The rate of case fatalities decreased slightly during Delta, and substantially during Omicron phase. CONCLUSION Morbidity caused by SARS-CoV-2 infections among children and adolescents in Germany decreased over the course of the COVID-19 pandemic, as different VOCs) emerged.
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Affiliation(s)
- Marietta Jank
- Department of Pediatrics, University Medical Center Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
- Department of Pediatric Surgery, University Medical Center Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
| | - Anna-Lisa Oechsle
- Division of Pediatric Epidemiology, Institute of Social Pediatrics and Adolescent Medicine, Ludwig-Maximilians-University Munich, 80336, Munich, Germany
| | - Jakob Armann
- Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Uta Behrends
- Department of Pediatrics, Faculty of Medicine, Technical University Munich, 80804, Munich, Germany
| | - Reinhard Berner
- Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Cho-Ming Chao
- Department of Pediatrics, Helios University Medical Center, Witten/Herdecke University, Heusnerstr. 40, 42283, Wuppertal, Germany
- Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Natalie Diffloth
- Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Maren Doenhardt
- Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Gesine Hansen
- Centre for Pediatrics and Adolescent Medicine, Hannover Medical School, Excellence Cluster RESIST, Deutsche Forschungsgemeinschaft (DFG), EXS 2155, 30625, Hannover, Germany
| | - Markus Hufnagel
- Department of Pediatrics and Adolescent Medicine, Medical Faculty, University Medical Center, University of Freiburg, Freiburg, Germany
| | - Fabian Lander
- Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Johannes G Liese
- Division of Paediatric Infectious Diseases, Department of Pediatrics, University Hospital of Wuerzburg, 97080, Würzburg, Germany
| | - Ania C Muntau
- Medical Center Hamburg-Eppendorf, University Children's Hospital, Martinistrasse 52, 20246, Hamburg, Germany
| | - Tim Niehues
- Department of Pediatrics, Helios Klinikum Krefeld, 47805, Krefeld, Germany
| | - Ulrich von Both
- Dr von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University, 80337, Munich, Germany
| | - Eva Verjans
- Department of Pediatrics, Medical Faculty, University Hospital RWTH Aachen, 52074, Aachen, Germany
| | - Katharina Weil
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, Medical Faculty, University Hospital, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Rüdiger von Kries
- Division of Pediatric Epidemiology, Institute of Social Pediatrics and Adolescent Medicine, Ludwig-Maximilians-University Munich, 80336, Munich, Germany
| | - Horst Schroten
- Department of Pediatrics, University Medical Center Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
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28
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Giannitsioti E, Mavroudis P, Speggos I, Katsoulidou A, Pantazis N, Loupis T, Daniil I, Rekleiti N, Damianidou S, Louka C, Sidiropoulou C, Kranidiotis G, Velentza L, Stamati A, Kasidiaraki M, Efstratiadi E, Linardaki G, Chrysos G, Zarkotou O, Zoi K, Tryfinopoulou K, Gerakari S. Real life treatment experience and outcome of consecutively hospitalised patients with SARS-CoV-2 pneumonia by Omicron-1 vs Delta variants. Infect Dis (Lond) 2023; 55:706-715. [PMID: 37427461 DOI: 10.1080/23744235.2023.2232445] [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: 12/26/2022] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/11/2023] Open
Abstract
BACKGROUND Omicron-1 COVID-19 is less invasive in the general population than previous viral variants. However, clinical course and outcome of hospitalised patients with SARS-CoV-2 pneumonia during the shift of the predominance from Delta to Omicron variants are not fully explored. METHODS During January 2022 consecutively hospitalised patients with SARS-CoV-2 pneumonia were analysed. SARS-CoV-2 variants were identified by a 2-step pre-screening protocol and randomly confirmed by whole genome sequencing analysis. Clinical, laboratory and treatment data split by type of variant were analysed along with logistic regression of factors associated to mortality. RESULTS 150 patients [mean age (SD) 67.2(15.8) years, male 54%] were analysed. Compared to Delta (n = 46), Omicron-1 patients (n = 104) were older [mean age (SD): 69.5(15.4) vs 61.9(15.8) years, p = 0.007], with more comorbidities (89.4% vs 65.2%, p = 0.001), less obesity (BMI >30Kg/m2 in 24% vs 43.5%, p = 0.034) but higher vaccination rates for COVID-19 (52.9% vs 8.7%, p < 0.001). Severe pneumonia (48.7%), pulmonary embolism (4.7%), need for invasive mechanical ventilation (8%), administration of dexamethasone (76%) and 60-day mortality (22.6%) did not significantly differ. Severe SARS-CoV-2 pneumonia independently predicted mortality [OR 8.297 (CI95% 2.080-33.095), p = 0.003]. Remdesivir administration (n = 135) was protective from death both in unadjusted and adjusted models [OR 0.157 (CI95% 0.026-0.945), p = 0.043. CONCLUSIONS In a COVID-19 department the severity of pneumonia that did not differ between Omicron-1 and Delta variants predicted mortality whilst remdesivir remained protective in all analyses. Death rates did not differ between SARS-CoV-2 variants. Vigilance and consistency with prevention and treatment guidelines for COVID-19 is mandatory regardless of the predominant SARS-CoV-2 variant.
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Affiliation(s)
- Efthymia Giannitsioti
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, ATTIKON University General Hospital, Athens, Greece
| | - Panagiotis Mavroudis
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Ioannis Speggos
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Antigoni Katsoulidou
- Central Public Health Laboratory, National Public Health Organization, Athens, Greece
| | - Nikos Pantazis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodoros Loupis
- Greek Genome Centre, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
- Haematology Research Laboratory, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Ioannis Daniil
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Nektaria Rekleiti
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Sofia Damianidou
- Central Public Health Laboratory, National Public Health Organization, Athens, Greece
| | - Christina Louka
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Chrysanthi Sidiropoulou
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Georgios Kranidiotis
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Lemonia Velentza
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Emergency Department, Tzaneio General Hospital, Piraeus, Greece
| | - Alexandra Stamati
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Maria Kasidiaraki
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Emergency Department, Tzaneio General Hospital, Piraeus, Greece
| | - Efrosini Efstratiadi
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Emergency Department, Tzaneio General Hospital, Piraeus, Greece
| | - Garyfallia Linardaki
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Georgios Chrysos
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Olympia Zarkotou
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Katerina Zoi
- Greek Genome Centre, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
- Haematology Research Laboratory, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Kyriaki Tryfinopoulou
- Central Public Health Laboratory, National Public Health Organization, Athens, Greece
| | - Styliani Gerakari
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Emergency Department, Tzaneio General Hospital, Piraeus, Greece
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Kim SM, Kim EH, Casel MAB, Kim YI, Sun R, Kwak MJ, Yoo JS, Yu M, Yu KM, Jang SG, Rollon R, Choi JH, Gil J, Eun K, Kim H, Ensser A, Hwang J, Song MS, Kim MH, Jung JU, Choi YK. SARS-CoV-2 variants with NSP12 P323L/G671S mutations display enhanced virus replication in ferret upper airways and higher transmissibility. Cell Rep 2023; 42:113077. [PMID: 37676771 DOI: 10.1016/j.celrep.2023.113077] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/02/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
With the emergence of multiple predominant SARS-CoV-2 variants, it becomes important to have a comprehensive assessment of their viral fitness and transmissibility. Here, we demonstrate that natural temperature differences between the upper (33°C) and lower (37°C) respiratory tract have profound effects on SARS-CoV-2 replication and transmissibility. Specifically, SARS-CoV-2 variants containing the NSP12 mutations P323L or P323L/G671S exhibit enhanced RNA-dependent RNA polymerase (RdRp) activity at 33°C compared with 37°C and high transmissibility. Molecular dynamics simulations and microscale thermophoresis demonstrate that the NSP12 P323L and P323L/G671S mutations stabilize the NSP12-NSP7-NSP8 complex through hydrophobic effects, leading to increased viral RdRp activity. Furthermore, competitive transmissibility assay reveals that reverse genetic (RG)-P323L or RG-P323L/G671S NSP12 outcompetes RG-WT (wild-type) NSP12 for replication in the upper respiratory tract, allowing markedly rapid transmissibility. This suggests that NSP12 P323L or P323L/G671S mutation of SARS-CoV-2 is associated with increased RdRp complex stability and enzymatic activity, promoting efficient transmissibility.
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Affiliation(s)
- Se-Mi Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Eun-Ha Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Mark Anthony B Casel
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Young-Il Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Rong Sun
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mi-Jeong Kwak
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ji-Seung Yoo
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Mina Yu
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Kwang-Min Yu
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Seung-Gyu Jang
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Rare Rollon
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Jeong Ho Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Juryeon Gil
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Kiyoung Eun
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hyunggee Kim
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Armin Ensser
- Institute for Clinical and Molecular Virology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Jungwon Hwang
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Min-Suk Song
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Young Ki Choi
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea; College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea.
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Maruyama K, Sekiya K, Yanagida N, Nakayama K, Kushida Y, Yasuda S, Fukumoto D, Hosoya S, Moriya H, Katsumi M. Analysis of the Factors That Affect the Detection Duration of SARS-CoV-2 in Loop Mediated Isothermal Amplification among COVID-19 Inpatients. Jpn J Infect Dis 2023; 76:282-288. [PMID: 37258175 DOI: 10.7883/yoken.jjid.2023.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In COVID-19 patients who are immunocompromised or have severe COVID-19, the duration of infectious viral shedding may be longer, and a longer isolation duration is recommended. At the National Sagamihara Hospital, a decline in the viral load to end the isolation of hospitalized patients with COVID-19 was confirmed using loop-mediated isothermal amplification (LAMP). However, a subset of patients displayed LAMP positivity for more than 20 days after symptom onset. Therefore, we conducted a retrospective observational study to investigate the factors that affect the persistence of LAMP positivity. This study included a total of 102 participants. The severity of COVID-19 was mild (25.5%), moderate (67.6%), or severe (6.9%). The median number (interquartile range) of days until negative LAMP results from symptom onset were 16 (14-19) days. Multivariate logistic regression analysis showed that patients ≥55 years and/or those with the delta variant were correlated with persistent LAMP positivity for more than 20 days after symptom onset. This study identified age, the delta variant, and oxygen requirement as factors that contribute to persistently positive LAMP results. Therefore, it is posited that in these patients, the implementation of LAMP for deisolation would result in a prolonged isolation duration.
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Affiliation(s)
- Kohei Maruyama
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Department of Pharmacy, National Hospital Organization Sagamihara National Hospital, Japan
| | - Kiyoshi Sekiya
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Japan
| | - Noriyuki Yanagida
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Department of Pediatrics, National Hospital Organization Sagamihara National Hospital, Japan
| | - Kanae Nakayama
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Department of Clinical Laboratory, National Hospital Organization Sagamihara National Hospital, Japan
| | - Yusuke Kushida
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Department of Pharmacy, National Hospital Organization Sagamihara National Hospital, Japan
| | - Shuhei Yasuda
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Department of Clinical Laboratory, National Hospital Organization Sagamihara National Hospital, Japan
| | - Daisuke Fukumoto
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Department of Nursing, National Hospital Organization Sagamihara National Hospital, Japan
| | - Satoshi Hosoya
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Department of Emergency and Critical Care Medicine, National Hospital Organization Sagamihara National Hospital, Japan
| | - Hiromitsu Moriya
- Department of Infection Control and Prevention, National Hospital Organization Sagamihara National Hospital, Japan
- Department of Surgery, National Hospital Organization Sagamihara National Hospital, Japan
| | - Manabu Katsumi
- Department of Pharmacy, National Hospital Organization Sagamihara National Hospital, Japan
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Yalci A, Doğan E, Kapici MA, Demirkıran BÇ, Filiz M, Artuk C. What we learned from steroid therapy in the COVID-19 pandemic. Niger J Clin Pract 2023; 26:1348-1353. [PMID: 37794549 DOI: 10.4103/njcp.njcp_110_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Background The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic named coronavirus disease 2019 (COVID-19) that has become the greatest worldwide public health threat. Although different treatment recommendations are offered for COVID-19 infection, steroid treatment remains important. Aim We aimed to demonstrate the effect of pulse steroid therapy (PST) on inflammatory markers and patient outcomes in moderate/severe COVID-19 pneumonia. Materials and Methods We retrospectively analyzed the patients 18 years and older hospitalized in our hospital's COVID-19 clinics between April 1, 2020, to June 30, 2020, and July 1, 2021, to November 30, 2021. Patients in the moderate/severe COVID-19 pneumonia category, according to the World Health Organization COVID-19 guidelines, were included in the study. The demographic characteristics of the patients, treatments, inflammatory markers, and patient outcomes (need for intensive care, length of hospital stay, high-flow nasal oxygen (HFNO) requirement, mechanical ventilation (MV), and mortality rates) were recorded and analyzed. Results Patients who received PST had more advanced age (P < 0.01), more comorbidities (P < 0.001), and more HFNO need (P < 001) compared with the patients who did not receive PST. There was no statistically significant difference between clinical outcomes: the need for intensive care, length of hospital stay, need for MV, and mortality rates (P = 0.54, P = 0.3, P = 0.14, and P = 0.09, respectively). When we evaluated the unvaccinated patients, there was a statistically significant difference in the MV need and mortality rates between those who received PST and those who did not (P = 0.017, P = 0.014, respectively). Conclusion It was observed that PST provided similar mortality, ICU, and MV requirements in patients with older age and comorbidities. Lower MV requirements and mortality were observed in the unvaccinated group receiving PST compared with the unvaccinated group not receiving steroids. PST is still promising in COVID-19 infection, and more studies are needed for standard doses and applications.
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Affiliation(s)
- A Yalci
- Department of Infectious Diseases and Clinical Microbiology, University of Health Science, Gülhane Educational and Research Hospital, Ankara, Turkey
| | - E Doğan
- Department of Infectious Diseases and Clinical Microbiology, University of Health Science, Gülhane Educational and Research Hospital, Ankara, Turkey
| | - M A Kapici
- Department of Infectious Diseases and Clinical Microbiology, University of Health Science, Gülhane Educational and Research Hospital, Ankara, Turkey
| | - B Ç Demirkıran
- Department of Infectious Diseases and Clinical Microbiology, University of Health Science, Gülhane Educational and Research Hospital, Ankara, Turkey
| | - M Filiz
- Department of Infectious Diseases and Clinical Microbiology, University of Health Science, Gülhane Educational and Research Hospital, Ankara, Turkey
| | - C Artuk
- Department of Infectious Diseases and Clinical Microbiology, University of Health Science, Gülhane Educational and Research Hospital, Ankara, Turkey
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Zhou Z, Li D, Zhao Z, Shi S, Wu J, Li J, Zhang J, Gui K, Zhang Y, Ouyang Q, Mei H, Hu Y, Li F. Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients. PLoS Comput Biol 2023; 19:e1011383. [PMID: 37656752 PMCID: PMC10501599 DOI: 10.1371/journal.pcbi.1011383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/14/2023] [Accepted: 07/24/2023] [Indexed: 09/03/2023] Open
Abstract
Once challenged by the SARS-CoV-2 virus, the human host immune system triggers a dynamic process against infection. We constructed a mathematical model to describe host innate and adaptive immune response to viral challenge. Based on the dynamic properties of viral load and immune response, we classified the resulting dynamics into four modes, reflecting increasing severity of COVID-19 disease. We found the numerical product of immune system's ability to clear the virus and to kill the infected cells, namely immune efficacy, to be predictive of disease severity. We also investigated vaccine-induced protection against SARS-CoV-2 infection. Results suggested that immune efficacy based on memory T cells and neutralizing antibody titers could be used to predict population vaccine protection rates. Finally, we analyzed infection dynamics of SARS-CoV-2 variants within the construct of our mathematical model. Overall, our results provide a systematic framework for understanding the dynamics of host response upon challenge by SARS-CoV-2 infection, and this framework can be used to predict vaccine protection and perform clinical diagnosis.
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Affiliation(s)
- Zhengqing Zhou
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Dianjie Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Ziheng Zhao
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Shuyu Shi
- Peking University Third Hospital, Peking University, Beijing, China
| | - Jianghua Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianwei Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Jingpeng Zhang
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Ke Gui
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yu Zhang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Qi Ouyang
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Heng Mei
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fangting Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
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Carroll TD, Wong T, Morris MK, Di Germanio C, Ma ZM, Stone M, Ball E, Fritts L, Rustagi A, Simmons G, Busch M, Miller CJ. Administration of vaccine-boosted COVID-19 convalescent plasma to SARS-CoV-2 infected hamsters decreases virus replication in lungs and hastens resolution of the infection despite transiently enhancing disease and lung pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.553458. [PMID: 37662344 PMCID: PMC10473650 DOI: 10.1101/2023.08.22.553458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The utility of COVID-19 convalescent plasma (CCP) for treatment of immunocompromised patients who are not able to mount a protective antibody response against SARS-CoV-2 and who have contraindications or adverse effects from currently available antivirals remains unclear. To better understand the mechanism of protection in CCP, we studied viral replication and disease progression in SARS-CoV-2 infected hamsters treated with CCP plasma obtained from recovered COVID patients that had also been vaccinated with an mRNA vaccine, hereafter referred to as Vaxplas. We found that Vaxplas dramatically reduced virus replication in the lungs and improved infection outcome in SARS-CoV-2 infected hamsters. However, we also found that Vaxplas transiently enhanced disease severity and lung pathology in treated animals likely due to the deposition of immune complexes, activation of complement and recruitment of increased numbers of macrophages with an M1 proinflammatory phenotype into the lung parenchyma.
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Affiliation(s)
- Timothy D. Carroll
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
- California National Primate Research Center, University of California Davis, Davis, California, USA
| | - Talia Wong
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Mary Kate Morris
- Division of Viral and Rickettsial Diseases, California Department of Public Health, Richmond, California, USA
| | | | - Zhong-min Ma
- California National Primate Research Center, University of California Davis, Davis, California, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
| | - Erin Ball
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Linda Fritts
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
- California National Primate Research Center, University of California Davis, Davis, California, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | | | | | - Christopher J. Miller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
- California National Primate Research Center, University of California Davis, Davis, California, USA
- Division of Infectious Diseases, Department of Internal Medicine, School of Medicine, University of California Davis, Sacramento, California, USA
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Kandeel A, Moatasim Y, Fahim M, Bahaaeldin H, El-Shesheny R, Roshdy WH, Kamel MN, Shawky S, Gomaa M, Naguib A, Guindy NE, Deghedy O, Kamel R, Khalifa M, Galal R, Hassany M, Mahmoud G, Kandeil A, Afifi S, Mohsen A, Fattah MA, Kayali G, Ali MA, Abdelghaffar K. Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020-2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality. BMC Infect Dis 2023; 23:542. [PMID: 37596534 PMCID: PMC10439637 DOI: 10.1186/s12879-023-08527-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed millions of people and caused widespread concern around the world. Multiple genetic variants of SARS-CoV-2 have been identified as the pandemic continues. Concerns have been raised about high transmissibility and lower vaccine efficacy against omicron. There is an urgent need to better describe how omicron will impact clinical presentation and vaccine efficacy. This study aims at comparing the epidemiologic, clinical, and genomic characteristics of the omicron variant prevalent during the fifth wave with those of other VOCs between May 2020 and April 2022. METHODS Epidemiological data were obtained from the National Electronic Diseases Surveillance System. Secondary data analysis was performed on all confirmed COVID-19 patients. Descriptive data analysis was performed for demographics and patient outcome and the incidence of COVID-19 was calculated as the proportion of SARS-CoV-2 confirmed patients out of the total population of Egypt. Incidence and characteristics of the omicron cohort from January- April 2022, were compared to those confirmed from May 2020-December 2021. We performed the whole-genome sequencing of SARS-CoV-2 on 1590 specimens using Illumina sequencing to describe the circulation of the virus lineages in Egypt. RESULTS A total of 502,629 patients enrolled, including 60,665 (12.1%) reported in the fifth wave. The incidence rate of omicron was significantly lower than the mean of incidences in the previous subperiod (60.1 vs. 86.3/100,000 population, p < 0.001). Symptoms were reported less often in the omicron cohort than in patients with other variants, with omicron having a lower hospitalization rate and overall case fatality rate as well. The omicron cohort tended to stay fewer days at the hospital than did those with other variants. We analyzed sequences of 2433 (1590 in this study and 843 were obtained from GISAID platform) Egyptian SARS-CoV-2 full genomes. The first wave that occurred before the emergence of global variants of concern belonged to the B.1 clade. The second and third waves were associated with C.36. Waves 4 and 5 included B.1.617.2 and BA.1 clades, respectively. CONCLUSIONS The study indicated that Omicron-infected patients had milder symptoms and were less likely to be hospitalized; however, patients hospitalized with omicron had a more severe course and higher fatality rates than those hospitalized with other variants. Our findings demonstrate the importance of combining epidemiological data and genomic analysis to generate actionable information for public health decision-making.
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Affiliation(s)
- Amr Kandeel
- Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Yassmin Moatasim
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Manal Fahim
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Hala Bahaaeldin
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt.
| | - Rabeh El-Shesheny
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Wael H Roshdy
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Mina N Kamel
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Shaymaa Shawky
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Mokhtar Gomaa
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Amel Naguib
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Nancy El Guindy
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Ola Deghedy
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Reham Kamel
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Mohamed Khalifa
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Ramy Galal
- Public Health Initiatives, Cairo, 11613, Egypt
| | - Mohamed Hassany
- National Hepatology and Tropical Medicine Research Institute, Ministry of Health and Population, Cairo, 11613, Egypt
| | - Galal Mahmoud
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Ahmed Kandeil
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Salma Afifi
- Ministry of Health and Population Consultant, Cairo, Egypt
| | - Amira Mohsen
- Community Medicine Department, National Research Centre, Cairo, Egypt
| | - Mohammad Abdel Fattah
- Preventive Sector, Central Administration for Preventive Affairs, Ministry of Health and Population, Cairo, Egypt
| | | | - Mohamed A Ali
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
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Agrawal P, Damania D, Cseh A, Grab J, Strom L, Frank B, Patel D, Clyatt G. Impact of COVID vaccine and comorbidities in patients receiving casirivimab-imdevimab monoclonal antibody during SARS-CoV-2 B.1.617.2 (Delta) surge: A real-world study. Vaccine 2023; 41:5195-5200. [PMID: 37451874 DOI: 10.1016/j.vaccine.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Several randomized trials and real-world studies depicted the role of monoclonal antibody infusion in reducing hospitalization, and halting progression from asymptomatic to symptomatic COVID pneumonia, viral titer, and death. No data exists to show outcomes of patients who received casirivimab-imdevimab infusion based on their vaccination status and underlying comorbidities. This study aims to provide outcomes of casirivimab-imdevimab treatment during the SARS-CoV-2 B1.617.2 (Delta) surge among fully vaccinated and not fully vaccinated individuals. METHODS COVID-19-positive patients who received casirivimab-imdevimab infusion during the Delta surge were analyzed to compare their underlying comorbidities and the rate of 28-days all-cause and COVID-related ED visits or hospitalization, among fully vaccinated and not fully vaccinated individuals. RESULTS A total of 3,586 patients received casirivimab-imdevimab infusion. COVID-related hospitalizations were directly related to the number of comorbidities (OR:1.745, 95 % CI:1.469-2.074). Vaccinated patients with ≥3 comorbidities had lower rates of 28-day COVID-related ED visits or hospitalization (p = 0.044) and those with ≥4 comorbidities had lower rates of 28-day All-cause ED visits or hospitalization (p = 0.029). Hypertension (OR:2.418, 95 %CI:1.341-4.360), immunocompromised state (OR:5.250, 95 %CI: 1.912-14.417), age ≥ 65 (OR:4.045, 95 %CI:2.224-7.358) increased the probability of hospitalization due to COVID and being fully vaccinated lowered the likelihood of hospitalization (OR: 0.472, 95 %CI: 0.239-0.933). Vaccinated patients had a lower length of COVID-related hospitalization (2 days vs 4.5 days, p < 0.001). CONCLUSION COVID vaccination status and comorbidities are significant predictors of outcomes after casirivimab-imdevimab treatment. Despite having higher comorbidities, patients who were fully vaccinated at the time of casirivimab-imdevimab infusion had a lower length of hospitalization and reduced 28-day COVID ED visits or hospitalizations. Future trials should also compare outcomes based on the patient's vaccination status.
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Affiliation(s)
- Pankaj Agrawal
- Department of Medicine, South Georgia Medical Center, 2501 N Patterson St., Valdosta, GA, United States.
| | - Dushyant Damania
- Pulmonary Critical Care, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Attila Cseh
- Economics, Valdosta State University, Valdosta, GA, United States
| | - John Grab
- Edward Via College of Osteopathic Medicine, Auburn, AL, United States
| | - Laura Strom
- Edward Via College of Osteopathic Medicine, Auburn, AL, United States
| | - Brianna Frank
- Edward Via College of Osteopathic Medicine, Auburn, AL, United States
| | - Dhruv Patel
- Philadelphia College of Osteopathic Medicine- Moultrie, GA, United States
| | - Griffin Clyatt
- Philadelphia College of Osteopathic Medicine- Moultrie, GA, United States
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Kim CY, Sardar Z, Ayele BA, Fleck‐Derderian S, Barrett CE, Sun Y, Clague M, Hurst HA, Boruah A, Zucker J, Maddox R, Sejvar J, Thakur KT. Neurological diagnoses in hospitalized COVID-19 patients during the B.1.1.529 surge. Ann Clin Transl Neurol 2023; 10:1433-1441. [PMID: 37350635 PMCID: PMC10424653 DOI: 10.1002/acn3.51833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
OBJECTIVE Emerging variants and sublineages of SARS-CoV-2 have differing disease severity, transmissibility, and immune evasion. The neurological conditions associated with the original strain of SARS-CoV-2 are well established. Our study assessed the neurological presentations specific to hospitalized patients during the B.1.1.529 (Omicron) variant surge in New York City. METHODS A total of 178 cases with positive RT-PCR result within 6 weeks before admission, and subsequent development of select neurological conditions during the SARS-CoV-2 B.1.1.529 (Omicron) surge between December 1, 2021 and February 28, 2022, were included from 12,800 SARS-CoV-2-positive hospital admissions. Clinical data from acute hospitalizations were compared to findings of inpatient neurological cases with COVID-19 infections from the initial surge in NYC in the same hospital system. RESULTS Compared to SARS-CoV-2 infections of the original strain, COVID-19 cases hospitalized during the Omicron surge (B.1.1.529) were associated with incidental and/or asymptomatic COVID-19 cases (96, 53.9%) and an increased incidence of pre-existing neurological and immunocompromising conditions. Encephalopathy, seizures, and stroke remained the most prevalent neurological conditions identified in hospitalized COVID-19 cases during the study period, reflecting a similar distribution of neurological presentations associated with the original strain. INTERPRETATION In our cohort of 178 admitted SARS-CoV-2-positive patients with select neurological conditions during the Omicron B.1.1.529 surge, 54% of COVID-19 cases were considered incidental and/or asymptomatic, and the identified neurological conditions resembled those associated with the original SARS-CoV-2 strain. Further studies characterizing neurological presentation in Omicron sublineages and other variants are warranted in an ongoing COVID-19 pandemic.
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Affiliation(s)
- Carla Y. Kim
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Zomer Sardar
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Biniyam A. Ayele
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | | | | | - Yifei Sun
- Department of BiostatisticsColumbia UniversityNew YorkNew YorkUSA
| | - Madison Clague
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Holly A. Hurst
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Abhilasha Boruah
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
- Case Western Reserve University School of MedicineClevelandOhioUSA
| | - Jason Zucker
- Department of Infectious DiseaseColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Ryan Maddox
- United States Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - James Sejvar
- United States Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Kiran T. Thakur
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
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Kim JM, Kim D, Lee NJ, Woo SH, Lee J, Lee H, Park AK, Kim JA, Lee CY, Kim ,IH, Yoo CK, Kim EJ. Increased viral load in patients infected with severe acute respiratory syndrome coronavirus 2 Omicron variant in the Republic of Korea. Osong Public Health Res Perspect 2023; 14:272-278. [PMID: 37652682 PMCID: PMC10493702 DOI: 10.24171/j.phrp.2023.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/12/2023] [Accepted: 06/12/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has been declared a global pandemic owing to the rapid spread of the causative agent, severe acute respiratory syndrome coronavirus 2. Its Delta and Omicron variants are more transmissible and pathogenic than other variants. Some debates have emerged on the mechanism of variants of concern. In the COVID-19 wave that began in December 2021, the Omicron variant, first reported in South Africa, became identifiable in most cases globally. The aim of this study was to provide data to inform effective responses to the transmission of the Omicron variant. METHODS The Delta variant and the spike protein D614G mutant were compared with the Omicron variant. Viral loads from 5 days after symptom onset were compared using epidemiological data collected at the time of diagnosis. RESULTS The Omicron variant exhibited a higher viral load than other variants, resulting in greater transmissibility within 5 days of symptom onset. CONCLUSION Future research should focus on vaccine efficacy against the Omicron variant and compare trends in disease severity associated with its high viral load.
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Affiliation(s)
- Jeong-Min Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Dongju Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Nam-Joo Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Sang Hee Woo
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jaehee Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Hyeokjin Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Ae Kyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jeong-Ah Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Chae Young Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - , Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Cheon Kwon Yoo
- Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
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Ryder JH, Van Schooneveld TC, Abdalhamid B, Wood MG, Wahlig TA, Starlin R, Gillett G, Balfour T, Pflueger L, Rupp ME. Nosocomial outbreak of SARS-CoV-2 delta variant among vaccinated healthcare workers and immunocompromised patients on a solid-organ transplant unit: Complexities of an epidemiologic and genomic investigation. Infect Control Hosp Epidemiol 2023; 44:1355-1357. [PMID: 36082695 PMCID: PMC9551180 DOI: 10.1017/ice.2022.233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022]
Abstract
In September 2021, a cluster of 6 patients with nosocomial coronavirus disease 2019 (COVID-19) were identified in a transplant unit. A visitor and 11 healthcare workers also tested positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2). Genomic sequencing identified 3 separate introductions of SARS-CoV-2 with related transmission among the identified patients and healthcare workers.
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Affiliation(s)
- Jonathan H. Ryder
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Trevor C. Van Schooneveld
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Baha Abdalhamid
- Nebraska Public Health Laboratory, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Macy G. Wood
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Taylor A. Wahlig
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Richard Starlin
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Gayle Gillett
- Department of Infection Control and Epidemiology, Nebraska Medicine, Omaha, Nebraska
| | | | | | - Mark E. Rupp
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska
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Quee FA, Hogema BM, Slot E, Kruijer S, Molier M, van den Hurk K, Zaaijer HL. Booster vaccinations and Omicron: the effects on SARS-CoV-2 antibodies in Dutch blood donors. BMC Infect Dis 2023; 23:464. [PMID: 37438703 DOI: 10.1186/s12879-023-08448-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023] Open
Abstract
INTRODUCTION The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) booster vaccination campaign and the emergence of SARS-CoV-2 Omicron variants impact the prevalence and levels of SARS-CoV-2 antibodies in the Netherlands. In this study we determined antibody levels across age groups, the impact of Omicron variant infections, and the effect of booster vaccinations on antibody levels. METHODS In September and December 2021 and in February 2022, over 2000 Dutch blood donors were tested for presence of SARS-CoV-2 antibodies. Donations were selected based on age, sex, and region of residence, to provide an optimal coverage and representation of the Dutch population. RESULTS Levels of vaccination-induced spike antibodies decreased over time in all age groups. Donors vaccinated with Janssen or AstraZeneca had significantly lower antibody levels than donors vaccinated with Pfizer or Moderna vaccine. Boostering with an mRNA vaccine elevated antibody levels in all age-groups irrespective of the initial vaccine. In donors aged < 56 years, the proportion of infected donors almost doubled between December 2021 and February 2022. CONCLUSION The booster vaccination campaign increased antibody levels in all age-groups. After a booster vaccination, donors initially vaccinated with AstraZeneca or Janssen vaccine showed antibody levels similar to donors initially vaccinated with an mRNA vaccine. The emergence of the SARS-CoV-2 Omicron variant in the Netherlands caused a substantial increase in donors with infection-induced antibodies, especially among younger donors.
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Affiliation(s)
- F A Quee
- Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
| | - B M Hogema
- Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
- Department of Virology, Sanquin Diagnostic Services, Amsterdam, the Netherlands
| | - E Slot
- Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
- Department of Medical Affairs, Sanquin Corporate Staff, Amsterdam, the Netherlands
| | - S Kruijer
- Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, the Netherlands
| | - M Molier
- Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
| | - K van den Hurk
- Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
| | - H L Zaaijer
- Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
- Department of Clinical Virology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
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Kim J, Choi G, Oh J, Park K, Yoo SJ. Comparative Study on Two COVID-19 Outbreaks at a Long-Term Mental Health Facility in Korea in 2020 and 2022. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1170. [PMID: 37374374 DOI: 10.3390/medicina59061170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
(1) Background and Objectives: There were two distinct coronavirus disease 2019 (COVID-19) outbreaks in 2020 and 2022 at a long-term mental health facility (LTMHF) in Gyeonggi Province, Korea. We aimed to compare the two outbreaks and identify differences in epidemiological and clinical outcomes due to changes in epidemic timing and management methods. (2) Materials and Methods: The structural, operational, and case-specific LTMHF data of COVID-19-confirmed patients during these outbreaks in 2020 and 2022 were retrospectively analyzed. (3) Results: Forty individuals (37 residents) in 2020 and thirty-nine (32 residents) in 2022 were confirmed to have COVID-19, and ten were infected twice. Facility isolation was implemented as an infection control measure, and one COVID-19-related death occurred in 2020. All residents and staff were vaccinated at least twice in 2022; moreover, in 2022, 38 patients (97.4%) received a third vaccination less than months before infection. The average Ct value of the cases in 2022 was significantly higher than that in 2020; however, vaccine-breakthrough (V-BT) and reinfection after vaccination rates were similar. (4) Conclusions: COVID-19 vaccination could help lower the viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was inversely correlated with Ct values, and ventilation system improvements in health facilities might reduce transmissibility.
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Affiliation(s)
- Jina Kim
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon 16508, Republic of Korea
| | - Gawon Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon 16508, Republic of Korea
| | - Jeonghyeon Oh
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon 16508, Republic of Korea
| | - Kunhee Park
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon 16508, Republic of Korea
| | - Seok-Ju Yoo
- Department of Preventive Medicine, College of Medicine, Dongguk University, Seoul 04620, Republic of Korea
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Salgado-Benvindo C, Leijs AA, Thaler M, Tas A, Arbiser JL, Snijder EJ, van Hemert MJ. Honokiol Inhibits SARS-CoV-2 Replication in Cell Culture at a Post-Entry Step. Microbiol Spectr 2023; 11:e0327322. [PMID: 37212560 PMCID: PMC10269499 DOI: 10.1128/spectrum.03273-22] [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: 08/18/2022] [Accepted: 04/10/2023] [Indexed: 05/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019, and the resulting pandemic has already caused the death of over 6 million people. There are currently few antivirals approved for treatment of the 2019 coronavirus disease (COVID-19), and more options would be beneficial, not only now but also to increase our preparedness for future coronavirus outbreaks. Honokiol is a small molecule from magnolia trees for which several biological effects have been reported, including anticancer and anti-inflammatory activities. Honokiol has also been shown to inhibit several viruses in cell culture. In this study, we determined that honokiol protected Vero E6 cells from SARS-CoV-2-mediated cytopathic effect, with a 50% effective concentration of 7.8 μM. In viral load reduction assays, honokiol decreased viral RNA copies as well as viral infectious progeny titers. The compound also inhibited SARS-CoV-2 replication in the more relevant human A549 cells expressing angiotensin converting enzyme 2 and transmembrane protease serine 2. Time-of-addition and other assays showed that honokiol inhibited virus replication at a post-entry step of the replication cycle. Honokiol was also effective against more recent variants of SARS-CoV-2, including Omicron, and it inhibited other human coronaviruses as well. Our study suggests that honokiol is an interesting molecule to be evaluated further in animal studies and, when successful, maybe even in clinical trials to investigate its effect on virus replication and pathogenic (inflammatory) host responses. IMPORTANCE Honokiol is a compound that shows both anti-inflammatory and antiviral effects, and therefore its effect on SARS-CoV-2 infection was assessed. This small molecule inhibited SARS-CoV-2 replication in various cell-based infection systems, with up to an ~1,000-fold reduction in virus titer. In contrast to earlier reports, our study clearly showed that honokiol acts on a postentry step of the replication cycle. Honokiol also inhibited different recent SARS-CoV-2 variants and other human coronaviruses (Middle East respiratory syndrome CoV and SARS-CoV), demonstrating its broad spectrum of antiviral activity. The anticoronavirus effect, combined with its anti-inflammatory properties, make honokiol an interesting compound to be further explored in animal coronavirus infection models.
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Affiliation(s)
| | - Anouk A. Leijs
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Melissa Thaler
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ali Tas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jack L. Arbiser
- Department of Dermatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Dermatology, Veterans Affairs Medical Center, Decatur, Georgia, USA
| | - Eric J. Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Martijn J. van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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Han W, Chen N, Xu X, Sahil A, Zhou J, Li Z, Zhong H, Gao E, Zhang R, Wang Y, Sun S, Cheung PPH, Gao X. Predicting the antigenic evolution of SARS-COV-2 with deep learning. Nat Commun 2023; 14:3478. [PMID: 37311849 DOI: 10.1038/s41467-023-39199-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
The relentless evolution of SARS-CoV-2 poses a significant threat to public health, as it adapts to immune pressure from vaccines and natural infections. Gaining insights into potential antigenic changes is critical but challenging due to the vast sequence space. Here, we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithms to predict the viral fitness landscape and explore antigenic evolution via in silico directed evolution. By analyzing existing SARS-CoV-2 variants, MLAEP accurately infers variant order along antigenic evolutionary trajectories, correlating with corresponding sampling time. Our approach identified novel mutations in immunocompromised COVID-19 patients and emerging variants like XBB1.5. Additionally, MLAEP predictions were validated through in vitro neutralizing antibody binding assays, demonstrating that the predicted variants exhibited enhanced immune evasion. By profiling existing variants and predicting potential antigenic changes, MLAEP aids in vaccine development and enhances preparedness against future SARS-CoV-2 variants.
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Affiliation(s)
- Wenkai Han
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ningning Chen
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xinzhou Xu
- Department of Chemical Pathology, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Adil Sahil
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juexiao Zhou
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Zhongxiao Li
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Huawen Zhong
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Elva Gao
- The KAUST School, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | | | - Yu Wang
- Syneron Technology, Guangzhou, 510000, China
| | - Shiwei Sun
- Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China.
- Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China.
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Wang X, Zhu X, Lin Y, He L, Yang J, Wang C, Zhu W. Tracking the first SARS-CoV-2 Omicron BA.5.1.3 outbreak in China. Front Microbiol 2023; 14:1183633. [PMID: 37275159 PMCID: PMC10232789 DOI: 10.3389/fmicb.2023.1183633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/28/2023] [Indexed: 06/07/2023] Open
Abstract
The SARS-CoV-2 is still undergoing rapid evolution, resulting in the emergence of several variants of concern, especially the Omicron variants (B.1.1.529), which are surging worldwide. In this study, we tracked Omicron subvariant BA.5.1.3 as the causative agent in the Hainan Province wave in China, which started on 1 August 2022. This was China's first case of Omicron subvariant BA.5.1.3 and led to an indefinite total lockdown in Hainan with more than 8,500 confirmed cases. We obtained 391 whole genomes from positive nasopharyngeal swab samples in the city of Sanya in Hainan Province, which was the center of this outbreak. More than half of the infected cases were female (58%, 227/391) with a median age of 37.0 years (IQR 23.0-53.0). Median Ct values were 24.9 (IQR 22.6-27.3) and 25.2 (IQR 22.9-27.6) for ORF1ab and N genes, respectively. The total single-nucleotide polymorphism (SNP) numbers of Omicron BA.5.1.3 sampled in Sanya (median 69.0, IQR = 69.0-70.0) compared to those worldwide (median 63.0, IQR = 61.0-64.0) showed a significant difference (p < 0.05). Unique core mutations, including three non-synonymous mutations in ORF1ab (Y1064N, S2844G, and R3574K) and one synonymous mutation in ORF3a (S74S), were found. Phylogenetic analysis showed that virus from Sanya formed an independent sub-clade within the BA.5.1.3 subvariant, and could be divided into 15 haplotypes based on the S gene. The most recent common ancestor for the virus from Sanya was estimated as appearing on 5 July 2022, with 95% HPD ranging from 15 May to 20 September 2022. Thanks to our results, we were also able to delineate the mutational profile of this outbreak and highlight the importance of global genomic surveillance and data sharing.
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Affiliation(s)
- Xiaoxia Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Xiong Zhu
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Yujin Lin
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Lvfen He
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chuan Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wentao Zhu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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Mahmoudi S, Pourakbari B, Benvari S, Hosseinpour Sadeghi R, Abdolsalehi MR, Shahbabaie MA, Jalali F, Safari F, Navaeian A, Mamishi S. Clinical and laboratory features of SARS-CoV-2 variants across multiple rounds of pandemic waves in hospitalized children in an Iranian referral hospital. BMC Pediatr 2023; 23:241. [PMID: 37193986 DOI: 10.1186/s12887-023-04042-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/27/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Since the onset of the COVID-19 pandemic, SARS-CoV-2 has evolved into independent new forms, variants of concern (VOCs). While epidemiological data showed increased transmissibility of VOCs, their impact on clinical outcomes is less clear. This study aimed to investigate the differences between the clinical and laboratory features of children infected with VOCs. METHODS This study included all cases with SARS-CoV-2-positive nasopharyngeal swabs obtained from patients referred to Children's Medical Center (CMC), an Iranian referral hospital, between July 2021 and March 2022. The inclusion criteria for this study included all patients, regardless of age, who had a positive test anywhere in the hospital setting. Exclusion criteria for the study included those whose data was obtained from non-hospital outpatient settings, or referred from another hospital. The SARS-CoV-2 genome area encoding the S1 domain was amplified and sequenced. The type of variant in each sample was identified based on the mutations in the S1 gene. Demographic characteristics, clinical data, and laboratory findings were collected from the patient's medical records. RESULTS This study included 87 pediatric cases with confirmed COVID-19, with a median age of 3.5 years (IQR: 1-8.12). Data from sequencing reveals the type of variants as 5 (5.7%) alpha, 53 (60.9%) Delta, and 29 (33.3%) Omicron. The incidence of seizure was higher in patients with Alpha and Omicron infection compared to the Delta group. A higher incidence of diarrhea was reported in Alpha-infected patients, and a higher risk of disease severity, distress, and myalgia was associated with Delta infection. CONCLUSION Laboratory parameters did not mostly differ among the patients infected with Alpha, Delta, and Omicron. However, these variants may manifest different clinical features. Further studies with larger sample sizes are required to fully understand the clinical manifestations of each variant.
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Affiliation(s)
- Shima Mahmoudi
- Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Biotechnology Centre, Silesian University of Technology, Gliwice, 44-100, Poland
| | - Babak Pourakbari
- Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Benvari
- Department of Microbiology, Faculty of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Mohammad Reza Abdolsalehi
- Department of Infectious Diseases, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Shahbabaie
- Department of Infectious Diseases, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Jalali
- Department of Infectious Diseases, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Safari
- Department of Infectious Diseases, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Amene Navaeian
- Department of Infectious Diseases, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Setareh Mamishi
- Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Infectious Diseases, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran.
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Robinson ML, Morris CP, Betz JF, Zhang Y, Bollinger R, Wang N, Thiemann DR, Fall A, Eldesouki RE, Norton JM, Gaston DC, Forman M, Luo CH, Zeger SL, Gupta A, Garibaldi BT, Mostafa HH. Impact of Severe Acute Respiratory Syndrome Coronavirus 2 Variants on Inpatient Clinical Outcome. Clin Infect Dis 2023; 76:1539-1549. [PMID: 36528815 PMCID: PMC10411930 DOI: 10.1093/cid/ciac957] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/21/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Prior observation has shown differences in COVID-19 hospitalization risk between SARS-CoV-2 variants, but limited information describes hospitalization outcomes. METHODS Inpatients with COVID-19 at 5 hospitals in the eastern United States were included if they had hypoxia, tachypnea, tachycardia, or fever, and SARS-CoV-2 variant data, determined from whole-genome sequencing or local surveillance inference. Analyses were stratified by history of SARS-CoV-2 vaccination or infection. The average effect of SARS-CoV-2 variant on 28-day risk of severe disease, defined by advanced respiratory support needs, or death was evaluated using models weighted on propensity scores derived from baseline clinical features. RESULTS Severe disease or death within 28 days occurred for 977 (29%) of 3369 unvaccinated patients and 269 (22%) of 1230 patients with history of vaccination or prior SARS-CoV-2 infection. Among unvaccinated patients, the relative risk of severe disease or death for Delta variant compared with ancestral lineages was 1.30 (95% confidence interval [CI]: 1.11-1.49). Compared with Delta, the risk for Omicron patients was .72 (95% CI: .59-.88) and compared with ancestral lineages was .94 (.78-1.1). Among Omicron and Delta infections, patients with history of vaccination or prior SARS-CoV-2 infection had half the risk of severe disease or death (adjusted hazard ratio: .40; 95% CI: .30-.54), but no significant outcome difference by variant. CONCLUSIONS Although risk of severe disease or death for unvaccinated inpatients with Omicron was lower than with Delta, it was similar to ancestral lineages. Severe outcomes were less common in vaccinated inpatients, with no difference between Delta and Omicron infections.
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Affiliation(s)
- Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - C Paul Morris
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua F Betz
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Yifan Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Robert Bollinger
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natalie Wang
- Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - David R Thiemann
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amary Fall
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Raghda E Eldesouki
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julie M Norton
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David C Gaston
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Forman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amita Gupta
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brian T Garibaldi
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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46
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Han MS, Kim KM, Oh KJ, Chang JY, Lee SY, Choi JE, Shin SM, Sun J. Distinct Clinical and Laboratory Features of COVID-19 in Children During the Pre-Delta, Delta and Omicron Wave. Pediatr Infect Dis J 2023; 42:423-428. [PMID: 36795583 PMCID: PMC10097473 DOI: 10.1097/inf.0000000000003872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/19/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND The SARS-CoV-2 variants of concern exhibit distinct features in terms of transmissibility and virulence. This study compared the clinical characteristics of COVID-19 in children during pre-Delta, Delta and Omicron waves. METHODS Medical records of 1163 children <19 years of age with COVID-19 admitted to a designated hospital in Seoul, South Korea, were analyzed. Clinical and laboratory findings during the pre-Delta (March 1, 2020, to June 30, 2021; 330 children), Delta (July 1, 2021, to December 31, 2021; 527 children) and Omicron (January 1, 2022, to May 10, 2022; 306 children) waves were compared. RESULTS Children during the Delta wave were older and had a higher proportion of fever ≥5 days and pneumonia than children during the pre-Delta and Omicron waves. The Omicron wave was characterized by younger age and a higher proportion of fever ≥39.0 °C, febrile seizure and croup. More children <2 years of age and adolescents aged 10 to <19 years experienced neutropenia and lymphopenia, respectively, during the Delta wave. Children aged 2 to <10 years had a higher incidence of leukopenia and lymphopenia during the Omicron wave. CONCLUSIONS Distinct features of COVID-19 were observed in children during the Delta and Omicron surges. Continuous scrutiny of the manifestations of variants of concern is needed for appropriate public health response and management.
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Affiliation(s)
- Mi Seon Han
- From the Department of Pediatrics, Seoul Metropolitan Government-Seoul National University Boramae Medical Center
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | - Kyung Min Kim
- Department of Pediatrics, Chungnam National University Hospital, Daejeon
| | - Kyung Jin Oh
- From the Department of Pediatrics, Seoul Metropolitan Government-Seoul National University Boramae Medical Center
| | - Ju Young Chang
- From the Department of Pediatrics, Seoul Metropolitan Government-Seoul National University Boramae Medical Center
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | - Seong Yong Lee
- From the Department of Pediatrics, Seoul Metropolitan Government-Seoul National University Boramae Medical Center
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | - Ji Eun Choi
- From the Department of Pediatrics, Seoul Metropolitan Government-Seoul National University Boramae Medical Center
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | | | - Jiyu Sun
- Medical Research Collaborating Center, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
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47
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García-García A, Pérez de Diego R, Flores C, Rinchai D, Solé-Violán J, Deyà-Martínez À, García-Solis B, Lorenzo-Salazar JM, Hernández-Brito E, Lanz AL, Moens L, Bucciol G, Almuqamam M, Domachowske JB, Colino E, Santos-Perez JL, Marco FM, Pignata C, Bousfiha A, Turvey SE, Bauer S, Haerynck F, Ocejo-Vinyals JG, Lendinez F, Prader S, Naumann-Bartsch N, Pachlopnik Schmid J, Biggs CM, Hildebrand K, Dreesman A, Cárdenes MÁ, Ailal F, Benhsaien I, Giardino G, Molina-Fuentes A, Fortuny C, Madhavarapu S, Conway DH, Prando C, Schidlowski L, Martínez de Saavedra Álvarez MT, Alfaro R, Rodríguez de Castro F, Meyts I, Hauck F, Puel A, Bastard P, Boisson B, Jouanguy E, Abel L, Cobat A, Zhang Q, Casanova JL, Alsina L, Rodríguez-Gallego C. Humans with inherited MyD88 and IRAK-4 deficiencies are predisposed to hypoxemic COVID-19 pneumonia. J Exp Med 2023; 220:e20220170. [PMID: 36880831 PMCID: PMC9998661 DOI: 10.1084/jem.20220170] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 11/11/2022] [Accepted: 01/30/2023] [Indexed: 03/08/2023] Open
Abstract
X-linked recessive deficiency of TLR7, a MyD88- and IRAK-4-dependent endosomal ssRNA sensor, impairs SARS-CoV-2 recognition and type I IFN production in plasmacytoid dendritic cells (pDCs), thereby underlying hypoxemic COVID-19 pneumonia with high penetrance. We report 22 unvaccinated patients with autosomal recessive MyD88 or IRAK-4 deficiency infected with SARS-CoV-2 (mean age: 10.9 yr; 2 mo to 24 yr), originating from 17 kindreds from eight countries on three continents. 16 patients were hospitalized: six with moderate, four with severe, and six with critical pneumonia, one of whom died. The risk of hypoxemic pneumonia increased with age. The risk of invasive mechanical ventilation was also much greater than in age-matched controls from the general population (OR: 74.7, 95% CI: 26.8-207.8, P < 0.001). The patients' susceptibility to SARS-CoV-2 can be attributed to impaired TLR7-dependent type I IFN production by pDCs, which do not sense SARS-CoV-2 correctly. Patients with inherited MyD88 or IRAK-4 deficiency were long thought to be selectively vulnerable to pyogenic bacteria, but also have a high risk of hypoxemic COVID-19 pneumonia.
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Affiliation(s)
- Ana García-García
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
| | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Jordi Solé-Violán
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Dept. of Intensive Care Medicine, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Àngela Deyà-Martínez
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
| | - Blanca García-Solis
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Elisa Hernández-Brito
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Anna-Lisa Lanz
- Dept. of Pediatrics, Division of Pediatric Immunology and Rheumatology, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Leen Moens
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
| | - Giorgia Bucciol
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Childhood Immunology, UZ Leuven, Leuven, Belgium
| | - Mohamed Almuqamam
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | | | - Elena Colino
- Unidad de Enfermedades Infecciosas, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - Juan Luis Santos-Perez
- Unidad de Gestión Clínica de Pediatría y Cirugía Pediátrica, Hospital Virgen de las Nieves-IBS, Granada, Spain
| | - Francisco M. Marco
- Dept. of Immunology, Alicante University General Hospital Doctor Balmis, Alicante, Spain
- Alicante Institute for Health and Biomedical Research, Alicante, Spain
| | - Claudio Pignata
- Dept. of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Aziz Bousfiha
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Stuart E. Turvey
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Stefanie Bauer
- Clinic for Children and Adolescents. Dept. of Hematology and Oncology. University Clinic Erlangen, Erlangen, Germany
| | - Filomeen Haerynck
- Dept. of Pediatric Immunology and Pulmonology, Centre for Primary Immune Deficiency Ghent, Ghent University Hospital, Ghent, Belgium
- Dept. of Internal Medicine and Pediatrics, PID Research Laboratory, Ghent University, Ghent, Belgium
| | | | - Francisco Lendinez
- Dept. of Pediatric Oncohematology, Hospital Materno Infantil Torrecárdenas, Almería, Spain
| | - Seraina Prader
- Division of Immunology and Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - Nora Naumann-Bartsch
- Clinic for Children and Adolescents. Dept. of Hematology and Oncology. University Clinic Erlangen, Erlangen, Germany
| | - Jana Pachlopnik Schmid
- Division of Immunology and Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - Catherine M. Biggs
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Kyla Hildebrand
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | | | - Miguel Ángel Cárdenes
- Dept. of Internal Medicine, Unit of Infectious Diseases, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Fatima Ailal
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Ibtihal Benhsaien
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Giuliana Giardino
- Dept. of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | | | - Claudia Fortuny
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain; Translational Research Network in Pediatric Infectious Diseases, Madrid, Spain
- Dept. of Surgery and Surgical Specializations, Facultat de Medicina i Ciències de la Salut, University of Barcelona, Barcelona, Spain
| | - Swetha Madhavarapu
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | - Daniel H. Conway
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | - Carolina Prando
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Hospital Pequeno Príncipe, Curitiba, Brazil
| | - Laire Schidlowski
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Hospital Pequeno Príncipe, Curitiba, Brazil
| | | | - Rafael Alfaro
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Felipe Rodríguez de Castro
- Dept. of Medical and Surgical Sciences, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Dept. of Respiratory Diseases, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Childhood Immunology, UZ Leuven, Leuven, Belgium
| | - Fabian Hauck
- Dept. of Pediatrics, Division of Pediatric Immunology and Rheumatology, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Pediatric Hematology and Immunology Unit, Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Laia Alsina
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
- Dept. of Surgery and Surgical Specializations, Facultat de Medicina i Ciències de la Salut, University of Barcelona, Barcelona, Spain
| | - Carlos Rodríguez-Gallego
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Dept. of Medical and Surgical Sciences, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
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Tu B, Gao Y, An X, Wang H, Huang Y. Localized delivery of nanomedicine and antibodies for combating COVID-19. Acta Pharm Sin B 2023; 13:1828-1846. [PMID: 36168329 PMCID: PMC9502448 DOI: 10.1016/j.apsb.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/01/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a major health burden in the world. So far, many strategies have been investigated to control the spread of COVID-19, including social distancing, disinfection protocols, vaccines, and antiviral treatments. Despite the significant achievement, due to the constantly emerging new variants, COVID-19 is still a great challenge to the global healthcare system. It is an urgent demand for the development of new therapeutics and technologies for containing the wild spread of SARS-CoV-2. Inhaled administration is useful for the treatment of lung and respiratory diseases, and enables the drugs to reach the site of action directly with benefits of decreased dose, improved safety, and enhanced patient compliance. Nanotechnology has been extensively applied in the prevention and treatment of COVID-19. In this review, the inhaled nanomedicines and antibodies, as well as intranasal nanodrugs, for the prevention and treatment of COVID-19 are summarized.
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Affiliation(s)
- Bin Tu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanrong Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinran An
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Huiyuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yongzhuo Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, SIMM, CAS, Zhongshan 528437, China
- NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients, Shanghai 201203, China
- Taizhou University, School of Advanced Study, Institute of Natural Medicine and Health Product, Taizhou 318000, China
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49
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Messiah SE, Swartz MD, Abbas RA, Talebi Y, Kohl HW, Valerio-Shewmaker M, DeSantis SM, Yaseen A, Kelder SH, Ross JA, Padilla LN, Gonzalez MO, Wu L, Lakey D, Shuford JA, Pont SJ, Boerwinkle E. SARS-CoV-2 Serostatus and COVID-19 Illness Characteristics by Variant Time Period in Non-Hospitalized Children and Adolescents. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10050818. [PMID: 37238366 DOI: 10.3390/children10050818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/13/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To describe COVID-19 illness characteristics, risk factors, and SARS-CoV-2 serostatus by variant time period in a large community-based pediatric sample. DESIGN Data were collected prospectively over four timepoints between October 2020 and November 2022 from a population-based cohort ages 5 to 19 years old. SETTING State of Texas, USA. PARTICIPANTS Participants ages 5 to 19 years were recruited from large pediatric healthcare systems, Federally Qualified Healthcare Centers, urban and rural clinical practices, health insurance providers, and a social media campaign. EXPOSURE SARS-CoV-2 infection. MAIN OUTCOME(S) AND MEASURE(S) SARS-CoV-2 antibody status was assessed by the Roche Elecsys® Anti-SARS-CoV-2 Immunoassay for detection of antibodies to the SARS-CoV-2 nucleocapsid protein (Roche N-test). Self-reported antigen or PCR COVID-19 test results and symptom status were also collected. RESULTS Over half (57.2%) of the sample (N = 3911) was antibody positive. Symptomatic infection increased over time from 47.09% during the pre-Delta variant time period, to 76.95% during Delta, to 84.73% during Omicron, and to 94.79% during the Omicron BA.2. Those who were not vaccinated were more likely (OR 1.71, 95% CI 1.47, 2.00) to be infected versus those fully vaccinated. CONCLUSIONS Results show an increase in symptomatic COVID-19 infection among non-hospitalized children with each progressive variant over the past two years. Findings here support the public health guidance that eligible children should remain up to date with COVID-19 vaccinations.
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Affiliation(s)
- Sarah E Messiah
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health in Dallas, The University of Texas (UT) Health Science Center at Houston, Dallas, TX 77030, USA
- Center for Pediatric Population Health, UTHealth School of Public Health, Dallas, TX 75207, USA
- Department of Pediatrics, McGovern Medical School, Houston, TX 77030, USA
| | - Michael D Swartz
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Rhiana A Abbas
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yashar Talebi
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Harold W Kohl
- School of Public Health in Austin, The University of Texas Health Science Center at Houston, Austin, TX 78701, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas at Austin, Austin, TX 78705, USA
| | - Melissa Valerio-Shewmaker
- School of Public Health in Brownville, The University of Texas Health Science Center at Houston, Brownsville, TX 78520, USA
| | - Stacia M DeSantis
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ashraf Yaseen
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Steven H Kelder
- School of Public Health in Austin, The University of Texas Health Science Center at Houston, Austin, TX 78701, USA
| | - Jessica A Ross
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lindsay N Padilla
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Michael O Gonzalez
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Leqing Wu
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - David Lakey
- Administration Division, University of Texas System, Austin, TX 78701, USA
- Department of Medicine, The University of Texas Health Science Center Tyler, Tyler, TX 75708, USA
| | | | - Stephen J Pont
- Texas Department of State Health Services, Austin, TX 78711, USA
| | - Eric Boerwinkle
- Department of Biostatistics and Data Sciences, School of Public Health in Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Metchurtchlishvili R, Chkhartishvili N, Abutidze A, Endeladze M, Ezugbaia M, Bakradze A, Tsertsvadze T. Effect of remdesivir on mortality and the need for mechanical ventilation among hospitalized patients with COVID-19: real-world data from a resource-limited country. Int J Infect Dis 2023; 129:63-69. [PMID: 36690139 PMCID: PMC9854141 DOI: 10.1016/j.ijid.2023.01.021] [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: 07/23/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVES Georgia introduced remdesivir for the treatment of COVID-19 in December 2020. We evaluated the real-world effect of remdesivir on mortality and the need for mechanical ventilation among inpatients with COVID-19. METHODS The study included 346 remdesivir recipients and 346 controls not receiving remdesivir selected through propensity score matching based on age, gender, presence of any chronic comorbid condition, and oxygen saturation at admission. Factors associated with in-hospital mortality and the need for mechanical ventilation were assessed in a multivariable logistic regression model. RESULTS The groups were comparable by age, gender, comorbidities, and baseline oxygen saturation. Among 346 remdesivir recipients, 265 (76.6%) received a generic formulation of the drug. Eight (2.3%) patients died in the remdesivir group and 18 (5.2%) in the control group (P = 0.046). In the multivariable analysis, remdesivir was associated with non-statistically significant reduced odds of death (odds ratio: 0.39, 95% confidence interval: 0.14-1.04, P = 0.06). Significantly fewer patients in the remdesivir group required mechanical ventilation compared to controls: 2.9% vs 6.4% (P = 0.03). Statistically significant difference was maintained in multivariable analysis (odds ratio: 0.40, 95% confidence interval: 1.04-5.60, P = 0.04). CONCLUSION Borderline reduction in the odds of death and statistically significant decrease in the need for mechanical ventilation support use of remdesivir in hospitalized patients with COVID-19.
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Affiliation(s)
| | | | - Akaki Abutidze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia; Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Marina Endeladze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia
| | - Marine Ezugbaia
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia
| | - Ana Bakradze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia
| | - Tengiz Tsertsvadze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia; Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
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