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Hartantri Y, Andriyoko B, Debora J, Rachman FR, Susandi E, Ferdian F, Ganiem AR, Alisjahbana B, Soeroto AY, Turbawaty DK. BA.5 sub-lineages associated with higher severity of COVID-19 infection: A cross-sectional study in Indonesia. IJID REGIONS 2024; 11:100379. [PMID: 38855022 PMCID: PMC11157273 DOI: 10.1016/j.ijregi.2024.100379] [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: 10/25/2023] [Revised: 02/21/2024] [Accepted: 05/07/2024] [Indexed: 06/11/2024]
Abstract
Objectives We aimed to compare the clinical severity and outcome among laboratory-confirmed Omicron variant cases admitted between January and December 2022. Methods This is a cross-sectional study conducted in Hasan Sadikin General Hospital between January and December 2022. We enrolled patients aged ≥18 years with laboratory-confirmed Omicron infection. Data were collected from clinical records and a whole genome sequencing database. We compared the risk of severe symptoms and mortality using a logistic regression analysis adjusted for sex, age, comorbidities, and vaccination status. Results We enrolled 255 patients and the main sub-lineages were BA.1 (16.1%), BA.2 (11.4%), BA.5 (35.7%), XBB (22.7%), and BQ.1 (14.1%). Compared with BA.1/BA.2, BA.5 sub-lineages were associated with severe symptoms (adjusted odds ratio of 2.9, 95% confidence interval 1.1-8.2, P <0.05). The highest risk of severe symptoms and mortality was linked with a high number of comorbidities (adjusted odds ratio of 7.8, 95% confidence interval 1.7-22.4, P <0.05). Booster vaccination was protective of severity and mortality. Conclusions Disease severity was associated with BA.5 sub-lineages and multiple comorbidities. Good management is particularly important for people with comorbidities. Furthermore, booster vaccination is also required to reduce severity and mortality.
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Affiliation(s)
- Yovita Hartantri
- Division of Tropical and Infectious Diseases, Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Basti Andriyoko
- Department of Clinical Pathology, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Josephine Debora
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Febi Ramdhani Rachman
- Research Center for Care and Control of Infectious Diseases (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
| | - Evan Susandi
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ferdy Ferdian
- Division of Pulmonology and Critical Illness, Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ahmad Rizal Ganiem
- Department of Neurology, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Bachti Alisjahbana
- Division of Tropical and Infectious Diseases, Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
- Research Center for Care and Control of Infectious Diseases (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
| | - Arto Yuwono Soeroto
- Division of Pulmonology and Critical Illness, Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Dewi Kartika Turbawaty
- Department of Clinical Pathology, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
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Pahlavan Y, Yeganeh O, Asghariazar V, Karami C. Multi-epitope vaccine against SARS-CoV-2 targeting the spike RBD: an immunoinformatics approach. Future Sci OA 2024; 10:FSO939. [PMID: 38827807 PMCID: PMC11140640 DOI: 10.2144/fsoa-2023-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/07/2023] [Indexed: 06/05/2024] Open
Abstract
Aim: We designed a SARS-CoV-2 epitope vaccine based on the receptor-binding domain (RBD) in virus spike protein. Methods: RT-PCR performed on nasopharyngeal swab COVID-19 patients. After registering RBD region in the GenBank, physicochemical parameters, secondary structure, homology modeling, 3D structure of RBD region and antigenicity were determined using ProtParam ExPASy, PSIPRED, MolProbity, IEDB and Vaxijen online tools, respectively. Results: B and T cell epitopes were predicted in terms of non-allergenicity and antigenicity. MolProbity analysis provided a qualitative model for RBD. The homology model showed that most of the residues are in optimal district of energy. Conclusion: High immunogenicity score of epitopes indicates promising candidates for the development of multi-epitope vaccines. It may help to develop an effective vaccine.
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Affiliation(s)
- Yasamin Pahlavan
- Biosensor Sciences and Technologies Research Center, Ardabil University of Medical Sciences, Ardabil, 56189-85991, Iran
| | - Omid Yeganeh
- Department of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, 16511-53311, Iran
| | - Vahid Asghariazar
- Cancer Immunology and Immunotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, 56189-85991, Iran
| | - Chiman Karami
- Department of Microbiology, Parasitology and Immunology, Ardabil University of Medical Sciences, Ardabil, 56189-85991, Iran
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Lewnard JA, Mahale P, Malden D, Hong V, Ackerson BK, Lewin BJ, Link-Gelles R, Feldstein LR, Lipsitch M, Tartof SY. Immune escape and attenuated severity associated with the SARS-CoV-2 BA.2.86/JN.1 lineage. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.17.24305964. [PMID: 38699313 PMCID: PMC11065027 DOI: 10.1101/2024.04.17.24305964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
The SARS-CoV-2 BA.2.86 lineage, and its sublineage JN.1 in particular, achieved widespread transmission in the US during winter 2023-24. However, the increase in infections was not accompanied by increases in COVID-19 hospitalizations and mortality commensurate with prior waves. To understand shifts in COVID-19 epidemiology associated with JN.1 emergence, we compared characteristics and clinical outcomes of time-matched cases infected with BA.2.86- derived lineages (predominantly representing JN.1) versus co-circulating XBB-derived lineages in December, 2023 and January, 2024. Cases infected with BA.2.86-derived lineages received greater numbers of COVID-19 vaccine doses, including XBB.1.5-targeted and BA.4/BA.5-targeted boosters, in comparison to cases infected with XBB-derived lineages. Additionally, cases infected with BA.2.86-derived lineages experienced greater numbers of documented prior SARS-CoV-2 infections. These associations of BA.2.86-derived lineages with immune escape were confirmed when comparing cases diagnosed during periods when JN.1 was the predominant circulating lineage to cases diagnosed during November, 2023. Cases infected with BA.2.86-derived lineages, or during periods when JN.1 was the predominant circulating lineage, also experienced lower risk of progression to severe clinical outcomes requiring emergency department consultations or hospital admission. Sensitivity analyses suggested under-ascertainment of prior infections, even if differential between cases infected with BA.2.86-derived lineages and non-BA.2.86 lineages, could not explain this apparent attenuation of severity. Our findings implicate escape from immunity acquired from prior vaccination or infection in the emergence of the JN.1 lineage and suggest infections with this lineage are less likely to experience clinically-severe disease. Monitoring of immune escape and clinical severity in emerging SARS-CoV-2 variants remains a priority to inform responses.
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Wang F, Liu D, Gao D, Yuan J, Zhao J, Yuan S, Cen Y, Lin GQ, Zhao J, Tian P. Discovery of natural catechol derivatives as covalent SARS-CoV-2 3CL pro inhibitors. Int J Biol Macromol 2024; 264:130377. [PMID: 38395279 DOI: 10.1016/j.ijbiomac.2024.130377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a threat to public health, and extensive research by scientists worldwide has also prompted the development of antiviral therapies. The 3C-like protease (3CLpro) is critical for SARS-CoV-2 replication and acts as an effective target for drug development. To date, numerous of natural products have been reported to exhibit inhibitory effects on 3CLpro, which encourages us to identify other novel inhibitors and elucidate their mechanism of action. In this study, we first screened an in-house compound library of 101 natural products using FRET assay, and found that oleuropein showed good inhibitory activity against SARS CoV-2 3CLpro with an IC50 value of 4.18 μM. Further studies revealed that the catechol core is essential for activity and can covalently bind to SARS-CoV-2 3CLpro. Among other 45 catechol derivatives, wedelolactone, capsazepine and brazilin showed better SARS-CoV-2 3CLpro inhibitory activities with IC50 values of 1.35 μM, 1.95 μM and 1.18 μM, respectively. These catechol derivatives were verified to be irreversible covalent inhibitors by time-dependent experiments, enzymatic kinetic studies, dilution and dialysis assays. It also exhibited good selectivity towards different cysteine proteases (SARS-CoV-2 PLpro, cathepsin B and cathepsin L). Subsequently, the binding affinity between brazilin and SARS-CoV-2 3CLpro was determined by SPR assay with KD value of 0.80 μM. Molecular dynamic (MD) simulations study showed the binding mode of brazilin in the target protein. In particular, brazilin displayed good anti-SARS-CoV-2 activity in A549-hACE2-TMPRSS2 cells with EC50 values of 7.85 ± 0.20 μM and 5.24 ± 0.21 μM for full time and post-infection treatments, respectively. This study provides a promising lead compound for the development of novel anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Feng Wang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China; Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China
| | - Dingding Gao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Jinwei Yuan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Shuai Yuan
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Center, Guangzhou 510700, China
| | - Yixin Cen
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China; Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Ping Tian
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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Kashiwado Y, Kimoto Y, Oku K, Yamamoto M, Ohshima S, Ito S, Horiuchi T, Takeuchi T. Prognostic improvement and treatment of COVID-19 in patients with rheumatic diseases until December 2022: Analysis of the JCR COVID-19 registry in Japan. Mod Rheumatol 2024; 34:576-583. [PMID: 37338284 DOI: 10.1093/mr/road057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/27/2023] [Accepted: 06/09/2023] [Indexed: 06/21/2023]
Abstract
OBJECTIVES The aim is to evaluate the treatment and prognosis of coronavirus disease 2019 (COVID-19) according to the time of onset and dominant strain in patients with rheumatic diseases. METHODS This study analysed a nationwide COVID-19 registry of Japanese patients with rheumatic diseases compiled between June 2020 and December 2022. The primary endpoints of the study were hypoxaemia incidence and mortality. Multivariate logistic regression analysis was performed to assess differences according to the period of onset. RESULTS A total of 760 patients were compared across four periods. Hypoxaemia rates were 34.9, 27.2, 13.8, and 6.1% and mortality rates were 5.6, 3.5, 1.8, and 0% until June 2021, between July and December 2021, January and June 2022, and July and December 2022, respectively. History of vaccination (odds ratio, 0.39; 95% confidence interval, 0.18-0.84) and onset during the July to December 2022 Omicron BA.5-dominant period (odds ratio, 0.17; 95% confidence interval, 0.07-0.41) were negatively associated with hypoxaemia in the multivariate model, adjusting for age, sex, obesity, glucocorticoid dose, and comorbidities. Over the Omicron-dominant period, antiviral treatment was administered in 30.5% of patients with a low probability of hypoxaemia. CONCLUSIONS COVID-19 prognosis improved over time in patients with rheumatic diseases, especially in the Omicron BA.5-dominant period. In the future, treatment of mild cases should be optimised.
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Affiliation(s)
- Yusuke Kashiwado
- Department of Internal Medicine, Kyushu University Beppu Hospital, Oita, Japan
| | - Yasutaka Kimoto
- Department of Internal Medicine, Kyushu University Beppu Hospital, Oita, Japan
| | - Kenji Oku
- Department of Rheumatology and Infectious Diseases, Kitasato University School of Medicine, Kanagawa, Japan
| | - Mari Yamamoto
- Department of Rheumatology and Nephrology, Chubu Rosai Hospital, Aichi, Japan
| | - Shiro Ohshima
- Department of Clinical Research, Rheumatology and Allergology, Osaka Minami Medical Center, Osaka, Japan
| | - Satoshi Ito
- Department of Rheumatology, Niigata Rheumatic Center, Niigata, Japan
| | - Takahiko Horiuchi
- Department of Internal Medicine, Kyushu University Beppu Hospital, Oita, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University, Tokyo, Japan
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Bouchnita A, Bi K, Fox SJ, Meyers LA. Projecting Omicron scenarios in the US while tracking population-level immunity. Epidemics 2024; 46:100746. [PMID: 38367285 DOI: 10.1016/j.epidem.2024.100746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/16/2023] [Accepted: 01/23/2024] [Indexed: 02/19/2024] Open
Abstract
Throughout the COVID-19 pandemic, changes in policy, shifts in behavior, and the emergence of new SARS-CoV-2 variants spurred multiple waves of transmission. Accurate assessments of the changing risks were vital for ensuring adequate healthcare capacity, designing mitigation strategies, and communicating effectively with the public. Here, we introduce a model of COVID-19 transmission and vaccination that provided rapid and reliable projections as the BA.1, BA.4 and BA.5 variants emerged and spread across the US. For example, our three-week ahead national projection of the early 2021 peak in COVID-19 hospitalizations was only one day later and 11.6-13.3% higher than the actual peak, while our projected peak in mortality was two days earlier and 0.22-4.7% higher than reported. We track population-level immunity from prior infections and vaccination in terms of the percent reduction in overall susceptibility relative to a completely naive population. As of October 1, 2022, we estimate that the US population had a 36.52% reduction in overall susceptibility to the BA.4/BA.5 variants, with 61.8%, 15.06%, and 23.54% of immunity attributable to infections, primary series vaccination, and booster vaccination, respectively. We retrospectively projected the potential impact of expanding booster coverage starting on July 15, 2022, and found that a five-fold increase in weekly boosting rates would have resulted in 70% of people over 65 vaccinated by Oct 10, 2022 and averted 25,000 (95% CI: 14,400-35,700) deaths during the BA.4/BA.5 surge. Our model provides coherent variables for tracking population-level immunity in the increasingly complex landscape of variants and vaccines and enables robust simulations of plausible scenarios for the emergence and mitigation of novel COVID variants.
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Affiliation(s)
- Anass Bouchnita
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Kaiming Bi
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Spencer J Fox
- Department of Epidemiology & Biostatistics, University of Georgia, Athens, GA 30602, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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7
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Rhoden J, Hoffmann AT, Stein JF, da Silva MS, Gularte JS, Filippi M, Demoliner M, Girardi V, Spilki FR, Fleck JD, Rigotto C. Diversity of Omicron sublineages and clinical characteristics in hospitalized patients in the southernmost state of Brazil. BMC Infect Dis 2024; 24:193. [PMID: 38350887 PMCID: PMC10863127 DOI: 10.1186/s12879-024-09089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 02/02/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Omicron has become the dominant variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since first reported in November 2021. From the initially detected Wuhan lineage, sublineages BA.2, BA.4, BA.5, BQ, XAG, and XBB have emerged over time and are dominant in many countries. Therefore, the aim is to evaluate which variants are circulating and the clinical characteristics of inpatients infected with the Omicron variant. METHODS This retrospective cohort study selected hospitalized patients admitted with respiratory symptoms to a hospital in the state of Rio Grande do Sul, Brazil, between June and July 2022. SARS-CoV-2 results were analyzed together with clinical outcomes and vaccination status. A viral genome library was prepared and forwarded to the Illumina MiSeq Platform for sequencing. RESULTS In total, 37 genomes were sequenced. Concerning the Omicron sublineages, our study detected: BA.1 (21 K), BA.2 (21 L), BA.4 (22A), BA.5 (22B), BA.2.12.1 (22C), BQ.1 (22E), XBB (22F), and XAG recombinant. Omicron BA.5 (30%), BA.2 (19%), and BQ.1 (19%) were the most frequent sublineages, respectively. In total, 38% of patients present hypertension, and the most common symptoms were coughing (62%). Analyzing the COVID-19 vaccination, 30% of patients were fully vaccinated, 49% had a partial vaccination status, and 21% were unvaccinated (no dose). CONCLUSIONS BA.5 was the most prevalent sublineage in our study and surpassed the predominance of BA.2, as reported by the national genomic surveillance program. BQ.1 was diagnosed earlier in this study than it was officially reported in the state. Current data have demonstrated that the Omicron variant causes less severe infections, with the high rate of transmissibility and mutational landscape causing the rapid emergence of new sublineages.
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Affiliation(s)
- Jaqueline Rhoden
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil.
- Santa Casa de Misericórdia de Porto Alegre, Hospital Dom Vicente Scherer, Centro Histórico. Av. Independência, n. 155, CEP 90035-074, Porto Alegre, Rio Grande do Sul, Brazil.
| | - Andressa Taíz Hoffmann
- Santa Casa de Misericórdia de Porto Alegre, Hospital Dom Vicente Scherer, Centro Histórico. Av. Independência, n. 155, CEP 90035-074, Porto Alegre, Rio Grande do Sul, Brazil
| | - Janaína Franciele Stein
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Caroline Rigotto
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
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Erabi G, Faridzadeh A, Parvin A, Deravi N, Rahmanian M, Fathi M, Aleebrahim‐Dehkordi E, Rezaei N. SARS-CoV-2 Omicron (BA.4, BA.5) variant: Lessons learned from a new variant during the COVID-19 pandemic. Health Sci Rep 2024; 7:e1873. [PMID: 38332930 PMCID: PMC10851086 DOI: 10.1002/hsr2.1873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 01/05/2024] [Accepted: 01/21/2024] [Indexed: 02/10/2024] Open
Abstract
Background and Aim In late 2021, the world faced the rapid spread of the SARS-CoV-2 Omicron variant, which quickly became the variant of concern. In April 2022, two new lineages of Omicron (BA.4/BA.5) emerged from Africa, where they caused the fifth wave of infection. Method We searched PubMed, Google Scholar, and Scopus online databases up to December 2023 for founding relevant studies. Results BA.4 and BA.5 subgroups, with changes in the spike protein, have a greater ability to escape from the immune system, which was possible with the help of L452R and F486V mutations. Epidemiologically, these evolving subtypes show similarities to seasonal influenza but with higher mortality rates. The symptoms of these subgroups are different from the previous types in the form of upper respiratory symptoms. Antiviral treatments, the use of antibodies such as bebtelovimab, and the development of vaccines are promising. Conclusion Consequently, we must continue to be vigilant in our joint surveillance efforts against COVID-19 in diagnosis and treatment.
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Affiliation(s)
- Gisou Erabi
- Student Research CommitteeUrmia University of Medical SciencesUrmiaIran
| | - Arezoo Faridzadeh
- Department of Immunology and AllergyMashhad University of Medical SciencesMashhadIran
- Immunology Research CenterMashhad University of Medical SciencesMashhadIran
| | - Ali Parvin
- Student Research CommitteeUrmia University of Medical SciencesUrmiaIran
| | - Niloofar Deravi
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Mohammad Rahmanian
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Mobina Fathi
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Elahe Aleebrahim‐Dehkordi
- Medical Plants Research Center, Basic Health Sciences instituteShahrekord University of Medical SciencesShahrekordIran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical CenterTehran University of Medical SciencesTehranIran
- Department of Immunology, School of MedicineTehran University of Medical SciencesTehranIran
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA)Universal Scientific Education and Research Network (USERN)TehranIran
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9
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Kitamura N, Otani K, Kinoshita R, Yan F, Takizawa Y, Fukushima K, Yoneoka D, Suzuki M, Kamigaki T. Protective effect of previous infection and vaccination against reinfection with BA.5 Omicron subvariant: a nationwide population-based study in Japan. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2023; 41:100911. [PMID: 38223396 PMCID: PMC10786644 DOI: 10.1016/j.lanwpc.2023.100911] [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: 05/29/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 01/16/2024]
Abstract
Background The Omicron variant of SARS-CoV-2 was reported to evade immunity derived from vaccination and previous infection. A better understanding of hybrid immunity informs effective infection control strategies. Since the reinfection risk was not well-assessed in East Asia, this study aims to evaluate the risk of infection with Omicron subvariant BA.5 among previously infected individuals in Japan. Methods All notified cases were extracted from the Japanese national COVID-19 surveillance database including 20,297,335 records up to 25 September 2022. Reinfection with BA.5 was defined as the infection notified during the BA.5 dominated period with any prior SARS-CoV-2 infection. The protective effect of prior infections against reinfections with BA.5 was estimated by applying a case-population design and the protective effect of vaccination was estimated by a multivariable Cox regression adjusting for age, sex, variants of prior infection, and the time since the last vaccination. Findings Among 19,830,548 SARS-CoV-2 first infections, 233,424 (1.2%) were reinfected with BA.5. The protective effect against BA.5 reinfection of prior infection with Wuhan strain was 46%, Alpha variant was 35%, Delta variant was 41%, and BA.1/BA.2 subvariant was 74%. The reduced risk of BA.5 reinfection by 7%, 33%, and 66% was associated with two, three, and four doses of vaccination, respectively, compared with one-dose vaccination. Interpretation The prior infections with Omicron subvariant BA.1/BA.2 protected BA.5 reinfection more than pre-Omicron variants. Increased frequency of vaccination led to more protection from reinfection with BA.5. Up-to-date vaccination may be encouraged to prevent future reinfection among the previously infected population. Funding None.
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Affiliation(s)
- Noriko Kitamura
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kanako Otani
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryo Kinoshita
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Fangyu Yan
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yu Takizawa
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kohei Fukushima
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Daisuke Yoneoka
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Taro Kamigaki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
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10
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Ramasamy R. Overview of immunological & virological factors driving the evolution & global spread of SARS-CoV-2 variants. Indian J Med Res 2023; 158:257-268. [PMID: 37815068 PMCID: PMC10720969 DOI: 10.4103/ijmr.ijmr_2591_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Indexed: 10/11/2023] Open
Abstract
The SARS-CoV-2, a highly infectious positive strand RNA virus first identified in December 2019, has produced multiple genetic variants that have rapidly and sequentially spread worldwide during the coronavirus disease 2019 (COVID-19) pandemic. Genetic changes in SARS-CoV-2 for greater infectivity, replication and transmission were selected during the early stages of the pandemic. More recently, after widespread infection and vaccination, SARS-CoV-2 variants that evade antigen-specific adaptive immunity, have begun to be selected. This article provides an overview of the molecular immunological and virological factors underlying the origin and global spread of important SARS-CoV-2 variant lineages.
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11
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Lewnard JA, Hong V, Kim JS, Shaw SF, Lewin B, Takhar H, Lipsitch M, Tartof SY. Increased vaccine sensitivity of an emerging SARS-CoV-2 variant. Nat Commun 2023; 14:3854. [PMID: 37386005 PMCID: PMC10310822 DOI: 10.1038/s41467-023-39567-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Host immune responses are a key source of selective pressure driving pathogen evolution. Emergence of many SARS-CoV-2 lineages has been associated with enhancements in their ability to evade population immunity resulting from both vaccination and infection. Here we show diverging trends of escape from vaccine-derived and infection-derived immunity for the emerging XBB/XBB.1.5 Omicron lineage. Among 31,739 patients tested in ambulatory settings in Southern California from December, 2022 to February, 2023, adjusted odds of prior receipt of 2, 3, 4, and ≥5 COVID-19 vaccine doses were 10% (95% confidence interval: 1-18%), 11% (3-19%), 13% (3-21%), and 25% (15-34%) lower, respectively, among cases infected with XBB/XBB.1.5 than among cases infected with other co-circulating lineages. Similarly, prior vaccination was associated with greater point estimates of protection against progression to hospitalization among cases with XBB/XBB.1.5 than among non-XBB/XBB.1.5 cases (70% [30-87%] and 48% [7-71%], respectively, for recipients of ≥4 doses). In contrast, cases infected with XBB/XBB.1.5 had 17% (11-24%) and 40% (19-65%) higher adjusted odds of having experienced 1 and ≥2 prior documented infections, respectively, including with pre-Omicron variants. As immunity acquired from SARS-CoV-2 infection becomes increasingly widespread, fitness costs associated with enhanced vaccine sensitivity in XBB/XBB.1.5 may be offset by increased ability to evade infection-derived host responses.
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Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology, School of Public Health, , University of California, Berkeley, Berkeley, CA, 94720, USA.
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA.
| | - Vennis Hong
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Jeniffer S Kim
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Sally F Shaw
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Bruno Lewin
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA
| | - Harpreet Takhar
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Marc Lipsitch
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Sara Y Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA.
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA.
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Lassan S, Tesar T, Tisonova J, Lassanova M. Pharmacological approaches to pulmonary fibrosis following COVID-19. Front Pharmacol 2023; 14:1143158. [PMID: 37397477 PMCID: PMC10308083 DOI: 10.3389/fphar.2023.1143158] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
Background: In the past few years, COVID-19 became the leading cause of morbidity and mortality worldwide. Although the World Health Organization has declared an end to COVID-19 as a public health emergency, it can be expected, that the emerging new cases at the top of previous ones will result in an increasing number of patients with post-COVID-19 sequelae. Despite the fact that the majority of patients recover, severe acute lung tissue injury can in susceptible individuals progress to interstitial pulmonary involvement. Our goal is to provide an overview of various aspects associated with the Post-COVID-19 pulmonary fibrosis with a focus on its potential pharmacological treatment options. Areas covered: We discuss epidemiology, underlying pathobiological mechanisms, and possible risk and predictive factors that were found to be associated with the development of fibrotic lung tissue remodelling. Several pharmacotherapeutic approaches are currently being applied and include anti-fibrotic drugs, prolonged use or pulses of systemic corticosteroids and non-steroidal anti-inflammatory and immunosuppressive drugs. In addition, several repurposed or novel compounds are being investigated. Fortunately, clinical trials focused on pharmacological treatment regimens for post-COVID-19 pulmonary fibrosis have been either designed, completed or are already in progress. However, the results are contrasting so far. High quality randomised clinical trials are urgently needed with respect to the heterogeneity of disease behaviour, patient characteristics and treatable traits. Conclusion: The Post-COVID-19 pulmonary fibrosis contributes to the burden of chronic respiratory consequences among survivors. Currently available pharmacotherapeutic approaches mostly comprise repurposed drugs with a proven efficacy and safety profile, namely, corticosteroids, immunosuppressants and antifibrotics. The role of nintedanib and pirfenidone is promising in this area. However, we still need to verify conditions under which the potential to prevent, slow or stop progression of lung damage will be fulfilled.
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Affiliation(s)
- Stefan Lassan
- Department of Pneumology, Phthisiology and Functional Diagnostics, Slovak Medical University and Bratislava University Hospital, Bratislava, Slovakia
| | - Tomas Tesar
- Department of Organisation and Management of Pharmacy, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Jana Tisonova
- Institute of Pharmacology and Clinical Pharmacology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Monika Lassanova
- Institute of Pharmacology and Clinical Pharmacology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
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