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Yan Q, Zhang Y, Hou R, Pan W, Liang H, Gao X, Deng W, Huang X, Qu L, Tang C, He P, Liu B, Wang Q, Zhao X, Lin Z, Chen Z, Li P, Han J, Xiong X, Zhao J, Li S, Niu X, Chen L. Deep immunoglobulin repertoire sequencing depicts a comprehensive atlas of spike-specific antibody lineages shared among COVID-19 convalescents. Emerg Microbes Infect 2024; 13:2290841. [PMID: 38044868 PMCID: PMC10810631 DOI: 10.1080/22221751.2023.2290841] [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: 09/07/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Neutralizing antibodies are a key component in protective humoral immunity against SARS-CoV-2. Currently, available technologies cannot track epitope-specific antibodies in global antibody repertoires. Thus, the comprehensive repertoire of spike-specific neutralizing antibodies elicited by SARS-CoV-2 infection is not fully understood. We therefore combined high-throughput immunoglobulin heavy chain (IgH) repertoire sequencing, and structural and bioinformatics analysis to establish an antibodyomics pipeline, which enables tracking spike-specific antibody lineages that target certain neutralizing epitopes. We mapped the neutralizing epitopes on the spike and determined the epitope-preferential antibody lineages. This analysis also revealed numerous overlaps between immunodominant neutralizing antibody-binding sites and mutation hotspots on spikes as observed so far in SARS-CoV-2 variants. By clustering 2677 spike-specific antibodies with 360 million IgH sequences that we sequenced, a total of 329 shared spike-specific antibody clonotypes were identified from 33 COVID-19 convalescents and 24 SARS-CoV-2-naïve individuals. Epitope mapping showed that the shared antibody responses target not only neutralizing epitopes on RBD and NTD but also non-neutralizing epitopes on S2. The immunodominance of neutralizing antibody response is determined by the occurrence of specific precursors in human naïve B-cell repertoires. We identified that only 28 out of the 329 shared spike-specific antibody clonotypes persisted for at least 12 months. Among them, long-lived IGHV3-53 antibodies are likely to evolve cross-reactivity to Omicron variants through accumulating somatic hypermutations. Altogether, we created a comprehensive atlas of spike-targeting antibody lineages in COVID-19 convalescents and antibody precursors in human naïve B cell repertoires, providing a valuable reference for future vaccine design and evaluation.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Ruitian Hou
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenjing Pan
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Weiqi Deng
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linbing Qu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qian Wang
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Zihan Lin
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Zhaoming Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jian Han
- iRepertoire Inc., Huntsville, AL, USA
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Song Li
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
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Tsai JJ, Chiou SS, Chen PC, Chen CH, Lin PC, Tsai CY, Chuang WL, Hwang SJ, Chong IW, Liu LT. The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan. J Infect Public Health 2024; 17:102556. [PMID: 39388868 DOI: 10.1016/j.jiph.2024.102556] [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: 05/24/2024] [Revised: 09/13/2024] [Accepted: 09/24/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Omicron, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, entered Taiwan at the end of 2021. The Taiwanese government ended its "zero-COVID" policy in March 2022. Multiple coronavirus disease 2019 (COVID-19) outbreaks began in April 2022. We monitored the replacement of Omicron subvariants after BA.1/BA.2 and analyzed their correlation with COVID-19 outbreaks. METHODS We collected SARS-CoV-2 real-time qRTPCR-positive nasopharyngeal swabs from Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, Taiwan, and performed sequencing for specimens exhibiting a cytopathic effect in Vero E6 cells to determine their clades and lineages. We analyzed the medical records of COVID-19 patients and identified hospitalization risk factor(s). We retrieved SARS-CoV-2 sequences identified in Taiwan from GISAID and analyzed their correlation with COVID-19 data from the Taiwan Centers for Disease Control. RESULTS We analyzed the phylogenesis of KMUH-47 to KMUH-104 (SARS-CoV-2 isolates identified herein) and all of the Omicron subvariants from BA.5 to XBB.1 (n = 1930). Age and comorbidities were hospitalization risk factors. Men generally exhibited a greater fatality rate than women. COVID-19-related deaths predominantly occurred in individuals over 70 years old. The COVID-19-related case fatality rate increased as nucleotide (NT) and amino acid (AA) substitutions increased. The number of COVID-19-related cases and deaths progressively decreased with each outbreak between August 2022 and October 2023. CONCLUSION Hospitalization was associated with age and the presence of comorbidities. COVID-19-related fatality was linked to sex, age, and the accumulation of NT and AA substitutions in emerging Omicron subvariants.
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Affiliation(s)
- Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shyh-Shin Chiou
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Po-Chih Chen
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, 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, Taiwan
| | - Ching-Yi Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wan-Long Chuang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shang-Jyh Hwang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Inn-Wen Chong
- Department of Internal Medicine and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pulmonary Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Li-Teh Liu
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan, Taiwan.
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Shorthouse D, Lister H, Freeman GS, Hall BA. Understanding large scale sequencing datasets through changes to protein folding. Brief Funct Genomics 2024; 23:517-524. [PMID: 38521964 PMCID: PMC11428155 DOI: 10.1093/bfgp/elae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/25/2024] Open
Abstract
The expansion of high-quality, low-cost sequencing has created an enormous opportunity to understand how genetic variants alter cellular behaviour in disease. The high diversity of mutations observed has however drawn a spotlight onto the need for predictive modelling of mutational effects on phenotype from variants of uncertain significance. This is particularly important in the clinic due to the potential value in guiding clinical diagnosis and patient treatment. Recent computational modelling has highlighted the importance of mutation induced protein misfolding as a common mechanism for loss of protein or domain function, aided by developments in methods that make large computational screens tractable. Here we review recent applications of this approach to different genes, and how they have enabled and supported subsequent studies. We further discuss developments in the approach and the role for the approach in light of increasingly high throughput experimental approaches.
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Affiliation(s)
- David Shorthouse
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Harris Lister
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
| | - Gemma S Freeman
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
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Sarkar M, Madabhavi I. COVID-19 mutations: An overview. World J Methodol 2024; 14:89761. [PMID: 39310238 PMCID: PMC11230071 DOI: 10.5662/wjm.v14.i3.89761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 06/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.
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Affiliation(s)
- Malay Sarkar
- Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Irappa Madabhavi
- Department of Medical and Pediatric Oncology and Hematology, J N Medical College, and KAHER, Belagavi, Karnataka 590010, India
- Department of Medical and Pediatric Oncology and Hematology, Kerudi Cancer Hospital, Bagalkot, Karnataka 587103, India
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5
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Verhagen NB, Geissler T, SenthilKumar G, Gehl C, Shaik T, Flitcroft MA, Yang X, Taylor BW, Ghaferi AA, Gould JC, Kothari AN. From Alpha to Omicron and Beyond: Associations Between SARS-CoV-2 Variants and Surgical Outcomes. J Surg Res 2024; 301:71-79. [PMID: 38917576 PMCID: PMC11427160 DOI: 10.1016/j.jss.2024.05.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION The COVID-19 pandemic has significantly influenced surgical practices, with SARS-CoV-2 variants presenting unique pathologic profiles and potential impacts on perioperative outcomes. This study explores associations between Alpha, Delta, and Omicron variants of SARS-CoV-2 and surgical outcomes. METHODS We conducted a retrospective analysis using the National COVID Cohort Collaborative database, which included patients who underwent selected major inpatient surgeries within eight weeks post-SARS-CoV-2 infection from January 2020 to April 2023. The viral variant was determined by the predominant strain at the time of the patient's infection. Multivariable logistic regression models explored the association between viral variants, COVID-19 severity, and 30-d major morbidity or mortality. RESULTS The study included 10,617 surgical patients with preoperative COVID-19, infected by the Alpha (4456), Delta (1539), and Omicron (4622) variants. Patients infected with Omicron had the highest vaccination rates, most mild disease, and lowest 30-d morbidity and mortality rates. Multivariable logistic regression demonstrated that Omicron was linked to a reduced likelihood of adverse outcomes compared to Alpha, while Delta showed odds comparable to Alpha. Inclusion of COVID-19 severity in the model rendered the odds of major morbidity or mortality equal across all three variants. CONCLUSIONS Our study examines the associations between the clinical and pathological characteristics of SARS-CoV-2 variants and surgical outcomes. As novel SARS-CoV-2 variants emerge, this research supports COVID-19-related surgical policy that assesses the severity of disease to estimate surgical outcomes.
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Affiliation(s)
- Nathaniel B Verhagen
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Thomas Geissler
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Gopika SenthilKumar
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; Department of Physiology and Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Carson Gehl
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Tahseen Shaik
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Madelyn A Flitcroft
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Xin Yang
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Bradley W Taylor
- Clinical and Translational Science Institute of Southeastern Wisconsin, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Amir A Ghaferi
- Division of Minimally Invasive and GI Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jon C Gould
- Division of Minimally Invasive and GI Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Anai N Kothari
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; Clinical and Translational Science Institute of Southeastern Wisconsin, Medical College of Wisconsin, Milwaukee, Wisconsin.
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Yan Q, Gao X, Liu B, Hou R, He P, Ma Y, Zhang Y, Zhang Y, Li Z, Chen Q, Wang J, Huang X, Liang H, Zheng H, Yao Y, Chen X, Niu X, He J, Chen L, Zhao J, Xiong X. Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants. Nat Commun 2024; 15:7585. [PMID: 39217172 PMCID: PMC11366018 DOI: 10.1038/s41467-024-51770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 08/17/2024] [Indexed: 09/04/2024] Open
Abstract
Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruitian Hou
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Guangzhou National Laboratory, Guangzhou, China
| | - Yong Ma
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Jingjing Wang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huiran Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yichen Yao
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xianying Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, 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, China.
- Guangzhou National Laboratory, Guangzhou, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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7
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Rostamzadeh S, Allafasghari A, Allafasghari A, Abouhossein A. Handgrip strength as a prognostic factor for COVID-19 mortality among older adult patients admitted to the intensive care unit (ICU): a comparison Alpha (B.1.1.7) and Delta (B.1.617.2) variants. Sci Rep 2024; 14:19927. [PMID: 39198687 PMCID: PMC11358457 DOI: 10.1038/s41598-024-71034-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: 12/14/2023] [Accepted: 08/23/2024] [Indexed: 09/01/2024] Open
Abstract
Handgrip strength (HGS) is a non-invasive and reliable biomarker of overall health, physical function, mobility, and mortality. This study aimed to investigate the possible relationship between HGS and mortality in older adult patients hospitalized with COVID-19 in the intensive care unit (ICU) by Alpha (B.1.1.7) and Delta (B.1.617.2) variants. This retrospective cohort study was conducted on 472 COVID-19 patients (222 female and 250 male) aged 60-85 years admitted to the ICU. Demographic data, underlying comorbidities, COVID-19-related symptoms, as well as laboratory and computed tomography (CT) findings were obtained from the patient's medical records. Using a JAMAR® hydraulic dynamometer, the average grip strength value (kg) after three measurements on the dominant side was recorded for subsequent analysis. Low grip strength (LGS) was defined as an arbitrary cut-off of two standard deviations below the gender-specific peak mean value of normative HGS in Iranian healthy population, i.e. < 26 kg in males and < 14 kg in females. The findings showed lower mean grip strength and high frequency of LGS in the non-survivors patients versus survivors group and in the Delta (B.1.617.2) variant vs. Alpha (B.1.1.7) variant, respectively (both p < 0.01). The binary logistic regression analysis showed that chronic obstructive pulmonary disease (COPD) (adjusted odds ratio [OR] 5.125, 95% CI 1.425-25.330), LGS (OR 4.805, 95% CI 1.624-10.776), SaO2 (OR - 3.501, 95% CI 2.452-1.268), C-reactive protein (CRP) level (OR 2.625, 95% CI 1.256-7.356), and age (OR 1.118, 95% CI 1.045-1.092) were found to be independent predictors for mortality of patients with Alpha (B.1.1.7) variant (all p < 0.05). However, only four independent predictors including COPD (OR 6.728, 95% CI 1.683-28.635), LGS (OR 5.405, 95% CI 1.461-11.768), SaO2 (OR - 4.120, 95% CI 2.924-1.428), and CRP level (OR 1.893, 95% CI 1.127-8.692) can be predicted the mortality of patients with Delta (B.1.617.2) variant (p < 0.05). Along with the well-known and common risk factors (i.e. COPD, CRP, and SaO2), handgrip strength can be a quick and low-cost prognostic tool in predicting chances of mortality in older adults who are afflicted with COVID-19 variants.
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Affiliation(s)
- Sajjad Rostamzadeh
- Department of Ergonomics, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atabak Allafasghari
- Department of Health, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Amin Allafasghari
- Department of Health, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Alireza Abouhossein
- Department of Ergonomics, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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8
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Wang Y, Qian J, Li Y, Wang D, Song X, Tian S, Zhou J, Wang W, Guo R, Li J, Zhang X, Wang X, Fan B, Li B. Genetic characterization and phylogenetic analysis of the S genes of porcine epidemic diarrhea virus isolates from China from 2020 to 2023. Arch Virol 2024; 169:180. [PMID: 39150572 DOI: 10.1007/s00705-024-06109-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 08/17/2024]
Abstract
Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus that has been the main cause of diarrhea in piglets since 2010 in China. The aim of this study was to investigate sequence variation and recombination events in the spike (S) gene of PEDV isolates from China. Thirty complete S gene sequences were obtained from PEDV-positive samples collected in six provinces in China from 2020 to 2023. Phylogenetic analysis showed that 10% (3/30) belonged to subtype GII-a, 6.67% (2/30) were categorized as subtype GII-b, 66.67% (20/30) were categorized as subtype GII-c, and 16.66% (5/30) were clustered with the S-INDEL strains. Amino acid sequence alignments showed that, when compared to strains of other subtypes, the GII-c strains had two characteristic amino acid substitutions (N139D and I289M). Five S-INDEL subtype strains had a single amino acid deletion (139N) and four amino acid substitutions (N118G, T137S, A138S, and D141G). Recombination analysis allowed six putative recombination events to be identified, one involving recombination between GII-c strains, two involving GII-c and GII-b strains, two involving GII-c and GI-a strains, and one involving GII-a and GI-b strains. These results suggest that recombination between PEDV strains has been common and complex in recent years and is one of the main reasons for the continuous variation of PEDV strains.
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Affiliation(s)
- Yi Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
- School of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jiali Qian
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Yupeng Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Dandan Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Xu Song
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Shuo Tian
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
- School of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Wei Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Xuehan Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
| | - Xianwei Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baochao Fan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China
| | - Bin Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, 50 Zhong-ling Street, Nanjing, 210014, China.
- School of Veterinary Medicine, Hebei Agricultural University, Baoding, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China.
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China.
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9
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Xiao B, Wu L, Sun Q, Shu C, Hu S. Dynamic analysis of SARS-CoV-2 evolution based on different countries. Gene 2024; 916:148426. [PMID: 38575101 DOI: 10.1016/j.gene.2024.148426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Since late 2019, COVID-19 has significantly impacted the world. Understanding the evolution of SARS-CoV-2 is crucial for protecting against future infectious pathogens. In this study, we conducted a comprehensive chronological analysis of SARS-CoV-2 evolution by examining mutation prevalence from the source countries of VOCs: United Kingdom, India, Brazil, South Africa, plus two countries: United States, Russia, utilizing genomic sequences from GISAID. Our methodological approach involved large-scale genomic sequence alignment using MAFFT, Python-based data processing on a high-performance computing platform, and advanced statistical methods the Maximal Information Coefficient (MIC), and also Long Short-Term Memory (LSTM) models for correlation analysis. Our findings elucidate the dynamics of SARS-CoV-2 evolution, highlighting the virus's changing behaviour over various pandemic stages. Key results include the discovery of three temporal mutation patterns-lineage distinct, long-span, and competitive mutations-with varying levels of impact on the virus. Notably, we observed a convergence of advantageous mutations in the spike protein, especially in the later stages of the pandemic, indicating a substantial evolutionary pressure on the virus. One of the most significant revelations is the predominant role of natural immunity over vaccination-induced immunity in driving these evolutionary changes. This emphasizes the critical need for regular vaccine updates to maintain efficacy against evolving strains. In conclusion, our study not only sheds light on the evolutionary trajectory of SARS-CoV-2 but also underscores the urgency for robust, continuous global data collection and sharing. It highlights the necessity for rapid adaptations in medical countermeasures, including vaccine development, to stay ahead of pathogen evolution. This research provides valuable insights for future pandemic preparedness and response strategies.
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Affiliation(s)
- Binghan Xiao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China.
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10
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Tramuto F, Marotta C, Stefanelli P, Cernigliaro A, Maida CM, Silenzi A, Angeloni U, Di Naro D, Randazzo G, Guzzetta V, Barone T, Brusaferro S, Severoni S, Rezza G, Vitale F, Mazzucco W. SARS-CoV-2 genomic surveillance of migrants arriving to Europe through the Mediterranean routes. J Glob Health 2024; 14:05017. [PMID: 38963881 PMCID: PMC11223754 DOI: 10.7189/jogh.14.05017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024] Open
Abstract
Background The implementation genomic-based surveillance on emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in low-income countries, which have inadequate molecular and sequencing capabilities and limited vaccine storage, represents a challenge for public health. To date, there is little evidence on molecular investigations of SARS-CoV-2 variants in areas where they might emerge. We report the findings of an experimental SARS-CoV-2 molecular surveillance programme for migrants, refugees, and asylum seekers arriving to Europe via Italy through the Mediterranean Sea. Methods We descriptively analysed data on migrants collected at entry points in Sicily from February 2021 to May 2022. These entry points are integrated with a network of laboratories fully equipped for molecular analyses, which performed next-generation sequencing and used Nextclade and the Pangolin coronavirus disease 2019 (COVID-19) tools for clade/lineage assignment. Results We obtained 472 full-length SARS-CoV-2 sequences and identified 12 unique clades belonging to 31 different lineages. The delta variant accounted for 43.6% of all genomes, followed by clades 21D (Eta) and 20A (25.4% and 11.4%, respectively). Notably, some of the identified lineages (A.23.1, A.27, and A.29) predicted their introduction into the migration area. The mutation analysis allowed us to identify 617 different amino acid substitutions, 156 amino acid deletions, 7 stop codons, and 6 amino acid insertions. Lastly, we highlighted the geographical distribution patterns of some mutational profiles occurring in the migrants' countries of origin. Conclusions Genome-based molecular surveillance dedicated to migrant populations from low-resource areas may be useful for forecasting new epidemiological scenarios related to SARS-CoV-2 variants or other emerging pathogens, as well as for informing the updating of vaccination strategies.
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Affiliation(s)
- Fabio Tramuto
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties ‘G. D’Alessandro’, University of Palermo, Italy
- Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital ‘P. Giaccone’, Palermo, Italy
| | - Claudia Marotta
- General Directorate of Health Prevention, Ministry of Health, Rome, Italy
| | - Paola Stefanelli
- National Institute of Health (Istituto Superiore di Sanità), Rome, Italy
| | | | - Carmelo Massimo Maida
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties ‘G. D’Alessandro’, University of Palermo, Italy
- Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital ‘P. Giaccone’, Palermo, Italy
| | - Andrea Silenzi
- General Directorate of Health Prevention, Ministry of Health, Rome, Italy
| | - Ulrico Angeloni
- General Directorate of Health Prevention, Ministry of Health, Rome, Italy
| | - Daniela Di Naro
- Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital ‘P. Giaccone’, Palermo, Italy
| | - Giulia Randazzo
- Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital ‘P. Giaccone’, Palermo, Italy
| | - Valeria Guzzetta
- Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital ‘P. Giaccone’, Palermo, Italy
| | - Teresa Barone
- Department of Laboratory Diagnostics, Local Health Unit of Palermo, Palermo, Italy
| | - Silvio Brusaferro
- National Institute of Health (Istituto Superiore di Sanità), Rome, Italy
- University of Udine, Udine, Italy
| | - Santino Severoni
- Health and Migration Programme (PHM), World Health Organization, Geneva, Switzerland
| | - Gianni Rezza
- General Directorate of Health Prevention, Ministry of Health, Rome, Italy
- Vita – Salute San Raffaele University, Milan, Italy
| | - Francesco Vitale
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties ‘G. D’Alessandro’, University of Palermo, Italy
- Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital ‘P. Giaccone’, Palermo, Italy
| | - Walter Mazzucco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties ‘G. D’Alessandro’, University of Palermo, Italy
- Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital ‘P. Giaccone’, Palermo, Italy
- Division of Biostatistics & Epidemiology Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, USA
| | - SAMI-Surv CollaborationAlbaDavideAmodioEmanueleCasuccioAlessandraCostantinoClaudioFruscioneSantoImmordinoPalmiraRestivoVincenzoSavatteriAlessandraD’AgostinoNadiaLa MiliaDanielePecoraroLauraPulvirentiClaudioStabileDomenicoCesariCarloZichichiSalvatoreLo PrestiAlessandraGrazianoGiorgioScondottoSalvatoreRealeStefanoScibettaSilviaVitaleFabrizioBarracoChiaraMistrettaGiuseppaPalmeriGiuliaRizzoAntonina PatriziaSparacoAntoninoAgnoneAnnalisaCascioFrancescoDi QuartoDaniela LauraMigliorisiCarmeloD’AmatoStefaniaCucchiaraValentinaGenoveseDarioFrisciaGiuseppeIacolinoGiorgiaSpotoVittorioZappiaMario
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties ‘G. D’Alessandro’, University of Palermo, Italy
- Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital ‘P. Giaccone’, Palermo, Italy
- General Directorate of Health Prevention, Ministry of Health, Rome, Italy
- National Institute of Health (Istituto Superiore di Sanità), Rome, Italy
- Regional Health Authority of Sicily, Palermo, Italy
- Department of Laboratory Diagnostics, Local Health Unit of Palermo, Palermo, Italy
- University of Udine, Udine, Italy
- Health and Migration Programme (PHM), World Health Organization, Geneva, Switzerland
- Vita – Salute San Raffaele University, Milan, Italy
- Division of Biostatistics & Epidemiology Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, USA
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11
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Simoneau CR, Chen PY, Xing GK, Hayashi JM, Chen IP, Khalid MM, Meyers NL, Taha TY, Leon KE, Suryawanshi RK, McCavitt-Malvido M, Ashuach T, Fontaine KA, Rodriguez L, Joehnk B, Walcott K, Vasudevan S, Fang X, Maishan M, Schultz S, Roose JP, Matthay MA, Sil A, Arjomandi M, Yosef N, Ott M. NF-κB inhibitor alpha controls SARS-CoV-2 infection in ACE2-overexpressing human airway organoids. Sci Rep 2024; 14:15351. [PMID: 38961189 PMCID: PMC11222426 DOI: 10.1038/s41598-024-66003-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that recapitulate the cell-intrinsic response to arising viral variants are needed. Here we describe an adult stem cell-derived human airway organoid model overexpressing the ACE2 receptor (ACE2-OE) that supports robust viral replication while maintaining 3D architecture and cellular diversity of the airway epithelium. ACE2-OE organoids were infected with SARS-CoV-2 variants and subjected to single-cell RNA-sequencing. Interferon-lambda was upregulated in cells with low-level infection while the NF-kB inhibitor alpha gene (encoding IkBa) was consistently upregulated in infected cells, and its expression positively correlated with infection levels. Confocal microscopy showed more IkBa expression in infected than bystander cells, but found concurrent nuclear translocation of NF-kB that IkBa usually prevents. Overexpressing a nondegradable IkBa mutant reduced NF-kB translocation and increased viral infection. These data demonstrate the functionality of ACE2-OE organoids in SARS-CoV-2 research and underscore that the strength of the NF-kB feedback loop in infected cells controls viral replication.
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Affiliation(s)
- Camille R Simoneau
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Galen K Xing
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Irene P Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Mir M Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Taha Y Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Kristoffer E Leon
- Gladstone Institute of Virology, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Tal Ashuach
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Lauren Rodriguez
- ImmunoX CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Bastian Joehnk
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | | | - Xiaohui Fang
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mazharul Maishan
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shawn Schultz
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Michael A Matthay
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mehrdad Arjomandi
- Medical Service, San Francisco VA Healthcare System, San Francisco, CA, USA
- Division of Pulmonary and Critical Care, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Melanie Ott
- Gladstone Institute of Virology, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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12
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Maiti AK. Progressive Evolutionary Dynamics of Gene-Specific ω Led to the Emergence of Novel SARS-CoV-2 Strains Having Super-Infectivity and Virulence with Vaccine Neutralization. Int J Mol Sci 2024; 25:6306. [PMID: 38928018 PMCID: PMC11204377 DOI: 10.3390/ijms25126306] [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: 05/06/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
An estimation of the proportion of nonsynonymous to synonymous mutation (dn/ds, ω) of the SARS-CoV-2 genome would indicate the evolutionary dynamics necessary to evolve into novel strains with increased infection, virulence, and vaccine neutralization. A temporal estimation of ω of the whole genome, and all twenty-nine SARS-CoV-2 genes of major virulent strains of alpha, delta and omicron demonstrates that the SARS-CoV-2 genome originally emerged (ω ~ 0.04) with a strong purifying selection (ω < 1) and reached (ω ~ 0.85) in omicron towards diversifying selection (ω > 1). A marked increase in the ω occurred in the spike gene from alpha (ω = 0.2) to omicron (ω = 1.97). The ω of the replication machinery genes including RDRP, NSP3, NSP4, NSP7, NSP8, NSP10, NSP13, NSP14, and ORF9 are markedly increased, indicating that these genes/proteins are yet to be evolutionary stabilized and are contributing to the evolution of novel virulent strains. The delta-specific maximum increase in ω in the immunomodulatory genes of NSP8, NSP10, NSP16, ORF4, ORF5, ORF6, ORF7A, and ORF8 compared to alpha or omicron indicates delta-specific vulnerabilities for severe COVID-19 related hospitalization and death. The maximum values of ω are observed for spike (S), NSP4, ORF8 and NSP15, which indicates that the gene-specific temporal estimation of ω identifies specific genes for its super-infectivity and virulency that could be targeted for drug development.
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Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 28475 Greenfield Rd, Southfield, MI 48076, USA
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13
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Wang D, Huot M, Mohanty V, Shakhnovich EI. Biophysical principles predict fitness of SARS-CoV-2 variants. Proc Natl Acad Sci U S A 2024; 121:e2314518121. [PMID: 38820002 PMCID: PMC11161772 DOI: 10.1073/pnas.2314518121] [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: 08/22/2023] [Accepted: 04/19/2024] [Indexed: 06/02/2024] Open
Abstract
SARS-CoV-2 employs its spike protein's receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBD's biophysical properties contribute to SARS-CoV-2's epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the identification of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by dissociation constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto an epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low-frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.
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Affiliation(s)
- Dianzhuo Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Marian Huot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- École Polytechnique, Institut Polytechnique de Paris, Palaiseau91128, France
| | - Vaibhav Mohanty
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA02115
- Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eugene I. Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
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14
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Jiao J, Chen W. Core health system measures response to COVID-19 among East Asian countries. Front Public Health 2024; 12:1385291. [PMID: 38887248 PMCID: PMC11180828 DOI: 10.3389/fpubh.2024.1385291] [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: 02/12/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Objective The purpose of this study is to summarize the health system response to COVID-19 in four East Asian countries, analyze the effectiveness of their health system response, and provide lessons for other countries to control the epidemic and optimize their health system response. Methods This study investigated and summarized COVID-19 data and health system response in four East Asian countries, China, Japan, Mongolia, and South Korea from national governments and ministries of health, WHO country offices, and official websites of international organizations, to assess the effectiveness of health system measures. Result As of June 30, 2022, all four countries are in a declining portion of COVID-19. China has two waves, and new cases increased slowly, with the total cases per million remaining within 4, indicating a low level. Japan has experienced six waves, with case growth at an all-time high, total cases per million of 250.994. Mongolia started the epidemic later, but also experienced four waves, with total cases per million of 632.658, the highest of the four countries. South Korea has seen an increasing number of new cases per wave, with a total case per million of 473.759. Conclusion In containment strategies adopted by China and Mongolia, and mitigation strategies adopted by Japan and South Korea, health systems have played important roles in COVID-19 prevention and control. While promoting vaccination, countries should pay attention to non-pharmaceutical health system measures, as evidenced by: focusing on public information campaigns to lead public minds; strengthening detection capabilities for early detection and identification; using technical ways to participate in contact tracing, and promoting precise judging isolation.
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Affiliation(s)
- Jun Jiao
- School of Population and Health, Renmin University of China, Beijing, China
| | - Wei Chen
- Yichun Hospital of Traditional Chinese Medicine, Yichun, Jiangxi, China
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15
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Porebski P, Venkatramanan S, Adiga A, Klahn B, Hurt B, Wilson ML, Chen J, Vullikanti A, Marathe M, Lewis B. Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections. Epidemics 2024; 47:100761. [PMID: 38555667 PMCID: PMC11205267 DOI: 10.1016/j.epidem.2024.100761] [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: 08/18/2023] [Revised: 01/30/2024] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Scenario-based modeling frameworks have been widely used to support policy-making at state and federal levels in the United States during the COVID-19 response. While custom-built models can be used to support one-off studies, sustained updates to projections under changing pandemic conditions requires a robust, integrated, and adaptive framework. In this paper, we describe one such framework, UVA-adaptive, that was built to support the CDC-aligned Scenario Modeling Hub (SMH) across multiple rounds, as well as weekly/biweekly projections to Virginia Department of Health (VDH) and US Department of Defense during the COVID-19 response. Building upon an existing metapopulation framework, PatchSim, UVA-adaptive uses a calibration mechanism relying on adjustable effective transmissibility as a basis for scenario definition while also incorporating real-time datasets on case incidence, seroprevalence, variant characteristics, and vaccine uptake. Through the pandemic, our framework evolved by incorporating available data sources and was extended to capture complexities of multiple strains and heterogeneous immunity of the population. Here we present the version of the model that was used for the recent projections for SMH and VDH, describe the calibration and projection framework, and demonstrate that the calibrated transmissibility correlates with the evolution of the pathogen as well as associated societal dynamics.
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Affiliation(s)
- Przemyslaw Porebski
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA.
| | | | - Aniruddha Adiga
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA
| | - Brian Klahn
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA
| | - Benjamin Hurt
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA
| | - Mandy L Wilson
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA
| | - Jiangzhuo Chen
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA
| | - Anil Vullikanti
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA; Department of Computer Science, University of Virginia, Charlottesville, 22904, VA, USA
| | - Madhav Marathe
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA; Department of Computer Science, University of Virginia, Charlottesville, 22904, VA, USA
| | - Bryan Lewis
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, 22911, VA, USA
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16
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Cui L, Li T, Xue W, Zhang S, Wang H, Liu H, Gu Y, Xia N, Li S. Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants. Viruses 2024; 16:900. [PMID: 38932192 PMCID: PMC11209230 DOI: 10.3390/v16060900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Currently, SARS-CoV-2 has evolved into various variants, including the numerous highly mutated Omicron sub-lineages, significantly increasing immune evasion ability. The development raises concerns about the possibly diminished effectiveness of available vaccines and antibody-based therapeutics. Here, we describe those representative categories of broadly neutralizing antibodies (bnAbs) that retain prominent effectiveness against emerging variants including Omicron sub-lineages. The molecular characteristics, epitope conservation, and resistance mechanisms of these antibodies are further detailed, aiming to offer suggestion or direction for the development of therapeutic antibodies, and facilitate the design of vaccines with broad-spectrum potential.
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Affiliation(s)
- Lingyan Cui
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Tingting Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Wenhui Xue
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Sibo Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hong Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hongjing Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ying Gu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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17
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Faraji N, Zeinali T, Joukar F, Aleali MS, Eslami N, Shenagari M, Mansour-Ghanaei F. Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies. Heliyon 2024; 10:e30208. [PMID: 38707429 PMCID: PMC11066641 DOI: 10.1016/j.heliyon.2024.e30208] [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: 07/08/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.
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Affiliation(s)
- Niloofar Faraji
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Tahereh Zeinali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Maryam Sadat Aleali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Narges Eslami
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Shenagari
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fariborz Mansour-Ghanaei
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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18
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Zhao Z, Bashiri S, Ziora ZM, Toth I, Skwarczynski M. COVID-19 Variants and Vaccine Development. Viruses 2024; 16:757. [PMID: 38793638 PMCID: PMC11125726 DOI: 10.3390/v16050757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), the global pandemic caused by severe acute respiratory syndrome 2 virus (SARS-CoV-2) infection, has caused millions of infections and fatalities worldwide. Extensive SARS-CoV-2 research has been conducted to develop therapeutic drugs and prophylactic vaccines, and even though some drugs have been approved to treat SARS-CoV-2 infection, treatment efficacy remains limited. Therefore, preventive vaccination has been implemented on a global scale and represents the primary approach to combat the COVID-19 pandemic. Approved vaccines vary in composition, although vaccine design has been based on either the key viral structural (spike) protein or viral components carrying this protein. Therefore, mutations of the virus, particularly mutations in the S protein, severely compromise the effectiveness of current vaccines and the ability to control COVID-19 infection. This review begins by describing the SARS-CoV-2 viral composition, the mechanism of infection, the role of angiotensin-converting enzyme 2, the host defence responses against infection and the most common vaccine designs. Next, this review summarizes the common mutations of SARS-CoV-2 and how these mutations change viral properties, confer immune escape and influence vaccine efficacy. Finally, this review discusses global strategies that have been employed to mitigate the decreases in vaccine efficacy encountered against new variants.
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Affiliation(s)
- Ziyao Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Sahra Bashiri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
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19
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Cao B, Wang X, Yin W, Gao Z, Xia B. The human microbiota is a beneficial reservoir for SARS-CoV-2 mutations. mBio 2024; 15:e0318723. [PMID: 38530031 PMCID: PMC11237538 DOI: 10.1128/mbio.03187-23] [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: 12/17/2023] [Accepted: 02/14/2024] [Indexed: 03/27/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging. In particular, beneficial mutations in the spike (S) protein, which can either make a person more infectious or enable immunological escape, are providing a significant obstacle to the prevention and treatment of pandemics. However, how the virus acquires a high number of beneficial mutations in a short time remains a mystery. We demonstrate here that variations of concern may be mutated due in part to the influence of the human microbiome. We searched the National Center for Biotechnology Information database for homologous fragments (HFs) after finding a mutation and the six neighboring amino acids in a viral mutation fragment. Among the approximate 8,000 HFs obtained, 61 mutations in S and other outer membrane proteins were found in bacteria, accounting for 62% of all mutation sources, which is 12-fold higher than the natural variable proportion. A significant proportion of these bacterial species-roughly 70%-come from the human microbiota, are mainly found in the lung or gut, and share a composition pattern with COVID-19 patients. Importantly, SARS-CoV-2 RNA-dependent RNA polymerase replicates corresponding bacterial mRNAs harboring mutations, producing chimeric RNAs. SARS-CoV-2 may collectively pick up mutations from the human microbiota that change the original virus's binding sites or antigenic determinants. Our study clarifies the evolving mutational mechanisms of SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging, in particular advantageous mutations in the spike (S) protein, which either increase transmissibility or lead to immune escape and are posing a major challenge to pandemic prevention and treatment. However, how the virus acquires a high number of advantageous mutations in a short time remains a mystery. Here, we provide evidence that the human microbiota is a reservoir of advantageous mutations and aids mutational evolution and host adaptation of SARS-CoV-2. Our findings demonstrate a conceptual breakthrough on the mutational evolution mechanisms of SARS-CoV-2 for human adaptation. SARS-CoV-2 may grab advantageous mutations from the widely existing microorganisms in the host, which is undoubtedly an "efficient" manner. Our study might open a new perspective to understand the evolution of virus mutation, which has enormous implications for comprehending the trajectory of the COVID-19 pandemic.
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Affiliation(s)
- Birong Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong Guangya High School, Guangzhou, China
| | - Xiaoxi Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wanchao Yin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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20
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Munson E. Biographical Feature: Charles Y. Chiu, M.D., Ph.D. J Clin Microbiol 2024; 62:e0140523. [PMID: 38619264 PMCID: PMC11077958 DOI: 10.1128/jcm.01405-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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21
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Kumar A, Tripathi P, Kumar P, Shekhar R, Pathak R. From Detection to Protection: Antibodies and Their Crucial Role in Diagnosing and Combatting SARS-CoV-2. Vaccines (Basel) 2024; 12:459. [PMID: 38793710 PMCID: PMC11125746 DOI: 10.3390/vaccines12050459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Understanding the antibody response to SARS-CoV-2, the virus responsible for COVID-19, is crucial to comprehending disease progression and the significance of vaccine and therapeutic development. The emergence of highly contagious variants poses a significant challenge to humoral immunity, underscoring the necessity of grasping the intricacies of specific antibodies. This review emphasizes the pivotal role of antibodies in shaping immune responses and their implications for diagnosing, preventing, and treating SARS-CoV-2 infection. It delves into the kinetics and characteristics of the antibody response to SARS-CoV-2 and explores current antibody-based diagnostics, discussing their strengths, clinical utility, and limitations. Furthermore, we underscore the therapeutic potential of SARS-CoV-2-specific antibodies, discussing various antibody-based therapies such as monoclonal antibodies, polyclonal antibodies, anti-cytokines, convalescent plasma, and hyperimmunoglobulin-based therapies. Moreover, we offer insights into antibody responses to SARS-CoV-2 vaccines, emphasizing the significance of neutralizing antibodies in order to confer immunity to SARS-CoV-2, along with emerging variants of concern (VOCs) and circulating Omicron subvariants. We also highlight challenges in the field, such as the risks of antibody-dependent enhancement (ADE) for SARS-CoV-2 antibodies, and shed light on the challenges associated with the original antigenic sin (OAS) effect and long COVID. Overall, this review intends to provide valuable insights, which are crucial to advancing sensitive diagnostic tools, identifying efficient antibody-based therapeutics, and developing effective vaccines to combat the evolving threat of SARS-CoV-2 variants on a global scale.
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Affiliation(s)
- Anoop Kumar
- Molecular Diagnostic Laboratory, National Institute of Biologicals, Noida 201309, India
| | - Prajna Tripathi
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Prashant Kumar
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Ritu Shekhar
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
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22
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Nguyen HL, Nguyen TQ, Li MS. SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study. J Phys Chem B 2024; 128:3340-3349. [PMID: 38564480 PMCID: PMC11017248 DOI: 10.1021/acs.jpcb.3c06270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high contagious ability. Studies have shown that the Omicron binds human ACE2 more strongly than the wild type. The prevalence of Omicron in new cases of COVID-19 promotes novel lineages with improved receptor binding affinity and immune evasion. To shed light on this open problem, in this work, we investigated the binding free energy of the receptor binding domain of the Omicron lineages BA.2, BA.2.3.20, BA.3, BA4/BA5, BA.2.75, BA.2.75.2, BA.4.6, XBB.1, XBB.1.5, BJ.1, BN.1, BQ.1.1, and CH.1.1 to human ACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. The results show that these lineages have increased binding affinity compared to the BA.1 lineage, and BA.2.75 and BA.2.75.2 subvariants bind ACE2 more strongly than others. However, in general, the binding affinities of the Omicron lineages do not differ significantly from each other. The electrostatic force dominates over the van der Waals force in the interaction between Omicron lineages and human cells. Based on our results, we argue that viral evolution does not further improve the affinity of SARS-CoV-2 for ACE2 but may increase immune evasion.
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Affiliation(s)
- Hoang Linh Nguyen
- Institute
of Fundamental and Applied Sciences, Duy
Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty
of Environmental and Natural Sciences, Duy
Tan University, Da Nang 550000, Vietnam
| | - Thai Quoc Nguyen
- Faculty
of Physics, VNU University of Science, Vietnam
National University, 334 Nguyen Trai, Hanoi 100000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap 81000, Vietnam
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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23
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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24
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Hussein HAM, Thabet AA, Wardany AA, El-Adly AM, Ali M, Hassan MEA, Abdeldayem MAB, Mohamed ARMA, Sobhy A, El-Mokhtar MA, Afifi MM, Fathy SM, Sultan S. SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression. Virol J 2024; 21:75. [PMID: 38539202 PMCID: PMC10967059 DOI: 10.1186/s12985-024-02342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 03/12/2024] [Indexed: 05/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.
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Affiliation(s)
- Hosni A M Hussein
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt.
| | - Ali A Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed A Wardany
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed M El-Adly
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed Ali
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed E A Hassan
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A B Abdeldayem
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | | | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos Campus, Lebanon
| | - Magdy M Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Samah M Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum, Egypt.
| | - Serageldeen Sultan
- Department of Microbiology, Virology Division, Faculty of Veterinary medicine, South Valley University, 83523, Qena, Egypt.
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25
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Oktavianthi S, Lages AC, Kusuma R, Kurniasih TS, Trimarsanto H, Andriani F, Rustandi D, Meriyanti T, Yusuf I, Malik SG, Jo J, Suriapranata I. Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia. Pathogens 2024; 13:279. [PMID: 38668234 PMCID: PMC11053823 DOI: 10.3390/pathogens13040279] [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: 11/06/2023] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 04/29/2024] Open
Abstract
The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolates collected from selected regions of Indonesia between January and October 2021 was performed to identify the distribution of SARS-CoV-2 variants and common mutations in Indonesia. During January-April 2021, Indonesian lineages B.1.466.2 and B.1.470 dominated, but from May 2021, Delta's AY.23 lineage outcompeted them. An analysis of 7515 published sequences from January 2021 to June 2022 revealed a decline in Delta in November 2021, followed by the emergence of Omicron variants in December 2021. We identified C241T (5'UTR), P314L (NSP12b), F106F (NSP3), and D614G (Spike) mutations in all sequences. The other common substitutions included P681R (76.4%) and T478K (60%) in Spike, D377Y in Nucleocapsid (61%), and I82T in Membrane (60%) proteins. Breakthrough infection and prolonged viral shedding cases were associated with Delta variants carrying the Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, and V1264L mutations. The dynamic of SARS-CoV-2 variants in Indonesia highlights the importance of continuous genomic surveillance in monitoring and identifying potential strains leading to disease outbreaks.
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Affiliation(s)
- Sukma Oktavianthi
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Aksar Chair Lages
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Rinaldy Kusuma
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Tri Shinta Kurniasih
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
- Menzies School of Health Research, Charles Darwin University, Darwin 0811, Australia
| | - Febi Andriani
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - David Rustandi
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Tandry Meriyanti
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Irawan Yusuf
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Safarina G. Malik
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Juandy Jo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Ivet Suriapranata
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
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26
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Bugalia S, Tripathi JP, Wang H. Mutations make pandemics worse or better: modeling SARS-CoV-2 variants and imperfect vaccination. J Math Biol 2024; 88:45. [PMID: 38507066 DOI: 10.1007/s00285-024-02068-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 07/04/2023] [Accepted: 02/18/2024] [Indexed: 03/22/2024]
Abstract
COVID-19 is a respiratory disease triggered by an RNA virus inclined to mutations. Since December 2020, variants of COVID-19 (especially Delta and Omicron) continuously appeared with different characteristics that influenced death and transmissibility emerged around the world. To address the novel dynamics of the disease, we propose and analyze a dynamical model of two strains, namely native and mutant, transmission dynamics with mutation and imperfect vaccination. It is also assumed that the recuperated individuals from the native strain can be infected with mutant strain through the direct contact with individual or contaminated surfaces or aerosols. We compute the basic reproduction number, R 0 , which is the maximum of the basic reproduction numbers of native and mutant strains. We prove the nonexistence of backward bifurcation using the center manifold theory, and global stability of disease-free equilibrium whenR 0 < 1 , that is, vaccine is effective enough to eliminate the native and mutant strains even if it cannot provide full protection. Hopf bifurcation appears when the endemic equilibrium loses its stability. An intermediate mutation rate ν 1 leads to oscillations. When ν 1 increases over a threshold, the system regains its stability and exhibits an interesting dynamics called endemic bubble. An analytical expression for vaccine-induced herd immunity is derived. The epidemiological implication of the herd immunity threshold is that the disease may effectively be eradicated if the minimum herd immunity threshold is attained in the community. Furthermore, the model is parameterized using the Indian data of the cumulative number of confirmed cases and deaths of COVID-19 from March 1 to September 27 in 2021, using MCMC method. The cumulative cases and deaths can be reduced by increasing the vaccine efficacies to both native and mutant strains. We observe that by considering the vaccine efficacy against native strain as 90%, both cumulative cases and deaths would be reduced by 0.40%. It is concluded that increasing immunity against mutant strain is more influential than the vaccine efficacy against it in controlling the total cases. Our study demonstrates that the COVID-19 pandemic may be worse due to the occurrence of oscillations for certain mutation rates (i.e., outbreaks will occur repeatedly) but better due to stability at a lower infection level with a larger mutation rate. We perform sensitivity analysis using the Latin Hypercube Sampling methodology and partial rank correlation coefficients to illustrate the impact of parameters on the basic reproduction number, the number of cumulative cases and deaths, which ultimately sheds light on disease mitigation.
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Affiliation(s)
- Sarita Bugalia
- Department of Mathematics, Central University of Rajasthan, Bandar Sindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Jai Prakash Tripathi
- Department of Mathematics, Central University of Rajasthan, Bandar Sindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
| | - Hao Wang
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, T6G 2G1, Canada
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27
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Magaret CA, Li L, deCamp AC, Rolland M, Juraska M, Williamson BD, Ludwig J, Molitor C, Benkeser D, Luedtke A, Simpkins B, Heng F, Sun Y, Carpp LN, Bai H, Dearlove BL, Giorgi EE, Jongeneelen M, Brandenburg B, McCallum M, Bowen JE, Veesler D, Sadoff J, Gray GE, Roels S, Vandebosch A, Stieh DJ, Le Gars M, Vingerhoets J, Grinsztejn B, Goepfert PA, de Sousa LP, Silva MST, Casapia M, Losso MH, Little SJ, Gaur A, Bekker LG, Garrett N, Truyers C, Van Dromme I, Swann E, Marovich MA, Follmann D, Neuzil KM, Corey L, Greninger AL, Roychoudhury P, Hyrien O, Gilbert PB. Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features. Nat Commun 2024; 15:2175. [PMID: 38467646 PMCID: PMC10928100 DOI: 10.1038/s41467-024-46536-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: 05/16/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
In the ENSEMBLE randomized, placebo-controlled phase 3 trial (NCT04505722), estimated single-dose Ad26.COV2.S vaccine efficacy (VE) was 56% against moderate to severe-critical COVID-19. SARS-CoV-2 Spike sequences were determined from 484 vaccine and 1,067 placebo recipients who acquired COVID-19. In this set of prespecified analyses, we show that in Latin America, VE was significantly lower against Lambda vs. Reference and against Lambda vs. non-Lambda [family-wise error rate (FWER) p < 0.05]. VE differed by residue match vs. mismatch to the vaccine-insert at 16 amino acid positions (4 FWER p < 0.05; 12 q-value ≤ 0.20); significantly decreased with physicochemical-weighted Hamming distance to the vaccine-strain sequence for Spike, receptor-binding domain, N-terminal domain, and S1 (FWER p < 0.001); differed (FWER ≤ 0.05) by distance to the vaccine strain measured by 9 antibody-epitope escape scores and 4 NTD neutralization-impacting features; and decreased (p = 0.011) with neutralization resistance level to vaccinee sera. VE against severe-critical COVID-19 was stable across most sequence features but lower against the most distant viruses.
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Affiliation(s)
- Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Li Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Allan C deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian D Williamson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Biostatistics Division, Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - James Ludwig
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cindy Molitor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Benkeser
- Departments of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Alex Luedtke
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Brian Simpkins
- Department of Computer Science, Pitzer College, Claremont, CA, USA
| | - Fei Heng
- University of North Florida, Jacksonville, FL, USA
| | - Yanqing Sun
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hongjun Bai
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Bethany L Dearlove
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Elena E Giorgi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mandy Jongeneelen
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Boerries Brandenburg
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Jerald Sadoff
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Cape Town, South Africa
| | - Sanne Roels
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - An Vandebosch
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Daniel J Stieh
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Mathieu Le Gars
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Johan Vingerhoets
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Beatriz Grinsztejn
- Evandro Chagas National Institute of Infectious Diseases-Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Paul A Goepfert
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leonardo Paiva de Sousa
- Evandro Chagas National Institute of Infectious Diseases-Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Mayara Secco Torres Silva
- Evandro Chagas National Institute of Infectious Diseases-Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Martin Casapia
- Facultad de Medicina Humana, Universidad Nacional de la Amazonia Peru, Iquitos, Peru
| | - Marcelo H Losso
- Hospital General de Agudos José María Ramos Mejia, Buenos Aires, Argentina
| | - Susan J Little
- Division of Infectious Diseases, University of California San Diego, La Jolla, CA, USA
| | - Aditya Gaur
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Carla Truyers
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Ilse Van Dromme
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Edith Swann
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mary A Marovich
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dean Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Biostatistics, University of Washington School of Public Health, Seattle, WA, USA.
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28
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Sow MS, Togo J, Simons LM, Diallo ST, Magassouba ML, Keita MB, Somboro AM, Coulibaly Y, Ozer EA, Hultquist JF, Murphy RL, Maiga AI, Maiga M, Lorenzo-Redondo R. Genomic characterization of SARS-CoV-2 in Guinea, West Africa. PLoS One 2024; 19:e0299082. [PMID: 38446806 PMCID: PMC10917296 DOI: 10.1371/journal.pone.0299082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
SARS-CoV-2 has claimed several million lives since its emergence in late 2019. The ongoing evolution of the virus has resulted in the periodic emergence of new viral variants with distinct fitness advantages, including enhanced transmission and immune escape. While several SARS-CoV-2 variants of concern trace their origins back to the African continent-including Beta, Eta, and Omicron-most countries in Africa remain under-sampled in global genomic surveillance efforts. In an effort to begin filling these knowledge gaps, we conducted retrospective viral genomic surveillance in Guinea from October 2020 to August 2021. We found that SARS-CoV-2 clades 20A, 20B, and 20C dominated throughout 2020 until the coincident emergence of the Alpha and Eta variants of concern in January 2021. The Alpha variant remained dominant throughout early 2021 until the arrival of the Delta variant in July. Surprisingly, despite the small sample size of our study, we also found the persistence of the early SARS-CoV-2 clade 19B as late as April 2021. Together, these data help fill in our understanding of the SARS-CoV-2 population dynamics in West Africa early in the COVID-19 pandemic.
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Affiliation(s)
- Mamadou Saliou Sow
- Service de Maladie Infectieuse du Centre Hospitalier de Donka, Conakry, Guinée
| | - Josue Togo
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Département de Biologie médicale, Centre Hospitalier Universitaire Gabriel Toure, Bamako, Mali
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | | | | | - Mamadou Bhoye Keita
- Département de laboratoire, Institut National de la Santé Publique, Conakry, Guinée
- Département de biologie, Université Gamal Abdel Nasser de Conakry, Conakry, Guinée
| | - Anou Moise Somboro
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Youssouf Coulibaly
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | - Judd F. Hultquist
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | - Robert Leo Murphy
- Institute for Global Health, Northwestern University, Chicago, IL, United States of America
| | - Almoustapha Issiaka Maiga
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Département de Biologie médicale, Centre Hospitalier Universitaire Gabriel Toure, Bamako, Mali
| | - Mamoudou Maiga
- Institute for Global Health, Northwestern University, Chicago, IL, United States of America
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
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29
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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30
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Gerashchenko GV, Hryshchenko NV, Melnichuk NS, Marchyshak TV, Chernushyn SY, Demchyshina IV, Chernenko LM, Kuzin IV, Tkachuk ZY, Kashuba VI, Tukalo MA. Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022. Heliyon 2024; 10:e25618. [PMID: 38380034 PMCID: PMC10877268 DOI: 10.1016/j.heliyon.2024.e25618] [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: 04/25/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
The aim of our study was to identify and characterize the SARS-CoV-2 variants in COVID-19 patients' samples collected from different regions of Ukraine to determine the relationship between SARS-CoV-2 phylogenetics and COVID-19 epidemiology. Patients and methods Samples were collected from COVID-19 patients during 2021 and the beginning of 2022 (401 patients). The SARS-CoV-2 genotyping was performed by parallel whole genome sequencing. Results The obtained SARS-CoV-2 genotypes showed that three waves of the COVID-19 pandemic in Ukraine were represented by three main variants of concern (VOC), named Alpha, Delta and Omicron; each VOC successfully replaced the earlier variant. The VOC Alpha strain was presented by one B.1.1.7 lineage, while VOC Delta showed a spectrum of 25 lineages that had different prevalence in 19 investigated regions of Ukraine. The VOC Omicron in the first half of the pandemic was represented by 13 lines that belonged to two different clades representing B.1 and B.2 Omicron strains. Each of the three epidemic waves (VOC Alpha, Delta, and Omicron) demonstrated their own course of disease, associated with genetic changes in the SARS-CoV-2 genome. The observed epidemiological features are associated with the genetic characteristics of the different VOCs, such as point mutations, deletions and insertions in the viral genome. A phylogenetic and transmission analysis showed the different mutation rates; there were multiple virus sources with a limited distribution between regions. Conclusions The evolution of SARS-CoV-2 virus and high levels of morbidity due to COVID-19 are still registered in the world. Observed multiple virus sourses with the limited distribution between regions indicates the high efficiency of the anti-epidemic policy pursued by the Ministry of Health of Ukraine to prevent the spread of the epidemic, despite the low level of vaccination of the Ukrainian population.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zenovii Yu Tkachuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Mykhailo A. Tukalo
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
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31
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Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [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: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
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Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
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Fauziah I, Nugroho HA, Yanthi ND, Tiffarent R, Saputra S. Potential zoonotic spillover at the human-animal interface: A mini-review. Vet World 2024; 17:289-302. [PMID: 38595670 PMCID: PMC11000462 DOI: 10.14202/vetworld.2024.289-302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/09/2024] [Indexed: 04/11/2024] Open
Abstract
Wildlife markets and wet wildlife markets, a type of human-animal interface, are commonly trading centers for wild-caught and captive-exotic animals as well as their products. These markets provide an ideal environment for spillovers of zoonotic and emerging infectious diseases (EIDs). These conditions may raise serious concerns, particularly in relation to wildlife species that frequently interact with humans and domestic animals. EIDs pose a significant risk to humans, ecosystems, and public health, as demonstrated by the current COVID-19 pandemic, and other previous outbreaks, including the highly pathogenic avian influenza H5N1. Even though it seems appears impossible to eliminate EIDs, we may still be able to minimalize the risks and take several measures to prevent new EIDs originated from animals. The aim of this study was to review several types of human-animal interfaces with a high risk of zoonotic spillover, infectious agents, and animal hosts or reservoirs. Identifying those factors will support the development of interventions and effective disease control in human-animal interface settings.
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Affiliation(s)
- Ima Fauziah
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Herjuno Ari Nugroho
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Nova Dilla Yanthi
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Rida Tiffarent
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
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Wang D, Huot M, Mohanty V, Shakhnovich EI. Biophysical principles predict fitness of SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.23.549087. [PMID: 37577536 PMCID: PMC10418099 DOI: 10.1101/2023.07.23.549087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
SARS-CoV-2 employs its spike protein's receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBD's biophysical properties contribute to SARS-CoV-2's epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the discovery of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by binding constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto a epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.
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Affiliation(s)
- Dianzhuo Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Marian Huot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Ecole Polytechnique, Institut Polytechnique de Paris
| | - Vaibhav Mohanty
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Harvard-MIT MD-PhD Program and Program in Health Sciences and Technology, Harvard Medical School, Boston, MA and Massachusetts Institute of Technology, Cambridge, MA
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34
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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Shi Y, Simpson S, Chen Y, Aull H, Benjamin J, Serra-Moreno R. Mutations accumulated in the Spike of SARS-CoV-2 Omicron allow for more efficient counteraction of the restriction factor BST2/Tetherin. PLoS Pathog 2024; 20:e1011912. [PMID: 38190411 PMCID: PMC10798645 DOI: 10.1371/journal.ppat.1011912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/19/2024] [Accepted: 12/19/2023] [Indexed: 01/10/2024] Open
Abstract
BST2/Tetherin is a restriction factor with broad antiviral activity against enveloped viruses, including coronaviruses. Specifically, BST2 traps nascent particles to membrane compartments, preventing their release and spread. In turn, viruses have evolved multiple mechanisms to counteract BST2. Here, we examined the interactions between BST2 and SARS-CoV-2. Our study shows that BST2 reduces SARS-CoV-2 virion release. However, the virus uses the Spike (S) protein to downregulate BST2. This requires a physical interaction between S and BST2, which routes BST2 for lysosomal degradation in a Clathtin- and ubiquitination-dependent manner. By surveying different SARS-CoV-2 variants of concern (Alpha-Omicron), we found that Omicron is more efficient at counteracting BST2, and that mutations in S account for its enhanced anti-BST2 activity. Mapping analyses revealed that several surfaces in the extracellular region of BST2 are required for an interaction with the Spike, and that the Omicron variant has changed its patterns of association with BST2 to improve its counteraction. Therefore, our study suggests that, besides enhancing receptor binding and evasion of neutralizing antibodies, mutations accumulated in the Spike afford more efficient counteraction of BST2, which highlights that BST2 antagonism is important for SARS-CoV-2 infectivity and spread.
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Affiliation(s)
- Yuhang Shi
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Sydney Simpson
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Yuexuan Chen
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Haley Aull
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jared Benjamin
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Ruth Serra-Moreno
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
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Zhao J, Kang M, Wu H, Sun B, Baele G, He WT, Lu M, Suchard MA, Ji X, He N, Su S, Veit M. Risk assessment of SARS-CoV-2 replicating and evolving in animals. Trends Microbiol 2024; 32:79-92. [PMID: 37541811 DOI: 10.1016/j.tim.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
The retransmissions of SARS-CoV-2 from several mammals - primarily mink and white-tailed deer - to humans have raised concerns for the emergence of a new animal-derived SARS-CoV-2 variant to worsen the pandemic. Here, we discuss animal species that are susceptible to natural or experimental infection with SARS-CoV-2 and can transmit the virus to mates or humans. We describe cutting-edge techniques to assess the impact of a mutation in the viral spike (S) protein on its receptor and on antibody binding. Our review of spike sequences of animal-derived viruses identified nine unique amino acid exchanges in the receptor-binding domain (RBD) that are not present in any variant of concern (VOC). These mutations are present in SARS-CoV-2 found in companion animals such as dogs and cats, and they exhibit a higher frequency in SARS-CoV-2 found in mink and white-tailed deer, suggesting that sustained transmissions may contribute to maintaining novel mutations. Four of these exchanges, such as Leu452Met, could undermine acquired immune protection in humans while maintaining high affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor. Finally, we discuss important avenues of future research into animal-derived viruses with public health risks.
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Affiliation(s)
- Jin Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Mei Kang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Wu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Bowen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Guy Baele
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Wan-Ting He
- School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Meng Lu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Na He
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany.
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y Castro TR, Piccoli BC, Vieira AA, Casarin BC, Tessele LF, Salvato RS, Gregianini TS, Martins LG, Resende PC, Pereira EC, Moreira FRR, de Jesus JG, Seerig AP, Lobato MAO, de Campos MMA, Goularte JS, da Silva MS, Demoliner M, Filippi M, Pereira VMAG, Schwarzbold AV, Spilki FR, Trindade PA. Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis. Microorganisms 2023; 11:2938. [PMID: 38138081 PMCID: PMC10745878 DOI: 10.3390/microorganisms11122938] [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: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Mutations in the SARS-CoV-2 genome can alter the virus' fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 × 10-4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.
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Affiliation(s)
- Thaís Regina y Castro
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Bruna C. Piccoli
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Andressa A. Vieira
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Bruna C. Casarin
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Luíza F. Tessele
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Richard S. Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Tatiana S. Gregianini
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Leticia G. Martins
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil
| | - Elisa C. Pereira
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil
| | - Filipe R. R. Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-853, Brazil
| | - Jaqueline G. de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05508-220, Brazil
| | - Ana Paula Seerig
- Vigilância em Saúde, Secretaria Municipal da Saúde de Santa Maria, Santa Maria 97060-001, Brazil
| | - Marcos Antonio O. Lobato
- Departamento de Saúde Coletiva, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Marli M. A. de Campos
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Juliana S. Goularte
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Mariana S. da Silva
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | | | - Alexandre V. Schwarzbold
- Departamento de Clínica Médica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Fernando R. Spilki
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Priscila A. Trindade
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
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Li M, Yuan Y, Zou T, Hou Z, Jin L, Wang B. Development trends of human organoid-based COVID-19 research based on bibliometric analysis. Cell Prolif 2023; 56:e13496. [PMID: 37218396 PMCID: PMC10693193 DOI: 10.1111/cpr.13496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a catastrophic threat to human health worldwide. Human stem cell-derived organoids serve as a promising platform for exploring SARS-CoV-2 infection. Several review articles have summarized the application of human organoids in COVID-19, but the research status and development trend of this field have seldom been systematically and comprehensively studied. In this review, we use bibliometric analysis method to identify the characteristics of organoid-based COVID-19 research. First, an annual trend of publications and citations, the most contributing countries or regions and organizations, co-citation analysis of references and sources and research hotspots are determined. Next, systematical summaries of organoid applications in investigating the pathology of SARS-CoV-2 infection, vaccine development and drug discovery, are provided. Lastly, the current challenges and future considerations of this field are discussed. The present study will provide an objective angle to identify the current trend and give novel insights for directing the future development of human organoid applications in SARS-CoV-2 infection.
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Affiliation(s)
- Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of BioengineeringChongqing UniversityChongqingChina
- Southwest Hospital/Southwest Eye HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Yuhan Yuan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of BioengineeringChongqing UniversityChongqingChina
| | - Ting Zou
- Southwest Hospital/Southwest Eye HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Zongkun Hou
- School of Basic Medical Sciences/School of Biology and Engineering (School of Modern Industry for Health and Medicine)Guizhou Medical UniversityGuiyangChina
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of BioengineeringChongqing UniversityChongqingChina
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of BioengineeringChongqing UniversityChongqingChina
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Wadford DA, Baumrind N, Baylis EF, Bell JM, Bouchard EL, Crumpler M, Foote EM, Gilliam S, Glaser CA, Hacker JK, Ledin K, Messenger SL, Morales C, Smith EA, Sevinsky JR, Corbett-Detig RB, DeRisi J, Jacobson K. Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance. Front Public Health 2023; 11:1249614. [PMID: 37937074 PMCID: PMC10627185 DOI: 10.3389/fpubh.2023.1249614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/27/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or "California COVIDNet". This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings. Methods California COVIDNet consists of 50 laboratory partners that include public health laboratories, private clinical diagnostic laboratories, and academic sequencing facilities as well as expert advisors, scientists, consultants, and contractors. Data management, sample sourcing and processing, and computational infrastructure were major challenges that had to be resolved in the midst of the pandemic chaos in order to conduct SARS-CoV-2 genomic surveillance. Data management, storage, and analytics needs were addressed with both conventional database applications and newer cloud-based data solutions, which also fulfilled computational requirements. Results Representative and randomly selected samples were sourced from state-sponsored community testing sites. Since March of 2021, California COVIDNet partners have contributed more than 450,000 SARS-CoV-2 genomes sequenced from remnant samples from both molecular and antigen tests. Combined with genomes from CDC-contracted WGS labs, there are currently nearly 800,000 genomes from all 61 local health jurisdictions (LHJs) in California in the COVIDNet sequence database. More than 5% of all reported positive tests in the state have been sequenced, with similar rates of sequencing across 5 major geographic regions in the state. Discussion Implementation of California COVIDNet revealed challenges and limitations in the public health system. These were overcome by engaging in novel partnerships that established a successful genomic surveillance program which provided valuable data to inform the COVID-19 public health response in California. Significantly, California COVIDNet has provided a foundational data framework and computational infrastructure needed to respond to future public health crises.
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Affiliation(s)
- Debra A. Wadford
- California Department of Public Health, Richmond, CA, United States
| | - Nikki Baumrind
- California Department of Public Health, Richmond, CA, United States
| | | | - John M. Bell
- California Department of Public Health, Richmond, CA, United States
| | | | - Megan Crumpler
- Orange County Public Health Laboratory, Santa Ana, CA, United States
| | - Eric M. Foote
- California Department of Public Health, Richmond, CA, United States
| | - Sabrina Gilliam
- California Department of Public Health, Richmond, CA, United States
| | - Carol A. Glaser
- California Department of Public Health, Richmond, CA, United States
| | - Jill K. Hacker
- California Department of Public Health, Richmond, CA, United States
| | - Katya Ledin
- California Department of Public Health, Richmond, CA, United States
| | | | | | | | | | | | - Joseph DeRisi
- University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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40
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Demirev AV, Lee K, Bae JY, Park H, Park S, Kim H, Lee J, Cho J, Yang JS, Kim KC, Lee JY, Kim K, Lemey P, Park MS, Kim JI. Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea. iScience 2023; 26:107689. [PMID: 37680469 PMCID: PMC10481354 DOI: 10.1016/j.isci.2023.107689] [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: 05/15/2023] [Revised: 07/28/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
SARS-CoV-2 variants have continuously emerged globally, including in South Korea. To characterize the molecular evolution of SARS-CoV-2 in South Korea, we performed phylogenetic and genomic recombination analyses using more than 12,000 complete genome sequences collected until October 2022. The variants in South Korea originated from globally identified variants of concern and harbored genetic clade-common and clade-specific amino acid mutations mainly around the N-terminal domain (NTD) or receptor binding domain (RBD) in the spike protein. Several point mutation residues in key antigenic sites were under positive selection persistently with changing genetic clades of SARS-CoV-2. Furthermore, we detected 17 potential genomic recombinants and 76.4% (13/17) retained the mosaic NTD or RBD genome. Our results suggest that point mutations and genomic recombination in the spike contributed to the molecular evolution of SARS-CoV-2 in South Korea, which will form an integral part of global prevention and control measures against SARS-CoV-2.
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Affiliation(s)
- Atanas V. Demirev
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyuyoung Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sejik Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyunbeen Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jungmin Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Junhyung Cho
- Division of Emerging Viral Diseases and Vector Research, Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea
| | - Jeong-Sun Yang
- Division of Emerging Viral Diseases and Vector Research, Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea
| | - Kyung-Chang Kim
- Division of Emerging Viral Diseases and Vector Research, Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea
| | - Joo-Yeon Lee
- Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea
| | - Kisoon Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Philippe Lemey
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
- Biosafety Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
- Biosafety Center, Korea University College of Medicine, Seoul, Republic of Korea
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41
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Curtis NC, Shin S, Hederman AP, Connor RI, Wieland-Alter WF, Ionov S, Boylston J, Rose J, Sakharkar M, Dorman DB, Dessaint JA, Gwilt LL, Crowley AR, Feldman J, Hauser BM, Schmidt AG, Ashare A, Walker LM, Wright PF, Ackerman ME, Lee J. Characterization of SARS-CoV-2 Convalescent Patients' Serological Repertoire Reveals High Prevalence of Iso-RBD Antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556349. [PMID: 37745524 PMCID: PMC10515772 DOI: 10.1101/2023.09.08.556349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
While our understanding of SARS-CoV-2 pathogenesis and antibody responses following infection and vaccination has improved tremendously since the outbreak in 2019, the sequence identities and relative abundances of the individual constituent antibody molecules in circulation remain understudied. Using Ig-Seq, we proteomically profiled the serological repertoire specific to the whole ectodomain of SARS-CoV-2 prefusion-stabilized spike (S) as well as to the receptor binding domain (RBD) over a 6-month period in four subjects following SARS-CoV-2 infection before SARS-CoV-2 vaccines were available. In each individual, we identified between 59 and 167 unique IgG clonotypes in serum. To our surprise, we discovered that ∼50% of serum IgG specific for RBD did not recognize prefusion-stabilized S (referred to as iso-RBD antibodies), suggesting that a significant fraction of serum IgG targets epitopes on RBD inaccessible on the prefusion-stabilized conformation of S. On the other hand, the abundance of iso-RBD antibodies in nine individuals who received mRNA-based COVID-19 vaccines encoding prefusion-stabilized S was significantly lower (∼8%). We expressed a panel of 12 monoclonal antibodies (mAbs) that were abundantly present in serum from two SARS-CoV-2 infected individuals, and their binding specificities to prefusion-stabilized S and RBD were all in agreement with the binding specificities assigned based on the proteomics data, including 1 iso-RBD mAb which bound to RBD but not to prefusion-stabilized S. 2 of 12 mAbs demonstrated neutralizing activity, while other mAbs were non-neutralizing. 11 of 12 mAbs also bound to S (B.1.351), but only 1 maintained binding to S (B.1.1.529). This particular mAb binding to S (B.1.1.529) 1) represented an antibody lineage that comprised 43% of the individual's total S-reactive serum IgG binding titer 6 months post-infection, 2) bound to the S from a related human coronavirus, HKU1, and 3) had a high somatic hypermutation level (10.9%), suggesting that this antibody lineage likely had been elicited previously by pre-pandemic coronavirus and was re-activated following the SARS-CoV-2 infection. All 12 mAbs demonstrated their ability to engage in Fc-mediated effector function activities. Collectively, our study provides a quantitative overview of the serological repertoire following SARS-CoV-2 infection and the significant contribution of iso-RBD antibodies, demonstrating how vaccination strategies involving prefusion-stabilized S may have reduced the elicitation of iso-RBD serum antibodies which are unlikely to contribute to protection.
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42
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Liu Y, Ye Q. The Key Site Variation and Immune Challenges in SARS-CoV-2 Evolution. Vaccines (Basel) 2023; 11:1472. [PMID: 37766148 PMCID: PMC10537874 DOI: 10.3390/vaccines11091472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide public health and economic threat, and virus variation amplifies the difficulty in epidemic prevention and control. The structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been studied extensively and is now well defined. The S protein is the most distinguishing feature in terms of infection and immunity, mediating virus entrance and inducing neutralizing antibodies. The S protein and its essential components are also the most promising target to develop vaccines and antibody-based drugs. Therefore, the key site mutation in the S gene is of high interest. Among them, RBD, NTD, and furin cleavage sites are the most mutable regions with the most mutation sites and the most serious consequences for SARS-CoV-2 biological characteristics, including infectivity, pathogenicity, natural immunity, vaccine efficacy, and antibody therapeutics. We are also aware that this outbreak may not be the last. Therefore, in this narrative review, we summarized viral variation and prevalence condition, discussed specific amino acid replacement and associated immune challenges and attempted to sum up some prevention and control strategies by reviewing the literature on previously published research about SARS-CoV-2 variation to assist in clarifying the mutation pathway and consequences of SARS-CoV-2 for developing countermeasures against such viruses as soon as possible.
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Affiliation(s)
| | - Qing Ye
- Department of ‘A’, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
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43
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Yamamoto S, Yamayoshi S, Ito M, Sakai-Tagawa Y, Nakachi I, Baba R, Kamimoto S, Ogura T, Hagiwara S, Kato H, Nakajima H, Uwamino Y, Yagi K, Sugaya N, Nagai H, Saito M, Adachi E, Koga M, Tsutsumi T, Duong C, Okuda M, Murakami J, Furusawa Y, Ujie M, Iwatsuki-Horimoto K, Yotsuyanagi H, Kawaoka Y. Differences among epitopes recognized by neutralizing antibodies induced by SARS-CoV-2 infection or COVID-19 vaccination. iScience 2023; 26:107208. [PMID: 37448563 PMCID: PMC10290734 DOI: 10.1016/j.isci.2023.107208] [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: 02/15/2023] [Revised: 04/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
SARS-CoV-2 has gradually acquired amino acid substitutions in its S protein that reduce the potency of neutralizing antibodies, leading to decreased vaccine efficacy. Here, we attempted to obtain mutant viruses by passaging SARS-CoV-2 in the presence of plasma samples from convalescent patients or vaccinees to determine which amino acid substitutions affect the antigenicity of SARS-CoV-2. Several amino acid substitutions in the S2 region, as well as the N-terminal domain (NTD) and receptor-binding domain (RBD), affected the neutralization potency of plasma samples collected from vaccinees, indicating that amino acid substitutions in the S2 region as well as those in the NTD and RBD affect neutralization by vaccine-induced antibodies. Furthermore, the neutralizing potency of vaccinee plasma samples against mutant viruses we obtained or circulating viruses differed among individuals. These findings suggest that genetic backgrounds of vaccinees influence the recognition of neutralizing epitopes.
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Affiliation(s)
- Shinya Yamamoto
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Mutsumi Ito
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Ichiro Nakachi
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Rie Baba
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Shigenobu Kamimoto
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Takayuki Ogura
- Department of Emergency and Intensive Care, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Shigehiro Hagiwara
- Department of Clinical Laboratory, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Hideaki Kato
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Hideaki Nakajima
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Yoshifumi Uwamino
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kazuma Yagi
- Department of Pulmonary Medicine, Keiyu Hospital, Kanagawa 220-8521, Japan
| | - Norio Sugaya
- Department of Pediatrics, Keiyu Hospital, Kanagawa 220-8521, Japan
| | - Hiroyuki Nagai
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Eisuke Adachi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Calvin Duong
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Moe Okuda
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jurika Murakami
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Michiko Ujie
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | | | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
- The University of Tokyo, Pandemic Preparedness, Infection and Advanced Research Center, Tokyo 108-8639, Japan
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Lin X, Sha Z, Trimpert J, Kunec D, Jiang C, Xiong Y, Xu B, Zhu Z, Xue W, Wu H. The NSP4 T492I mutation increases SARS-CoV-2 infectivity by altering non-structural protein cleavage. Cell Host Microbe 2023; 31:1170-1184.e7. [PMID: 37402373 DOI: 10.1016/j.chom.2023.06.002] [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: 01/29/2023] [Revised: 04/13/2023] [Accepted: 06/09/2023] [Indexed: 07/06/2023]
Abstract
The historically dominant SARS-CoV-2 Delta variant and the currently dominant Omicron variants carry a T492I substitution within the non-structural protein 4 (NSP4). Based on in silico analyses, we hypothesized that the T492I mutation increases viral transmissibility and adaptability, which we confirmed with competition experiments in hamster and human airway tissue culture models. Furthermore, we showed that the T492I mutation increases the replication capacity and infectiveness of the virus and improves its ability to evade host immune responses. Mechanistically, the T492I mutation increases the cleavage efficiency of the viral main protease NSP5 by enhancing enzyme-substrate binding, which increases production of nearly all non-structural proteins processed by NSP5. Importantly, the T492I mutation suppresses viral-RNA-associated chemokine production in monocytic macrophages, which may contribute to the attenuated pathogenicity of Omicron variants. Our results highlight the importance of NSP4 adaptation in the evolutionary dynamics of SARS-CoV-2.
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Affiliation(s)
- Xiaoyuan Lin
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China; Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Zhou Sha
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Chen Jiang
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China
| | - Binbin Xu
- School of Pharmaceutical Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China
| | - Zhenglin Zhu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China.
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China.
| | - Haibo Wu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China.
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45
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Hamdy ME, El Deeb AH, Hagag NM, Shahein MA, Alaidi O, Hussein HA. Interspecies transmission of SARS CoV-2 with special emphasis on viral mutations and ACE-2 receptor homology roles. Int J Vet Sci Med 2023; 11:55-86. [PMID: 37441062 PMCID: PMC10334861 DOI: 10.1080/23144599.2023.2222981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 07/15/2023] Open
Abstract
COVID-19 outbreak was first reported in 2019, Wuhan, China. The spillover of the disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to a wide range of pet, zoo, wild, and farm animals has emphasized potential zoonotic and reverse zoonotic viral transmission. Furthermore, it has evoked inquiries about susceptibility of different animal species to SARS-CoV-2 infection and role of these animals as viral reservoirs. Therefore, studying susceptible and non-susceptible hosts for SARS-CoV-2 infection could give a better understanding for the virus and will help in preventing further outbreaks. Here, we review structural aspects of SARS-CoV-2 spike protein, the effect of the different mutations observed in the spike protein, and the impact of ACE2 receptor variations in different animal hosts on inter-species transmission. Moreover, the SARS-CoV-2 spillover chain was reviewed. Combination of SARS-CoV-2 high mutation rate and homology of cellular ACE2 receptors enable the virus to transcend species barriers and facilitate its transmission between humans and animals.
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Affiliation(s)
- Mervat E. Hamdy
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Ayman H. El Deeb
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
- Department of Virology, Faculty of Veterinary Medicine, King Salman International University, South Sinai, Egypt
| | - Naglaa M. Hagag
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Momtaz A. Shahein
- Department of Virology, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Osama Alaidi
- Biocomplexity for Research and Consulting Co., Cairo, Egypt
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hussein A. Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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46
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Zhang Q, Qiao R, Niu J, Xiong X, Wang N, Zhang R, Luo S, Guo Y, Liu Z, Peng L, Zhang S, Tan G, Song K, Sun M, Xu L, Zhang R, Wu X. Evaluation of an identification method for the SARS-CoV-2 Delta variant based on the amplification-refractory mutation system. Front Cell Infect Microbiol 2023; 13:1180297. [PMID: 37475960 PMCID: PMC10354518 DOI: 10.3389/fcimb.2023.1180297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023] Open
Abstract
The Delta variant of SARS-CoV-2 dominated the COVID-19 pandemic due to its high viral replication capacity and immune evasion, causing massive outbreaks of cases, hospitalizations, and deaths. Currently, variant identification is performed mainly by sequencing. However, the high requirements for equipment and operators as well as its high cost have limited its application in underdeveloped regions. To achieve an economical and rapid method of variant identification suitable for undeveloped areas, we applied an amplification-refractory mutation system (ARMS) based on PCR for the detection of novel coronavirus variants. The results showed that this method could be finished in 90 min and detect as few as 500 copies/mL and not react with SARS-Coronavirus, influenza A H1N1(2009), and other cross-pathogens or be influenced by fresh human blood, α- interferon, and other interfering substances. In a set of double-blind trials, tests of 262 samples obtained from patients confirmed with Delta variant infection revealed that our method was able to accurately identify the Delta variant with high sensitivity and specificity. In conclusion, the ARMS-PCR method applied in Delta variant identification is rapid, sensitive, specific, economical, and suitable for undeveloped areas. In our future study, ARMS-PCR will be further applied in the identification of other variants, such as Omicron.
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Affiliation(s)
- Qin Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Runjie Qiao
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jiaojiao Niu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xia Xiong
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Nan Wang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Ruixian Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Sha Luo
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yuwan Guo
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Zhonghua Liu
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Li Peng
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Shaoduo Zhang
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Guolei Tan
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Keyu Song
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Mei Sun
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Lulu Xu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Rong Zhang
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Xuping Wu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
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47
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Wu CY, Yang YH, Lin YS, Shu LH, Cheng YC, Liu HT, Lin YY, Lee IY, Shih WT, Yang PR, Tsai YY, Chang GH, Hsu CM, Yeh RA, Wu YH, Wu YH, Shen RC, Tsai MS. The anti-SARS-CoV-2 effect and mechanism of Chiehyuan herbal oral protection solution. Heliyon 2023; 9:e17701. [PMID: 37483781 PMCID: PMC10359827 DOI: 10.1016/j.heliyon.2023.e17701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
The Chiehyuan herbal oral protection solution (GB-2) is a herbal mixture commonly utilized in Taiwan for combating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as per traditional Chinese medicine practices. This study assessed the clinical impact of GB-2 through prospective clinical trials. With twice-daily use for a week, GB-2 was shown to diminish the expression of angiotensin-converting enzyme 2 (ACE2) in oral mucosal cells. Moreover, after two weeks of use, it could reduce transmembrane protease, serine 2 (TMRPSS2) expression in these cells. Additionally, in vitro experiments demonstrated that GB-2 lessened the entry efficiency of the Omicron, L452R-D614G, T478K-D614G, and L452R-T478K-D614G variants of the SARS-CoV-2 pseudotyped lentivirus. It also impeded the interaction between ACE2 and the receptor-binding domain (RBD) presenting N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R and L452R-T478K mutations. Glycyrrhizic acid, a major compound in GB-2, also hindered the entry of the Omicron variant (BA.1) of the SARS-CoV-2 pseudotyped lentivirus by obstructing the binding between ACE2 and the RBD presenting the N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R mutation. To sum up, these findings suggest that GB-2 can decrease ACE2 and TMPRSS2 expression in oral mucosal cells. Both glycyrrhizic acid and GB-2 were found to reduce the entry efficiency of the Omicron variant (BA.1) of the SARS-CoV-2 pseudotyped lentivirus and block the binding between ACE2 and the RBD with the N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R mutation. This evidence implies that GB-2 might be a potential candidate for further study as a preventative measure against SARS-CoV-2 infection.
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Affiliation(s)
- Ching-Yuan Wu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- School of Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Yao-Hsu Yang
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- School of Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Shih Lin
- Department of Pharmacy, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Li-Hsin Shu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yu-Ching Cheng
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Hung-Te Liu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yin-Yin Lin
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - I-Yun Lee
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Wei-Tai Shih
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Pei-Rung Yang
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ying-Ying Tsai
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Geng-He Chang
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- Faculty of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Health Information and Epidemiology Laboratory, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Cheng-Ming Hsu
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- Faculty of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Reming-Albert Yeh
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yu-Huei Wu
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Heng Wu
- Department of Electrical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Rou-Chen Shen
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ming-Shao Tsai
- Department of Otolaryngology, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
- Faculty of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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48
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Miteva D, Kitanova M, Batselova H, Lazova S, Chervenkov L, Peshevska-Sekulovska M, Sekulovski M, Gulinac M, Vasilev GV, Tomov L, Velikova T. The End or a New Era of Development of SARS-CoV-2 Virus: Genetic Variants Responsible for Severe COVID-19 and Clinical Efficacy of the Most Commonly Used Vaccines in Clinical Practice. Vaccines (Basel) 2023; 11:1181. [PMID: 37514997 PMCID: PMC10385722 DOI: 10.3390/vaccines11071181] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Although the chief of the World Health Organization (WHO) has declared the end of the coronavirus disease 2019 (COVID-19) as a global health emergency, the disease is still a global threat. To be able to manage such pandemics in the future, it is necessary to develop proper strategies and opportunities to protect human life. The data on the SARS-CoV-2 virus must be continuously analyzed, and the possibilities of mutation and the emergence of new, more infectious variants must be anticipated, as well as the options of using different preventive and therapeutic techniques. This is because the fast development of severe acute coronavirus 2 syndrome (SARS-CoV-2) variants of concern have posed a significant problem for COVID-19 pandemic control using the presently available vaccinations. This review summarizes data on the SARS-CoV-2 variants that are responsible for severe COVID-19 and the clinical efficacy of the most commonly used vaccines in clinical practice. The consequences after the disease (long COVID or post-COVID conditions) continue to be the subject of studies and research, and affect social and economic life worldwide.
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Affiliation(s)
- Dimitrina Miteva
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Meglena Kitanova
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Hristiana Batselova
- Department of Epidemiology and Disaster Medicine, University Hospital "Saint George", Medical University, 6000 Plovdiv, Bulgaria
| | - Snezhina Lazova
- Pediatric Department, University Hospital "N. I. Pirogov," 21 "General Eduard I. Totleben" Blvd, 1606 Sofia, Bulgaria
- Department of Healthcare, Faculty of Public Health "Prof. Tsekomir Vodenicharov, MD, DSc", Medical University of Sofia, Bialo More 8 str., 1527 Sofia, Bulgaria
| | - Lyubomir Chervenkov
- Department of Diagnostic Imaging, Medical University Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, 1407 Sofia, Bulgaria
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
| | - Metodija Sekulovski
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
- Department of Anesthesiology and Intensive Care, University Hospital Lozenetz, 1 Kozyak str., 1407 Sofia, Bulgaria
| | - Milena Gulinac
- Department of General and Clinical Pathology, Medical University of Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Georgi V Vasilev
- Clinic of Endocrinology and Metabolic Disorders, UMHAT "Sv. Georgi", 4000 Plovdiv, Bulgaria
| | - Luchesar Tomov
- Department of Informatics, New Bulgarian University, Montevideo 21 str., 1618 Sofia, Bulgaria
| | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
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Addetia A, Park YJ, Starr T, Greaney AJ, Sprouse KR, Bowen JE, Tiles SW, Van Voorhis WC, Bloom JD, Corti D, Walls AC, Veesler D. Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Cell Rep 2023; 42:112621. [PMID: 37300832 PMCID: PMC10213294 DOI: 10.1016/j.celrep.2023.112621] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/18/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is eroding antibody responses elicited by prior vaccination and infection. The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-COV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the AZD1061 (COV2-2130) mAb. Here, we show that this mutation remodels the receptor-binding site allosterically, thereby altering the epitopes recognized by these three mAbs and vaccine-elicited neutralizing antibodies while remaining functional. Our results demonstrate the spectacular structural and functional plasticity of the SARS-CoV-2 RBD, which is continuously evolving in emerging SARS-CoV-2 variants, including currently circulating strains that are accumulating mutations in the antigenic sites remodeled by the E406W substitution.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA; Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Tyler Starr
- Howard Hughes Medical Institute, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sasha W Tiles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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50
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Zhou B, Sun Y, Mao H, Su L, Lou Y, Yan H, Yao W, Chen H, Zhang Y. Molecular epidemiological characteristics of SARS-CoV-2 in imported cases from 2021 to 2022 in Zhejiang Province, China. Front Public Health 2023; 11:1189969. [PMID: 37427288 PMCID: PMC10323361 DOI: 10.3389/fpubh.2023.1189969] [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: 03/22/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
Backgrounds The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a global threat since 2020. The emergence of the Omicron variant in 2021, which replaced Delta as the dominant variant of concern, has had a significant adverse impact on the global economy and public health. During this period, Zhejiang Province implemented dynamic zeroing and focused on preventing imported cases. This study aimed to gain clear insight into the characteristics of imported COVID-19 cases in Zhejiang Province. Methods We conducted a systematic molecular epidemiological analysis of 146 imported cases between July 2021 and November 2022 in Zhejiang Province. Virus samples with cycle threshold (Ct) value less than 32 were performed next generation sequencing. Basing the whole genome sequence obtained after quality control and assembly of reads, the whole genome variation map and phylogenetic tree were constructed and further analyzed. Results Our study identified critical months and populations for surveillance, profiled the variation of various lineages, determined the evolutionary relationships among various lineages of SARS-CoV-2, and compared the results in Zhejiang with those obtained worldwide during this period. Conclusion The continuous molecular epidemiological surveillance of imported cases of COVID-19 in Zhejiang Province during 2021 to 2022 is consistent with the global epidemic trend.
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