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Zheng K, Chong AY, Mentzer AJ. How could our genetics impact COVID-19 vaccine response? Expert Rev Clin Immunol 2024; 20:1027-1039. [PMID: 38676712 DOI: 10.1080/1744666x.2024.2346584] [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: 12/22/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024]
Abstract
INTRODUCTION The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has posed unprecedented global health challenges since its emergence in December 2019. The rapid availability of vaccines has been estimated to save millions of lives, but there is variation in how individuals respond to vaccines, influencing their effectiveness at an individual, and population level. AREAS COVERED This review focuses on human genetic factors influencing the immune response and effectiveness of vaccines, highlighting the importance of associations across the HLA locus. Genome-Wide Association Studies (GWAS) and other genetic association analyses have identified statistically significant associations between specific HLA alleles including HLA-DRB1*13, DBQ1*06, and A*03 impacting antibody responses and the risk of breakthrough infections post-vaccination. Relationships between these associations and potential mechanisms and links with risks of natural infection or disease are explored, and this review concludes by emphasizing how understanding the mechanisms of these genetic determinants may inform the development of tailored vaccination strategies. EXPERT OPINION Although complex, we believe these findings from the SARS-CoV2 pandemic offer a unique opportunity to understand the relationships between HLA and infection and vaccine response, with a goal of optimizing individual protection against COVID-19 in the ongoing pandemic, and possibly influencing wider vaccine development in the future.
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Affiliation(s)
- Keyi Zheng
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
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Wang Z, Sun W, Li D, Sun Y, Zhu M, Wang W, Zhang Y, Li E, Yan F, Wang T, Feng N, Yang S, Xia X, Gao Y. A live attenuated influenza B virus vaccine expressing RBD elicits protective immunity against SARS-CoV-2 in mice. Virus Res 2024; 345:199378. [PMID: 38643857 PMCID: PMC11059473 DOI: 10.1016/j.virusres.2024.199378] [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: 05/11/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/23/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to human health globally. It is crucial to develop a vaccine to reduce the effect of the virus on public health, economy, and society and regulate the transmission of SARS-CoV-2. Influenza B virus (IBV) can be used as a vector that does not rely on the current circulating influenza A strains. In this study, we constructed an IBV-based vector vaccine by inserting a receptor-binding domain (RBD) into a non-structural protein 1 (NS1)-truncated gene (rIBV-NS110-RBD). Subsequently, we assessed its safety, immunogenicity, and protective efficacy against SARS-CoV-2 in mice, and observed that it was safe in a mouse model. Intranasal administration of a recombinant rIBV-NS110-RBD vaccine induced high levels of SARS-CoV-2-specific IgA and IgG antibodies and T cell-mediated immunity in mice. Administering two doses of the intranasal rIBV-NS110-RBD vaccine significantly reduced the viral load and lung damage in mice. This novel IBV-based vaccine offers a novel approach for controlling the SARS-CoV-2 pandemic.
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MESH Headings
- Animals
- Mice
- Influenza B virus/immunology
- Influenza B virus/genetics
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- COVID-19/prevention & control
- COVID-19/immunology
- Vaccines, Attenuated/immunology
- Vaccines, Attenuated/administration & dosage
- Vaccines, Attenuated/genetics
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- Mice, Inbred BALB C
- Female
- Administration, Intranasal
- Humans
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Influenza Vaccines/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Immunoglobulin A/blood
- Disease Models, Animal
- Immunoglobulin G/blood
- Viral Load
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
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Affiliation(s)
- Zhenfei Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; College of Animal Science and Technology, College of Veterinary and Medicine, Jilin Agricultural University, Changchun, China
| | - Weiyang Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Dongxu Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yue Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, PR China
| | - Menghan Zhu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, School of Basic Medical Sciences, Kaifeng, China
| | - Wenqi Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yiming Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Songtao Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
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3
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Lee J, Naoe Y, Bang U, Nakagama Y, Saito A, Kido Y, Hotta A. Neutralization sensitivity of SARS-CoV-2 Omicron variants FL.1 and GE.1 by therapeutic antibodies and XBB sera. Virology 2024; 595:110067. [PMID: 38653156 DOI: 10.1016/j.virol.2024.110067] [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: 05/18/2023] [Revised: 02/22/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Two SARS-CoV-2 XBB sub-variants, FL.1 and GE.1, have been increasing in prevalence worldwide, but limited information is available about their ability to evade the immune system. FL.1 and GE.1 are emerging Omicron XBB variants possessing additional mutations in the spike RBD raising concerns of increased neutralization escape. In this study, we assessed the neutralizing ability of eleven FDA-approved monoclonal antibody combinations against different Omicron variants, including BA.2.75, BA.2.76, BA.4/5, XBB.1.5, and CH.1.1. Among the eleven antibodies, Sotrovimab was the only antibody to show broad neutralization ability against XBB.1.5. However, Sotrovimab showed attenuated neutralization efficiency against recently emerging XBB sub-lineages EG.5, FL.1, and GE.1 compared to XBB.1.5. Additionally, XBB.1.5 seropositive convalescent sera displayed lower neutralization activity against EG.5, FL.1, and GE.1. Overall, our findings present enhanced immune evasion capacity of emerging XBB variants and emphasize the importance of continued monitoring of novel variants.
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Affiliation(s)
- Joseph Lee
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Youichi Naoe
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Uikyu Bang
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Yu Nakagama
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Yasutoshi Kido
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan.
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4
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Bai R, Chen Y, Ou J, Dong W, Zhong T, Li Y, Li C, Liu C, Ji C, Li H, Luo Y, Mei YF, Wu J, Seto D, Yin A, Zhang Q, Luo M. Clinical characteristics and phylogenetic analysis of human enteric adenovirus type 41 (HAdV-F41) from children with gastroenteritis during SARS-CoV-2 pandemic. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105619. [PMID: 38906518 DOI: 10.1016/j.meegid.2024.105619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024]
Abstract
Human adenovirus type 41 (HAdV-F41) usually causes pediatrics gastroenteritis. However, it was reported to be associated with the outbreaks of severe acute hepatitis of unknown aetiology (SAHUA) in pediatrics during COVID-19 pandemic. In this study, we investigated the prevalence of enteric HAdV-F41 in 37,920 paediatric gastroenteritis cases from 2017 to 2022 in Guangzhou, China. All children presented were tested negative for SARS-CoV-2 during the "zero-COVID" period. The main clinical symptom of the children was diarrhea (96.5%). No fatalities nor liver abnormal symptoms was found. In 2021, one year since the pandemic of COVID-19, the prevalence of HAdV-F41 abruptly increased from 3.71% to 8.64% (P < 0.001). All of HAdV-F41 circulating worldwide were classified into eight different subtypes (G1-G8) based on the phylogenetic clustering permutation of the four capsid genes of HAdV-F41. G3 was the predominant subtype (56.2%; 77/137). CRV5 isolates from SAHUA cases belong to this subtype, in which N312D and H335D mutations in the short fiber knob were identified in both Guangzhou and CRV5 isolates, presumably changing the virus tropism by directly interacting with the heparin sulfate (HS) receptor. Additionally, a novel recombinant G6 subtype, which is unique and only circulating in China was first identified in this study. This is the first study highlighting the prevalence of HAdV-F41 in paediatric cases of gastroenteritis during COVID-19 pandemic in China. The clinical and viral evolution finding of HAdV-F41 provide insight into the clinical characteristics of children with HAdV-F41 infections as well as the uncertain role of HAdV-F41 in the cause of SAHUA.
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Affiliation(s)
- Ru Bai
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China; The Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yanyuan Chen
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China
| | - Junxian Ou
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Institute of Medical Microbiology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wenya Dong
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China
| | - Tianhua Zhong
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China
| | - Yiqiang Li
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Institute of Medical Microbiology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Congrong Li
- Biosafety Laboratory, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Chengyi Liu
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China
| | - Cunwei Ji
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China
| | - Huan Li
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China
| | - Yasha Luo
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China
| | - Ya-Fang Mei
- Department of Clinical Microbiology, Section of Virology, Umeå University, SE-90185 Umeå, Sweden
| | - Jie Wu
- Guangdong Center for Disease Control and Prevention, Guangzhou, China
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Aihua Yin
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China; Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou 511443, China.
| | - Qiwei Zhang
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Institute of Medical Microbiology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Mingyong Luo
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou 511443, China.
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5
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Khan P, Aufdembrink LM, Adamala KP, Engelhart AE. PACRAT: pathogen detection with aptamer-observed cascaded recombinase polymerase amplification-in vitro transcription. RNA (NEW YORK, N.Y.) 2024; 30:891-900. [PMID: 38637016 PMCID: PMC11182012 DOI: 10.1261/rna.079891.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024]
Abstract
The SARS-CoV-2 pandemic underscored the need for early, rapid, and widespread pathogen detection tests that are readily accessible. Many existing rapid isothermal detection methods use the recombinase polymerase amplification (RPA), which exhibits polymerase chain reaction (PCR)-like sensitivity, specificity, and even higher speed. However, coupling RPA to other enzymatic reactions has proven difficult. For the first time, we demonstrate that with tuning of buffer conditions and optimization of reagent concentrations, RPA can be cascaded into an in vitro transcription reaction, enabling detection using fluorescent aptamers in a one-pot reaction. We show that this reaction, which we term PACRAT (pathogen detection with aptamer-observed cascaded recombinase polymerase amplification-in vitro transcription) can be used to detect SARS-CoV-2 RNA with single-copy detection limits, Escherichia coli with single-cell detection limits, and 10-min detection times. Further demonstrating the utility of our one-pot, cascaded amplification system, we show PACRAT can be used for multiplexed detection of the pathogens SARS-CoV-2 and E. coli, along with multiplexed detection of two variants of SARS-CoV-2.
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Affiliation(s)
- Pavana Khan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Lauren M Aufdembrink
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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6
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Shen J, Xu X, Fan J, Chen H, Zhao Y, Huang W, Liu W, Zhang Z, Cui Q, Li Q, Niu Z, Jiang D, Cao G. APOBEC3-related mutations in the spike protein-encoding region facilitate SARS-CoV-2 evolution. Heliyon 2024; 10:e32139. [PMID: 38868014 PMCID: PMC11168432 DOI: 10.1016/j.heliyon.2024.e32139] [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: 12/10/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
SARS-CoV-2 evolves gradually to cause COVID-19 epidemic. One of driving forces of SARS-CoV-2 evolution might be activation of apolipoprotein B mRNA editing catalytic subunit-like protein 3 (APOBEC3) by inflammatory factors. Here, we aimed to elucidate the effect of the APOBEC3-related viral mutations on the infectivity and immune evasion of SARS-CoV-2. The APOBEC3-related C > U mutations ranked as the second most common mutation types in the SARS-CoV-2 genome. mRNA expression of APOBEC3A (A3A), APOBEC3B (A3B), and APOBEC3G (A3G) in peripheral blood cells increased with disease severity. A3B, a critical member of the APOBEC3 family, was significantly upregulated in both severe and moderate COVID-19 patients and positively associated with neutrophil proportion and COVID-19 severity. We identified USP18 protein, a key molecule centralizing the protein-protein interaction network of key APOBEC3 proteins. Furthermore, mRNA expression of USP18 was significantly correlated to ACE2 and TMPRSS2 expression in the tissue of upper airways. Knockdown of USP18 mRNA significantly decreased A3B expression. Ectopic expression of A3B gene increased SARS-CoV-2 infectivity. C > U mutations at S371F, S373L, and S375F significantly conferred with the immune escape of SARS-CoV-2. Thus, APOBEC3, whose expression are upregulated by inflammatory factors, might promote SARS-CoV-2 evolution and spread via upregulating USP18 level and facilitating the immune escape. A3B and USP18 might be therapeutic targets for interfering with SARS-CoV-2 evolution.
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Affiliation(s)
- Jiaying Shen
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Xinxin Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongsen Chen
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Weijin Huang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Zihan Zhang
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Qianqian Cui
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Qianqian Li
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Zheyun Niu
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Dongming Jiang
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Guangwen Cao
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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Penrice-Randal R, Bentley EG, Sharma P, Kirby A, Donovan-Banfield I, Kipar A, Mega DF, Bramwell C, Sharp J, Owen A, Hiscox JA, Stewart JP. The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582110. [PMID: 38464327 PMCID: PMC10925244 DOI: 10.1101/2024.02.27.582110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Objectives Immunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context during the first 7 days of infection. Methods Mice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed. Results Treatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of A>G and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs). Conclusions Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development, especially by taking persistence into consideration, and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.
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Affiliation(s)
| | - Eleanor G. Bentley
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - I’ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Daniele F. Mega
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Chloe Bramwell
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
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8
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Shempela DM, Chambaro HM, Sikalima J, Cham F, Njuguna M, Morrison L, Mudenda S, Chanda D, Kasanga M, Daka V, Kwenda G, Musonda K, Munsaka S, Chilengi R, Sichinga K, Simulundu E. Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study. Int J Mol Sci 2024; 25:6338. [PMID: 38928045 PMCID: PMC11203853 DOI: 10.3390/ijms25126338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.
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Affiliation(s)
| | - Herman M. Chambaro
- Virology Unit, Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka 10101, Zambia;
| | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Fatim Cham
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Michael Njuguna
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Linden Morrison
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia;
| | - Duncan Chanda
- University Teaching Hospital, Ministry of Health, Lusaka 10101, Zambia;
| | - Maisa Kasanga
- Department of Epidemiology and Biostatistics, School of Public Health, Zhengzhou University, Zhengzhou 450001, China;
| | - Victor Daka
- Public Health Department, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola 21692, Zambia;
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Karen Sichinga
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Macha Research Trust, Choma 20100, Zambia
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9
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Silva T, Oliveira E, Oliveira A, Menezes A, Jeremias WDJ, Grenfell RF, Monte-Neto RLD, Pascoal-Xavier MA, Campos MA, Fernandes G, Alves P. Enhancing the epidemiological surveillance of SARS-CoV-2 using Sanger sequencing to identify circulating variants and recombinants. Braz J Microbiol 2024:10.1007/s42770-024-01387-x. [PMID: 38802687 DOI: 10.1007/s42770-024-01387-x] [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: 12/12/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Since the emergence of SARS-CoV-2 in December 2019, more than 12,000 mutations in the virus have been identified. These could cause changes in viral characteristics and directly impact global public health. The emergence of variants is a great concern due to the chance of increased transmissibility and infectivity. Sequencing for surveillance and monitoring circulating strains is extremely necessary as the early identification of new variants allows public health agencies to make faster and more effective decisions to contain the spread of the virus. In the present study, we identified circulating variants in samples collected in Belo Horizonte, Brazil, and detected a recombinant lineage using the Sanger method. The identification of lineages was done through gene amplification of SARS-CoV-2 by Reverse Transcription-Polymerase Chain Reaction (RT-PCR). By using these specific fragments, we were able to differentiate one variant of interest and five circulating variants of concern. We were also able to detect recombinants. Randomly selected samples were sequenced by either Sanger or Next Generation Sequencing (NGS). Our findings validate the effectiveness of Sanger sequencing as a powerful tool for monitoring variants. It is easy to perform and allows the analysis of a larger number of samples in countries that cannot afford NGS.
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Affiliation(s)
- Thaís Silva
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Eneida Oliveira
- Secretaria Municipal de Saúde, 2336, Afonso Pena Avenue, Belo Horizonte, Minas Gerais, 30130-007, Brazil
| | - Alana Oliveira
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - André Menezes
- Secretaria Municipal de Saúde, 2336, Afonso Pena Avenue, Belo Horizonte, Minas Gerais, 30130-007, Brazil
| | - Wander de Jesus Jeremias
- Department of Pharmacy, Federal University of Ouro Preto (UFOP), 27, Nine Street, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Rafaella Fq Grenfell
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA, 30602, USA
| | - Rubens Lima do Monte-Neto
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Marcelo A Pascoal-Xavier
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
- Department of Anatomic Pathology, College of Medicine, Federal University of Minas Gerais, 6627, Presidente Antônio Carlos Avenue, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Marco A Campos
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Gabriel Fernandes
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Pedro Alves
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil.
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10
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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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11
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Glenet M, Lebreil AL, N'Guyen Y, Meyer I, Baud S, Andreoletti L. Structural impact of a new spike Y170W mutation detected in early emerging SARS-CoV-2 Omicron variants in France. Virus Res 2024; 343:199354. [PMID: 38492859 PMCID: PMC10957500 DOI: 10.1016/j.virusres.2024.199354] [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: 01/30/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
To assess the genetic characteristics of the early emerging SARS-CoV-2 Omicron variant strains, we retrospectively analyzed a collection of 150 nasopharyngeal samples taken from a series of outpatient cases tested positive by a referenced qRT-PCR assay during the reported period of Omicron variant emergence in December 2021, in northeastern region of France. Next Generation Sequencing (NGS) analysis of SARS-CoV-2 spike sequences revealed that only 3 (2 %) of these detected strains were Omicron variants, while 147 (98 %) were identified as previously described delta variants. Our phylogenetic analyzes of SARS-CoV-2 RNA genomes showed that these French early emerging Omicron variants may have originated from South Africa or India. In addition, whole viral genome sequences NGS comparison analyzes allowed us to identify an original and uncharacterized Y170W spike mutation that was weakly and transiently detected during the period of SARS-CoV-2 Omicron variant emergence in human populations. Molecular modeling and docking experiments indicated that this original mutated residue Y170W was neither directly involved in binding to the SARS-CoV-2 receptor ACE2 nor in interacting with known neutralizing antibody sites. However, this new mutation may be responsible for preventing the transition from the closed to the open Spike conformation, thus promoting the early emergence of the Omicron variant. Overall, these results underscore the epidemiological utility of a routine whole-genome viral NGS strategy that enables genotypic characterization of emerging or mutant SARS-CoV-2 variants, which could have significant implications for public health policy.
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Affiliation(s)
- Marie Glenet
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France.
| | - Anne-Laure Lebreil
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France
| | - Yohan N'Guyen
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France; Infectious Diseases and Internal Medicine Department, CHU Reims, Hôpital Robert Debré, Reims, France
| | - Ittah Meyer
- Unilabs BioCT, Private Laboratory Group, Château-Thierry, France
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, CNRS, MEDyC UMR 7369, Reims, France
| | - Laurent Andreoletti
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France; Virology Department, CHU Reims, Hôpital Robert Debré, Reims, France
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12
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Duan H, Zhang E, Ren G, Cheng Y, Yang B, Liu L, Jolicoeur N, Hu H, Xu Y, Liu B. Exploring immune evasion of SARS-CoV-2 variants using a pseudotyped system. Heliyon 2024; 10:e29939. [PMID: 38699727 PMCID: PMC11063423 DOI: 10.1016/j.heliyon.2024.e29939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/18/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
In the United States, coronavirus disease 2019 (COVID-19) cases have consistently been linked to the prevailing variant XBB.1.5 of SARS-CoV-2 since late 2022. A system has been developed for producing and infecting cells with a pseudovirus (PsV) of SARS-CoV-2 to investigate the infection in a Biosafety Level 2 (BSL-2) laboratory. This system utilizes a lentiviral vector carrying ZsGreen1 and Firefly luciferase (Fluc) dual reporter genes, facilitating the analysis of experimental results. In addition, we have created a panel of PsV variants that depict both previous and presently circulating mutations found in circulating SARS-CoV-2 strains. A series of PsVs includes the prototype SARS-CoV-2, Delta B.1.617.2, BA.5, XBB.1, and XBB.1.5. To facilitate the study of infections caused by different variants of SARS-CoV-2 PsV, we have developed a HEK-293T cell line expressing mCherry and human angiotensin converting enzyme 2 (ACE2). To validate whether different SARS-CoV-2 PsV variants can be used for neutralization assays, we employed serum from rats immunized with the PF-D-Trimer protein vaccine to investigate its inhibitory effect on the infectivity of various SARS-CoV-2 PsV variants. According to our observations, the XBB variant, particularly XBB.1.5, exhibits stronger immune evasion capabilities than the prototype SARS-CoV-2, Delta B.1.617.2, and BA.5 PsV variants. Hence, utilizing the neutralization test, this study has the capability to forecast the effectiveness in preventing future SARS-CoV-2 variants infections.
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Affiliation(s)
- Haixiao Duan
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Ershuai Zhang
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Ge Ren
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Yining Cheng
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Binfeng Yang
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Lirong Liu
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | | | - Han Hu
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Yan Xu
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Binlei Liu
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
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13
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Inson JGM, Malla B, Amalin DM, Carvajal TM, Enriquez MLD, Hirai S, Raya S, Rahmani AF, Angga MS, Sthapit N, Shrestha S, Ruti AA, Takeda T, Kitajima M, Alam ZF, Haramoto E. Detection of SARS-CoV-2 and Omicron variant RNA in wastewater samples from Manila, Philippines. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170921. [PMID: 38350577 DOI: 10.1016/j.scitotenv.2024.170921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/15/2024]
Abstract
Manila, a highly urbanized city, is listed as one of the top cities with the highest recorded number of coronavirus disease 2019 (COVID-19) cases in the Philippines. This study aimed to detect and quantify the RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the Omicron variant in 51 wastewater samples collected from three locations in Manila, namely Estero de Santa Clara, Estero de Pandacan, which are open drainages, and a sewage treatment plant (STP) at De La Salle University-Manila, between July 2022 and February 2023. Using one-step reverse transcription-quantitative polymerase chain reaction, SARS-CoV-2 and Omicron variant RNA were detected in 78 % (40/51; 4.9 ± 0.5 log10 copies/L) and 60 % (24/40; 4.4 ± 0.3 log10 copies/L) of wastewater samples collected from all sampling sites, respectively. SARS-CoV-2 RNA was detected frequently at Estero de Santa Clara (88 %, 15/17); its highest concentration was at the STP (6.3 log10 copies/L). The Omicron variant RNA was present in the samples collected (4.4 ± 0.3 log10 copies/L) from all sampling sites, with the highest concentration at the STP (4.9 log10 copies/L). Regardless of normalization, using concentrations of pepper mild mottle virus RNA, SARS-CoV-2 RNA concentrations exhibited the highest positive correlation with COVID-19 reported cases in Manila 5 days after the clinical report. These findings revealed that wastewater-based epidemiology may aid in identifying and monitoring of the presence of pathogens in open drainages and STPs in the Philippines. This paper provides the first documentation on SARS-CoV-2 and the Omicron variant in wastewater from Manila.
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Affiliation(s)
- Jessamine Gail M Inson
- Department of Biology, De La Salle University, Manila 1004, Philippines; Environmental Biomonitoring Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Divina M Amalin
- Department of Biology, De La Salle University, Manila 1004, Philippines; Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Thaddeus M Carvajal
- Department of Biology, De La Salle University, Manila 1004, Philippines; Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | | | - Soichiro Hirai
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
| | - Sunayana Raya
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Aulia Fajar Rahmani
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Made Sandhyana Angga
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Niva Sthapit
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Annisa Andarini Ruti
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan.
| | - Zeba F Alam
- Department of Biology, De La Salle University, Manila 1004, Philippines; Environmental Biomonitoring Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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14
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Prasad R, Kadam A, Padippurackal VV, Pulikuttymadom Balasubramanian A, Kumar Chandrakumaran N, Suresh Rangari K, Dnyaneshwar Khangar P, Ajith H, Natarajan K, Chandramohanadas R, Nelson-Sathi S. Discovery of small molecule entry inhibitors targeting the linoleic acid binding pocket of SARS-CoV-2 spike protein. J Biomol Struct Dyn 2024:1-15. [PMID: 38520147 DOI: 10.1080/07391102.2024.2327537] [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: 10/05/2023] [Accepted: 03/02/2024] [Indexed: 03/25/2024]
Abstract
Spike glycoprotein has a significant role in the entry of SARS-CoV-2 to host cells, which makes it a potential drug target. Continued accumulation of non-synonymous mutations in the receptor binding domain of spike protein poses great challenges in identifying antiviral drugs targeting this protein. This study aims to identify potential entry inhibitors of SARS-CoV-2 using virtual screening and molecular dynamics (MD) simulations from three distinct chemical libraries including Pandemic Response Box, Drugbank and DrugCentral, comprising 6971 small molecules. The molecules were screened against a binding pocket identified in the receptor-binding domain (RBD) region of the spike protein which is known as the linoleic acid binding pocket, a highly conserved motif among several SARS-CoV-2 variants. Through virtual screening and binding free energy calculations, we identified four top-scoring compounds, MMV1579787 ([2-Oxo-2-[2-(3-phenoxyphenyl)ethylamino]ethyl]phosphonic acid), Tretinoin, MMV1633963 ((2E,4E)-5-[3-(3,5-dichlorophenoxy)phenyl]penta-2,4-dienoic acid) and Polydatin, which were previously reported to have antibacterial, antifungal or antiviral properties. These molecules showed stable binding on MD simulations over 100 ns and maintained stable interactions with TYR365, PHE338, PHE342, PHE377, TYR369, PHE374 and LEU368 of the spike protein RBD that are found to be conserved among SARS-CoV-2 variants. Our findings were further validated with free energy landscape, principal component analysis and dynamic cross-correlation analysis. Our in silico analysis of binding mode and MD simulation analyses suggest that the identified compounds may impede viral entrance by interacting with the linoleic acid binding site of the spike protein of SARS-CoV-2 regardless of its variants, and they thus demand for further in vitro and in vivo research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshny Prasad
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Anil Kadam
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | | | | | - Kartik Suresh Rangari
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | - Harikrishnan Ajith
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Kathiresan Natarajan
- Trans-disciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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15
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Lopez PA, Nziza N, Chen T, Shook LL, Burns MD, Demidkin S, Jasset O, Akinwunmi B, Yonker LM, Gray KJ, Elovitz MA, Lauffenburger DA, Julg BD, Edlow AG. Placental transfer dynamics and durability of maternal COVID-19 vaccine-induced antibodies in infants. iScience 2024; 27:109273. [PMID: 38444609 PMCID: PMC10914478 DOI: 10.1016/j.isci.2024.109273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
Completion of a COVID-19 vaccination series during pregnancy effectively reduces COVID-19 hospitalization among infants less than 6 months of age. The dynamics of transplacental transfer of maternal vaccine-induced antibodies, and their persistence in infants at 2, 6, 9, and 12 months, have implications for new vaccine development and optimal timing of vaccine administration in pregnancy. We evaluated anti-COVID antibody IgG subclass, Fc-receptor binding profile, and activity against wild-type Spike and RBD plus five variants of concern (VOCs) in 153 serum samples from 100 infants. Maternal IgG1 and IgG3 responses persisted in 2- and 6-month infants to a greater extent than the other IgG subclasses, with high persistence of antibodies binding placental neonatal Fc-receptor and FcγR3A. Lowest persistence was observed against the Omicron RBD-specific region. Maternal vaccine timing, placental Fc-receptor binding capabilities, antibody subclass, fetal sex, and VOC all impact the persistence of antibodies in infants through 12 months of age.
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Affiliation(s)
- Paola A. Lopez
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nadège Nziza
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Tina Chen
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Lydia L. Shook
- Massachusetts General Hospital, Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Boston, MA 02114, USA
- Massachusetts General Hospital, Vincent Center for Reproductive Biology, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Madeleine D. Burns
- Massachusetts General Hospital for Children, Department of Pediatric, Boston, MA 02114, USA
| | - Stepan Demidkin
- Massachusetts General Hospital, Vincent Center for Reproductive Biology, Boston, MA 02114, USA
| | - Olyvia Jasset
- Massachusetts General Hospital, Vincent Center for Reproductive Biology, Boston, MA 02114, USA
| | - Babatunde Akinwunmi
- Brigham and Women’s Hospital, Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Boston, MA 02115, USA
| | - Lael M. Yonker
- Harvard Medical School, Boston, MA 02115, USA
- Massachusetts General Hospital for Children, Department of Pediatric, Boston, MA 02114, USA
| | - Kathryn J. Gray
- Harvard Medical School, Boston, MA 02115, USA
- Brigham and Women’s Hospital, Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Boston, MA 02115, USA
| | - Michal A. Elovitz
- Women’s Biomedical Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Boris D. Julg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Andrea G. Edlow
- Massachusetts General Hospital, Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Boston, MA 02114, USA
- Massachusetts General Hospital, Vincent Center for Reproductive Biology, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
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16
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Aguilar Ticona JP, Nery N, Hitchings M, Belitardo EMMA, Fofana MO, Dorión M, Victoriano R, Cruz JS, Oliveira Santana J, de Moraes LEP, Cardoso CW, Ribeiro GS, Reis MG, Khouri R, Costa F, Ko AI, Cummings DAT. Overestimation of Severe Acute Respiratory Syndrome Coronavirus 2 Household Transmission in Settings of High Community Transmission: Insights From an Informal Settlement Community in Salvador, Brazil. Open Forum Infect Dis 2024; 11:ofae065. [PMID: 38516384 PMCID: PMC10957159 DOI: 10.1093/ofid/ofae065] [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: 08/30/2023] [Accepted: 01/31/2024] [Indexed: 03/23/2024] Open
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread globally. However, the contribution of community versus household transmission to the overall risk of infection remains unclear. Methods Between November 2021 and March 2022, we conducted an active case-finding study in an urban informal settlement with biweekly visits across 1174 households with 3364 residents. Individuals displaying coronavirus disease 2019 (COVID-19)-related symptoms were identified, interviewed along with household contacts, and defined as index and secondary cases based on reverse-transcription polymerase chain reaction (RT-PCR) and symptom onset. Results In 61 households, we detected a total of 94 RT-PCR-positive cases. Of 69 sequenced samples, 67 cases (97.1%) were attributed to the Omicron BA.1* variant. Among 35 of their households, the secondary attack rate was 50.0% (95% confidence interval [CI], 37.0%-63.0%). Women (relative risk [RR], 1.6 [95% CI, .9-2.7]), older individuals (median difference, 15 [95% CI, 2-21] years), and those reporting symptoms (RR, 1.73 [95% CI, 1.0-3.0]) had a significantly increased risk for SARS-CoV-2 secondary infection. Genomic analysis revealed substantial acquisition of viruses from the community even among households with other SARS-CoV-2 infections. After excluding community acquisition, we estimated a household secondary attack rate of 24.2% (95% CI, 11.9%-40.9%). Conclusions These findings underscore the ongoing risk of community acquisition of SARS-CoV-2 among households with current infections. The observed high attack rate necessitates swift booster vaccination, rapid testing availability, and therapeutic options to mitigate the severe outcomes of COVID-19.
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Affiliation(s)
- Juan P Aguilar Ticona
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nivison Nery
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Matt Hitchings
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | | | - Mariam O Fofana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Murilo Dorión
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Renato Victoriano
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Jaqueline S Cruz
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Juliet Oliveira Santana
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
| | | | - Cristiane W Cardoso
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
- Centro de Informações Estratégicas de Vigilância em Saúde (CIEVS), Secretaria Municipal de Saúde de Salvador, Salvador, Brazil
| | - Guilherme S Ribeiro
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Mitermayer G Reis
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Ricardo Khouri
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Federico Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Albert I Ko
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Ministério da Saúde, Salvador, Bahia, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Derek A T Cummings
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
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Kim JW, Lee JH, Kim HJ, Heo K, Lee Y, Jang HJ, Lee HY, Park JW, Cho YB, Shin HG, Yang HR, Lee HE, Song JY, Lee S. Empowering SARS-CoV-2 variant neutralization with a bifunctional antibody engineered with tandem heptad repeat 2 peptides. J Med Virol 2024; 96:e29506. [PMID: 38445718 DOI: 10.1002/jmv.29506] [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: 11/17/2023] [Revised: 01/28/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
With the global pandemic and the continuous mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the need for effective and broadly neutralizing treatments has become increasingly urgent. This study introduces a novel strategy that targets two aspects simultaneously, using bifunctional antibodies to inhibit both the attachment of SARS-CoV-2 to host cell membranes and viral fusion. We developed pioneering IgG4-(HR2)4 bifunctional antibodies by creating immunoglobulin G4-based and phage display-derived human monoclonal antibodies (mAbs) that specifically bind to the SARS-CoV-2 receptor-binding domain, engineered with four heptad repeat 2 (HR2) peptides. Our in vitro experiments demonstrate the superior neutralization efficacy of these engineered antibodies against various SARS-CoV-2 variants, ranging from original SARS-CoV-2 strain to the recently emerged Omicron variants, as well as SARS-CoV, outperforming the parental mAb. Notably, intravenous monotherapy with the bifunctional antibody neutralizes a SARS-CoV-2 variant in a murine model without causing significant toxicity. In summary, this study unveils the significant potential of HR2 peptide-driven bifunctional antibodies as a potent and versatile strategy for mitigating SARS-CoV-2 infections. This approach offers a promising avenue for rapid development and management in the face of the continuously evolving SARS-CoV-2 variants, holding substantial promise for pandemic control.
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Affiliation(s)
- Ji Woong Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ji Hyun Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Kyun Heo
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
| | - Yoonwoo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Yea Bin Cho
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Gyeong Shin
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hee Eon Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Jin Young Song
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
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18
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Essabbar A, El Mazouri S, Boumajdi N, Bendani H, Aanniz T, Mouna O, Lahcen B, Ibrahimi A. Temporal Dynamics and Genomic Landscape of SARS-CoV-2 After Four Years of Evolution. Cureus 2024; 16:e53654. [PMID: 38327721 PMCID: PMC10849819 DOI: 10.7759/cureus.53654] [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] [Accepted: 02/05/2024] [Indexed: 02/09/2024] Open
Abstract
Introduction Since its emergence, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive genomic evolution, impacting public health policies, diagnosis, medication, and vaccine development. This study leverages advanced bioinformatics to assess the virus's temporal and regional genomic evolution from December 2019 to October 2023. Methods Our analysis incorporates 16,575 complete SARS-CoV-2 sequences collected from 214 countries. These samples were comparatively analyzed, with a detailed characterization of nucleic mutations, lineages, distribution, and evolutionary patterns during each year, using the Wuhan-Hu-1 strain as the reference. Results Our analysis has identified a total of 21,580 mutations that we classified into transient mutations, which diminished over time, and persistent mutations with steadily increasing frequencies. This mutation landscape led to a notable surge in the evolutionary rate, rising from 13 mutations per sample in 2020 to 96 by 2023, with minor geographic variations. The phylogenetic analysis unveiled three distinct evolutionary branches, each representing unique viral evolution pathways. These lineages exhibited a tendency for a reduced duration of dominance with a shortening prevalence period over time, as dominant strains were consistently replaced by more fit variants. Notably, the emergence of the Alpha and Delta variants in 2021 was followed by the subsequent dominance of Omicron clade variants that have branched into several recombinant variants in 2022, marking a significant shift in the viral landscape. Conclusion This study sheds light on the dynamic nature of SARS-CoV-2 evolution, emphasizing the importance of continuous and vigilant genomic surveillance. The dominance of recombinant lineages, coupled with the disappearance of local variants, underscores the virus's adaptability.
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Affiliation(s)
- Abdelmounim Essabbar
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
- Toulouse Cancer Research Center, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, FRA
| | - Safae El Mazouri
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Nassma Boumajdi
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Houda Bendani
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Tarik Aanniz
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Ouadghiri Mouna
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Belyamani Lahcen
- Émergency Department, Military Hospital Rabat Morocco, Rabat, MAR
- Mohammed VI Center For Research and Innovation, Mohammed VI University of Sciences and Health, Rabat, MAR
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
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Hakim MS, Gunadi, Rahayu A, Wibawa H, Eryvinka LS, Supriyati E, Vujira KA, Iskandar K, Afiahayati, Daniwijaya EW, Oktoviani FN, Annisa L, Utami FDT, Amadeus VC, Nurhidayah SS, Leksono TP, Halim FV, Arguni E, Nuryastuti T, Wibawa T. Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia. Virus Genes 2024:10.1007/s11262-023-02048-1. [PMID: 38244104 DOI: 10.1007/s11262-023-02048-1] [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: 06/25/2023] [Accepted: 12/22/2023] [Indexed: 01/22/2024]
Abstract
During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.
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Affiliation(s)
- Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Directorate General of Livestok Services, Ministry of Agriculture, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health and Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Farida Nur Oktoviani
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Luthvia Annisa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Verrell Christopher Amadeus
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Setiani Silvy Nurhidayah
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tiara Putri Leksono
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fiqih Vidiantoro Halim
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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20
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Outteridge M, Nunn CM, Devine K, Patel B, McLean GR. Antivirals for Broader Coverage against Human Coronaviruses. Viruses 2024; 16:156. [PMID: 38275966 PMCID: PMC10820748 DOI: 10.3390/v16010156] [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: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.
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Affiliation(s)
- Mia Outteridge
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Christine M. Nunn
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Kevin Devine
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Bhaven Patel
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
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21
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Sam S, Ofoghi H, Farahmand B. Developing of SARS-CoV-2 fusion protein expressed in E. coli Shuffle T7 for enhanced ELISA detection sensitivity - an integrated experimental and bioinformatic approach. J Biomol Struct Dyn 2024:1-16. [PMID: 38234051 DOI: 10.1080/07391102.2024.2302941] [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: 07/24/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
In the recent COVID-19 pandemic, developing effective diagnostic assays is crucial for controlling the spread of the SARS-CoV-2 virus. Multi-domain fusion proteins are a promising approach to detecting SARS-CoV-2 antibodies. In this study, we designed an antigen named CoV2-Pro, containing two RBD domains from SARS-CoV-2 Omicron and Delta variants and one CTD domain of the nucleoprotein in the order of RBD-RBD-N, linked by a super flexible glycine linker. We evaluated the suitability of E. coli Shuffle T7 and BL21 (DE3) strain for expressing CoV2-Pro. Moreover, Bioinformatic studies were conducted first to analyze the tertiary structure of CoV2-Pro. The CoV2-Pro sequences were cloned into a pET-32b (+) vector for expression in E. coli Shuffle T7 and BL21 (DE3). SDS-PAGE and western blot confirmed the protein expression and folding structure. The CoV2-Pro-TRX was purified by Ni-NTA affinity chromatography. Dot blot analysis was performed to evaluate the antigenic characterization of the CoV2-Pro. A molecular docking simulation was conducted to assess the binding affinity of CoV2-Pro with LY-COV555 (Bamlanivimab) monoclonal antibody. A molecular dynamic was performed to analyze the stability of the structure. Bioinformatic and experimental studies revealed a stable conformational 3D structure of the CoV2-Pro. The CoV2-Pro interacted with SARS-CoV-2 antibodies, confirming the correct antigenic structure. We assert with confidence that CoV2-Pro is ideal for developing an ELISA assay for precise diagnosis and rigorous vaccine evaluation during the COVID-19 prevalence.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sohrab Sam
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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22
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Conway MJ, Yang H, Revord LA, Novay MP, Lee RJ, Ward AS, Abel JD, Williams MR, Uzarski RL, Alm EW. Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater. BMC Genomics 2024; 25:59. [PMID: 38218804 PMCID: PMC10787452 DOI: 10.1186/s12864-024-09977-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Central Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program since 2021. Wastewater samples were collected from on-campus sites and nine off-campus wastewater treatment plants servicing small metropolitan and rural communities. SARS-CoV-2 genome copies were quantified using droplet digital PCR and results were reported to the health department. RESULTS One rural, off-campus site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced and contained predominately a derivative of Alpha variant lineage B.1.1.7, detected from fall 2021 through summer 2023. Mutational analysis of reconstructed genes revealed divergence from the Alpha variant lineage sequence over time, including numerous mutations in the Spike RBD and NTD. CONCLUSIONS We discuss the possibility that a chronic SARS-CoV-2 infection accumulated adaptive mutations that promoted long-term infection. This study reveals that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences.
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Affiliation(s)
- Michael J Conway
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA.
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA.
| | - Hannah Yang
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Lauren A Revord
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Michael P Novay
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Rachel J Lee
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Avery S Ward
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Jackson D Abel
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Maggie R Williams
- School of Engineering & Technology, Central Michigan University, Mt. Pleasant, MI, USA
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA
| | - Rebecca L Uzarski
- Department of Biology and Herbert H. and Grace A. Dow College of Health, Professions, Central Michigan University, Mt. Pleasant, MI, USA
| | - Elizabeth W Alm
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA
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23
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Li D, Sun C, Zhuang P, Mei X. Revolutionizing SARS-CoV-2 omicron variant detection: Towards faster and more reliable methods. Talanta 2024; 266:124937. [PMID: 37481886 DOI: 10.1016/j.talanta.2023.124937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The emergence of the highly contagious Omicron variant of SARS-CoV-2 has inflicted significant damage during the ongoing COVID-19 pandemic. This new variant's significant sequence changes and mutations in both proteins and RNA have rendered many existing rapid detection methods ineffective in identifying it accurately. As the world races to control the spread of the virus, researchers are urgently exploring new diagnostic strategies to specifically detect Omicron variants with high accuracy and sensitivity. In response to this challenge, we have compiled a comprehensive overview of the latest reported rapid detection techniques. These techniques include strategies for the simultaneous detection of multiple SARS-CoV-2 variants and methods for selectively distinguishing Omicron variants. By categorizing these diagnostic techniques based on their targets, which encompass protein antigens and nucleic acids, we aim to offer a comprehensive understanding of the utilization of various recognition elements in identifying these targets. We also highlight the advantages and limitations of each approach. Our work is crucial in providing a more nuanced understanding of the challenges and opportunities in detecting Omicron variants and emerging variants.
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Affiliation(s)
- Dan Li
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
| | - Cai Sun
- AECC Shenyang Liming Aero-Engine Co., Ltd., Shenyang, China
| | - Pengfei Zhuang
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Key Laboratory of Medical Tissue Engineering of Liaoning Province, Jinzhou Medical University, Jinzhou, Liaoning, China.
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24
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Choga WT, Kurusa Gasenna GK, San JE, Ookame T, Gobe I, Chand M, Phafane B, Seru K, Matshosi P, Zuze B, Ndlovu N, Matsuru T, Maruapula D, Bareng OT, Macheke K, Kuate-Lere L, Tlale L, Lesetedi O, Tau M, Mbulawa MB, Smith-Lawrence P, Matshaba M, Shapiro R, Makhema J, Martin DP, de Oliveira T, Lessells RJ, Lockman S, Gaseitsiwe S, Moyo S. Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection. Int J Infect Dis 2024; 138:91-96. [PMID: 37952911 PMCID: PMC10719116 DOI: 10.1016/j.ijid.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023] Open
Abstract
We investigated intra-host genetic evolution using two SARS-CoV-2 isolates from a fully vaccinated (primary schedule x2 doses of AstraZeneca plus a booster of Pfizer), >70-year-old woman with a history of lymphoma and hypertension who presented a SARS-CoV-2 infection for 3 weeks prior to death due to COVID-19. Two full genome sequences were determined from samples taken 13 days apart with both belonging to Pango lineage FL.2: the first detection of this Omicron sub-variant in Botswana. FL.2 is a sub-lineage of XBB.1.9.1. The repertoire of mutations and minority variants in the Spike protein differed between the two time points. Notably, we also observed deletions within the ORF1a and Membrane proteins; both regions are associated with high T-cell epitope density. The internal milieu of immune-suppressed individuals may accelerate SARS-CoV-2 evolution; hence, close monitoring is warranted.
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Affiliation(s)
- Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - James Emmanuel San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Irene Gobe
- School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana
| | - Mohammed Chand
- Diagnofirm Medical Laboratories, Plot 12583, Nyerere Drive MiddleStar, Gaborone, Botswana
| | - Badisa Phafane
- Diagnofirm Medical Laboratories, Plot 12583, Nyerere Drive MiddleStar, Gaborone, Botswana
| | - Kedumetse Seru
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Boitumelo Zuze
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Teko Matsuru
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana
| | | | | | | | | | - Modiri Tau
- National Health laboratory, Gaborone, Botswana
| | | | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, USA
| | - Richard J Lessells
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA; School of Health Systems and Public Health, University of Pretoria, South Africa; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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25
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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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26
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Pennisi R, Gentile D, Rescifina A, Napoli E, Trischitta P, Piperno A, Sciortino MT. An Integrated In Silico and In Vitro Approach for the Identification of Natural Products Active against SARS-CoV-2. Biomolecules 2023; 14:43. [PMID: 38254643 PMCID: PMC10813393 DOI: 10.3390/biom14010043] [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: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has provoked a global health crisis due to the absence of a specific therapeutic agent. 3CLpro (also known as the main protease or Mpro) and PLpro are chymotrypsin-like proteases encoded by the SARS-CoV-2 genome, and play essential roles during the virus lifecycle. Therefore, they are recognized as a prospective therapeutic target in drug discovery against SARS-CoV-2 infection. Thus, this work aims to collectively present potential natural 3CLpro and PLpro inhibitors by in silico simulations and in vitro entry pseudotype-entry models. We screened luteolin-7-O-glucuronide (L7OG), cynarin (CY), folic acid (FA), and rosmarinic acid (RA) molecules against PLpro and 3CLpro through a luminogenic substrate assay. We only reported moderate inhibitory activity on the recombinant 3CLpro and PLpro by L7OG and FA. Afterward, the entry inhibitory activity of L7OG and FA was tested in cell lines transduced with the two different SARS-CoV-2 pseudotypes harboring alpha (α) and omicron (o) spike (S) protein. The results showed that both compounds have a consistent inhibitory activity on the entry for both variants. However, L7OG showed a greater degree of entry inhibition against α-SARS-CoV-2. Molecular modeling studies were used to determine the inhibitory mechanism of the candidate molecules by focusing on their interactions with residues recognized by the protease active site and receptor-binding domain (RBD) of spike SARS-CoV-2. This work allowed us to identify the binding sites of FA and L7OG within the RBD domain in the alpha and omicron variants, demonstrating how FA is active in both variants. We have confidence that future in vivo studies testing the safety and effectiveness of these natural compounds are warranted, given that they are effective against a variant of concerns.
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Affiliation(s)
- Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
| | - Davide Gentile
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, V.le A. Doria 6, 95125 Catania, Italy;
| | - Edoardo Napoli
- Istituto di Chimica Biomolecolare—Consiglio Nazionale delle Ricerche, 95126 Catania, Italy;
| | - Paola Trischitta
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
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27
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Yagüe Relimpio A, Fink A, Bui DT, Fabritz S, Schröter M, Ruggieri A, Platzman I, Spatz JP. Bottom-up Assembled Synthetic SARS-CoV-2 Miniviruses Reveal Lipid Membrane Affinity of Omicron Variant Spike Glycoprotein. ACS NANO 2023; 17:23913-23923. [PMID: 37976416 PMCID: PMC10722588 DOI: 10.1021/acsnano.3c08323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
The ongoing COVID-19 pandemic has been brought on by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike glycoprotein (S), which decorates the viral envelope forming a corona, is responsible for the binding to the angiotensin-converting enzyme 2 (ACE2) receptor and initiating the infection. In comparison to previous variants, Omicron S presents additional binding sites as well as a more positive surface charge. These changes hint at additional molecular targets for interactions between virus and cell, such as the cell membrane or proteoglycans on the cell surface. Herein, bottom-up assembled synthetic SARS-CoV-2 miniviruses (MiniVs), with a lipid composition similar to that of infectious particles, are implemented to study and compare the binding properties of Omicron and Alpha variants. Toward this end, a systematic functional screening is performed to study the binding ability of Omicron and Alpha S proteins to ACE2-functionalized and nonfunctionalized planar supported lipid bilayers. Moreover, giant unilamellar vesicles are used as a cell membrane model to perform competitive interaction assays of the two variants. Finally, two cell lines with and without presentation of the ACE2 receptor are used to confirm the binding properties of the Omicron and Alpha MiniVs to the cellular membrane. Altogether, the results reveal a significantly higher affinity of Omicron S toward both the lipid membrane and ACE2 receptor. The research presented here highlights the advantages of creating and using bottom-up assembled SARS-CoV-2 viruses to understand the impact of changes in the affinity of S for ACE2 in infection studies.
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Affiliation(s)
- Ana Yagüe Relimpio
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Andreas Fink
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Duc Thien Bui
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Department
for Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Martin Schröter
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Alessia Ruggieri
- Heidelberg
University, Medical Faculty, Centre for Integrative Infectious Disease Research (CIID), Department
of Infectious Diseases, Molecular Virology, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Ilia Platzman
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
- Max
Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, U.K.
| | - Joachim P. Spatz
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
- Max
Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, U.K.
- Max Planck
School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
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28
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Ealand CS, Gordhan BG, Machowski EE, Kana BD. Development of primer-probe sets to rapidly distinguish single nucleotide polymorphisms in SARS-CoV-2 lineages. Front Cell Infect Microbiol 2023; 13:1283328. [PMID: 38130775 PMCID: PMC10733533 DOI: 10.3389/fcimb.2023.1283328] [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: 08/25/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Ongoing SARS-CoV-2 infections are driven by the emergence of various variants, with differential propensities to escape immune containment. Single nucleotide polymorphisms (SNPs) in the RNA genome result in altered protein structures and when these changes occur in the S-gene, encoding the spike protein, the ability of the virus to penetrate host cells to initiate an infection can be significantly altered. As a result, vaccine efficacy and prior immunity may be diminished, potentially leading to new waves of infection. Early detection of SARS-CoV-2 variants using a rapid and scalable approach will be paramount for continued monitoring of new infections. In this study, we developed minor groove-binding (MGB) probe-based qPCR assays targeted to specific SNPs in the S-gene, which are present in variants of concern (VOC), namely the E484K, N501Y, G446S and D405N mutations. A total of 95 archived SARS-CoV-2 positive clinical specimens collected in Johannesburg, South Africa between February 2021 and March 2022 were assessed using these qPCR assays. To independently confirm SNP detection, Sanger sequencing of the relevant region in the S-gene were performed. Where a PCR product could be generated and sequenced, qPCR assays were 100% concordant highlighting the robustness of the approach. These assays, and the approach described, offer the opportunity for easy detection and scaling of targeted detection of variant-defining SNPs in the clinical setting.
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Affiliation(s)
| | | | | | - Bavesh D. Kana
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and The National Health Laboratory Service, Johannesburg, South Africa
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29
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Lanyon HE, Todd BP, Downard KM. Distinguishing common SARS-CoV2 omicron and recombinant variants with high resolution mass spectrometry. Analyst 2023; 148:6306-6314. [PMID: 37936487 DOI: 10.1039/d3an01376f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
A selected ion monitoring (SIM) approach combined with high resolution mass spectrometry is employed to identify and distinguish common SARS-CoV2 omicron and recombinant variants in clinical specimens. Mutations within the receptor binding domain (RBD) within the surface spike protein of the virus result in a combination of peptide segments of unique sequence and mass that were monitored to detect BA.2.75 (including CH.1.1) and XBB (including 1.5) variants prevalent in the state's population in early 2023. SIM detection of pairs of peptides unique to each variant were confidently detected and differentiated in 57.3% of the specimens, with a further 10 or 17.5% (for a total of 74.8%) detected based on a single peptide biomarker. The BA.2.75 sub-variant was detected in 18.7%, while recombinant variants XBB and XBB.1.5 were detected in 13.3% and 25.3% of the specimens respectively, consistent with circulating levels in the population characterised by RT-PCR. Virus was detected in 75 SARS-CoV2 positive specimens by mass spectrometry down to the low or mid 104 copy level, with a single false positive and no false negative identified. This article is the first paper to characterise recombinant strains of the SARS-CoV2 virus by this, or any other, MS method.
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Affiliation(s)
- Henry E Lanyon
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
| | - Benjamin P Todd
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
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30
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Suryawanshi RK, Taha TY, McCavitt-Malvido M, Silva I, Khalid MM, Syed AM, Chen IP, Saldhi P, Sreekumar B, Montano M, Foresythe K, Tabata T, Kumar GR, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Kojima N, Arellanor T, Bussanich A, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Wang Y, Ghazarian S, Davis G, Rodriguez D, Doudna J, Spraggon L, Chiu CY, Ott M. Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination. Emerg Microbes Infect 2023; 12:2270071. [PMID: 37869789 PMCID: PMC10619466 DOI: 10.1080/22221751.2023.2270071] [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: 05/10/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
The emergence of SARS-CoV-2 recombinants is of particular concern as they can result in a sudden increase in immune evasion due to antigenic shift. Recent recombinants XBB and XBB.1.5 have higher transmissibility than previous recombinants such as "Deltacron." We hypothesized that immunity to a SARS-CoV-2 recombinant depends on prior exposure to its parental strains. To test this hypothesis, we examined whether Delta or Omicron (BA.1 or BA.2) immunity conferred through infection, vaccination, or breakthrough infection could neutralize Deltacron and XBB/XBB.1.5 recombinants. We found that Delta, BA.1, or BA.2 breakthrough infections provided better immune protection against Deltacron and its parental strains than did the vaccine booster. None of the sera were effective at neutralizing the XBB lineage or its parent BA.2.75.2, except for the sera from the BA.2 breakthrough group. These results support our hypothesis. In turn, our findings underscore the importance of multivalent vaccines that correspond to the antigenic profile of circulating variants of concern and of variant-specific diagnostics that may guide public health and individual decisions in response to emerging SARS-CoV-2 recombinants.
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Affiliation(s)
| | | | | | | | | | - Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Irene P. Chen
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | - Kafaya Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | | | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Amelia Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jennifer Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | | | - Charles Y. Chiu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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31
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Zaman N, Parvaiz N, Gul F, Yousaf R, Gul K, Azam SS. Dynamics of water-mediated interaction effects on the stability and transmission of Omicron. Sci Rep 2023; 13:20894. [PMID: 38017052 PMCID: PMC10684572 DOI: 10.1038/s41598-023-48186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.
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Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Fouzia Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rimsha Yousaf
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Kainat Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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32
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Nakagawa S, Katayama T, Jin L, Wu J, Kryukov K, Oyachi R, Takeuchi JS, Fujisawa T, Asano S, Komatsu M, Onami JI, Abe T, Arita M. SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan. Genes Genet Syst 2023; 98:221-237. [PMID: 37839865 DOI: 10.1266/ggs.23-00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.
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Affiliation(s)
- So Nakagawa
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Molecular Life Science, Tokai University School of Medicine
- Micro/Nano Technology Center, Tokai University
- Institute of Medical Sciences, Tokai University
| | | | | | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Kirill Kryukov
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
| | - Rise Oyachi
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Junko S Takeuchi
- Center for Clinical Sciences, National Center for Global Health and Medicine
| | | | - Satomi Asano
- Department of Informatics, National Institute of Genetics
| | - Momoka Komatsu
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Jun-Ichi Onami
- Research Center for Open Science and Data Platform, National Institute of Informatics
| | - Takashi Abe
- Bioinformation and DDBJ Center, National Institute of Genetics
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
- RIKEN Center for Sustainable Resource Science
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Hu S, Luo D, Zhu Q, Pan J, Chen B, Furian M, Harkare HV, Sun S, Fansa A, Wu X, Yu B, Ma T, Wang F, Shi S. An updated meta-analysis of Chinese herbal medicine for the prevention of COVID-19 based on Western-Eastern medicine. Front Pharmacol 2023; 14:1257345. [PMID: 38044944 PMCID: PMC10693348 DOI: 10.3389/fphar.2023.1257345] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/13/2023] [Indexed: 12/05/2023] Open
Abstract
Background and aims: Chinese herbal medicine (CHM) was used to prevent and treat coronavirus disease 2019 (COVID-19) in clinical practices. Many studies have demonstrated that the combination of CHM and Western medicine can be more effective in treating COVID-19 compared to Western medicine alone. However, evidence-based studies on the prevention in undiagnosed or suspected cases remain scarce. This systematic review and meta-analysis aimed to investigate the effectiveness of CHM in preventing recurrent, new, or suspected COVID-19 diseases. Methods: We conducted a comprehensive search using ten databases including articles published between December 2019 and September 2023. This search aimed to identify studies investigating the use of CHM to prevent COVID-19. Heterogeneity was assessed by a random-effects model. The relative risk (RR) and mean differences were calculated using 95% confidence intervals (CI). The modified Jadad Scale and the Newcastle-Ottawa Scale (NOS) were employed to evaluate the quality of randomized controlled trials and cohort studies, respectively. Results: Seventeen studies with a total of 47,351 patients were included. Results revealed that CHM significantly reduced the incidence of COVID-19 (RR = 0.24, 95% CI = 0.11-0.53, p = 0.0004), influenza (RR = 0.37, 95% CI = 0.18-0.76, p = 0.007), and severe pneumonia exacerbation rate (RR = 0.17, 95% CI = 0.05-0.64, p = 0.009) compared to non-treatment or conventional control group. Evidence evaluation indicated moderate quality evidence for COVID-19 incidence and serum complement components C3 and C4 in randomized controlled trials. For the incidence of influenza and severe pneumonia in RCTs as well as the ratio of CD4+/CD8+ lymphocytes, the evidence quality was low. The remaining outcomes including the disappearance rate of symptoms and adverse reactions were deemed to be of very low quality. Conclusion: CHM presents a promising therapeutic option for the prevention of COVID-19. However, additional high-quality clinical trials are needed to further strengthen evidential integrity.
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Affiliation(s)
- Siying Hu
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dan Luo
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qikui Zhu
- Department of Biomedical Engineering and Computer and Data Science, Case Western Reserve University, Cleveland, OH, United States
| | - Jie Pan
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Bonan Chen
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Michael Furian
- Research Department, Swiss University of Traditional Chinese Medicine, Bad Zurzach, Switzerland
| | - Harsh Vivek Harkare
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Shoukai Sun
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Adel Fansa
- Charité Universitätsmedizin Berlin, Berlin, Germany
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Xiaoping Wu
- National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baili Yu
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tianhong Ma
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fei Wang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shihua Shi
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Balupuri A, Kim JM, Choi KE, No JS, Kim IH, Rhee JE, Kim EJ, Kang NS. Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants. Int J Mol Sci 2023; 24:16069. [PMID: 38003257 PMCID: PMC10671153 DOI: 10.3390/ijms242216069] [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: 10/04/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike (S) protein mutations pose serious threats to current coronavirus disease 2019 (COVID-19) therapies. A comprehensive understanding of the structural stability of SARS-CoV-2 variants is vital for the development of effective therapeutic strategies as it can offer valuable insights into their potential impact on viral infectivity. S protein mediates a virus' attachment to host cells by binding to angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD), and mutations in this protein can affect its stability and binding affinity. We analyzed S protein structural stability in various Omicron subvariants computationally. Notably, the S protein sequences analyzed in this work were obtained directly from our own sample collection. We evaluated the binding free energy between S protein and ACE2 in several complex forms. Additionally, we measured distances between the RBD of each chain in S protein to analyze conformational changes. Unlike most of the prior studies, we analyzed full-length S protein-ACE2 complexes instead of only RBD-ACE2 complexes. Omicron subvariants including BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, BA.2.75_K147E, BA.4.6 and BA.4.6_N658S showed enhanced stability compared to wild type, potentially due to distinct S protein mutations. Among them, BA.2.75 and BA.4.6_N658S exhibited the highest and lowest level of stability, respectively.
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Affiliation(s)
- Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
| | - Jeong-Min Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Kwang-Eun Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
| | - Jin Sun No
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Jee Eun Rhee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
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Kim D, Kim J, Kim M, Park H, Park S, Maharjan S, Baek K, Kang BM, Kim S, Park MS, Lee Y, Kwon HJ. Analysis of spike protein variants evolved in a novel in vivo long-term replication model for SARS-CoV-2. Front Cell Infect Microbiol 2023; 13:1280686. [PMID: 38029235 PMCID: PMC10655031 DOI: 10.3389/fcimb.2023.1280686] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The spectrum of SARS-CoV-2 mutations have increased over time, resulting in the emergence of several variants of concern. Persistent infection is assumed to be involved in the evolution of the variants. Calu-3 human lung cancer cells persistently grow without apoptosis and release low virus titers after infection. Methods We established a novel in vivo long-term replication model using xenografts of Calu-3 human lung cancer cells in immunodeficient mice. Virus replication in the tumor was monitored for 30 days and occurrence of mutations in the viral genome was determined by whole-genome deep sequencing. Viral isolates with mutations were selected after plaque forming assays and their properties were determined in cells and in K18-hACE2 mice. Results After infection with parental SARS-CoV-2, viruses were found in the tumor tissues for up to 30 days and acquired various mutations, predominantly in the spike (S) protein, some of which increased while others fluctuated for 30 days. Three viral isolates with different combination of mutations produced higher virus titers than the parental virus in Calu-3 cells without cytopathic effects. In K18-hACE2 mice, the variants were less lethal than the parental virus. Infection with each variant induced production of cross-reactive antibodies to the receptor binding domain of parental SARS-CoV-2 S protein and provided protective immunity against subsequent challenge with parental virus. Discussion These results suggest that most of the SARS-CoV-2 variants acquired mutations promoting host adaptation in the Calu-3 xenograft mice. This model can be used in the future to further study SARS-CoV-2 variants upon long-term replication in vivo.
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Affiliation(s)
- Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
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Oyola S. Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population. RESEARCH SQUARE 2023:rs.3.rs-3457875. [PMID: 37961584 PMCID: PMC10635312 DOI: 10.21203/rs.3.rs-3457875/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.
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Li Y, Mo J, Liu J, Liang Y, Deng C, Huang Z, Jiang J, Liu M, Liu X, Shang L, Wang X, Xie X, Wang J. A micro-electroporation/electrophoresis-based vaccine screening system reveals the impact of vaccination orders on cross-protective immunity. iScience 2023; 26:108086. [PMID: 37860767 PMCID: PMC10582514 DOI: 10.1016/j.isci.2023.108086] [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: 07/13/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
The constant emergence of mutated pathogens poses great challenges to the existing vaccine system. A screening system is needed to screen for antigen designs and vaccination strategies capable of inducing cross-protective immunity. Herein, we report a screening system based on DNA vaccines and a micro-electroporation/electrophoresis system (MEES), which greatly improved the efficacy of DNA vaccines, elevating humoral and cellular immune responses by over 400- and 35-fold respectively. Eighteen vaccination strategies were screened simultaneously by sequential immunization with vaccines derived from wildtype (WT) SARS-CoV-2, Delta, or Omicron BA.1 variant. Sequential vaccination of BA.1-WT-Delta vaccines with MEES induced potent neutralizing antibodies against all three viral strains and BA.5 variant, demonstrating that cross-protective immunity against future mutants can be successfully induced by existing strain-derived vaccines when a proper combination and order of sequential vaccination are used. Our screening system could be used for fast-seeking vaccination strategies for emerging pathogens in the future.
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Affiliation(s)
- Yongyong Li
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Jingshan Mo
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
- School of Electronic and Information Engineering, Guangdong Ocean University, Zhanjiang 524088, People’s Republic of China
| | - Jing Liu
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Ying Liang
- Department of Nephrology, GuangZhou Eighth People′s Hospital, GuangZhou Medical University, Guangzhou 510060, People’s Republic of China
| | - Caiguanxi Deng
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Zhangping Huang
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Juan Jiang
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Ming Liu
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Xinmin Liu
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Liru Shang
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Xiafeng Wang
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
| | - Xi Xie
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Ji Wang
- Division of Pulmonary and Critical Care Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, Peoples Republic of China
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Megha KB, Reshma S, Amir S, Krishnan MJA, Shimona A, Alka R, Mohanan PV. Comprehensive Risk Assessment of Infection Induced by SARS-CoV-2. Mol Neurobiol 2023:10.1007/s12035-023-03682-4. [PMID: 37817031 DOI: 10.1007/s12035-023-03682-4] [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: 06/19/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
The pandemic COVID-19 (coronavirus disease 2019) is caused by the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), which devastated the global economy and healthcare system. The infection caused an unforeseen rise in COVID-19 patients and increased the mortality rate globally. This study gives an overall idea about host-pathogen interaction, immune responses to COVID-19, recovery status of infection, targeted organs and complications associated, and comparison of post-infection immunity in convalescent subjects and non-infected individuals. The emergence of the variants and episodes of COVID-19 infections made the situation worsen. The timely introduction of vaccines and precautionary measures helped control the infection's severity. Later, the population that recovered from COVID-19 grew significantly. However, understanding the impact of healthcare issues resulting after infection is paramount for improving an individual's health status. It is now recognised that COVID-19 infection affects multiple organs and exhibits a broad range of clinical manifestations. So, post COVID-19 infection creates a high risk in individuals with already prevailing health complications. The identification of post-COVID-19-related health issues and their appropriate management is of greater importance to improving patient's quality of life. The persistence, sequelae and other medical complications that normally last from weeks to months after the recovery of the initial infection are involved with COVID-19. A multi-disciplinary approach is necessary for the development of preventive measures, techniques for rehabilitation and strategies for clinical management when it comes to long-term care.
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Affiliation(s)
- K B Megha
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India
| | - S Reshma
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India
| | - S Amir
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India
| | - M J Ajai Krishnan
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India
| | - A Shimona
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad, 201002, India
| | - Rao Alka
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad, 201002, India
| | - P V Mohanan
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India.
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Kosenko M, Onkhonova G, Susloparov I, Ryzhikov A. SARS-CoV-2 proteins structural studies using synchrotron radiation. Biophys Rev 2023; 15:1185-1194. [PMID: 37974992 PMCID: PMC10643813 DOI: 10.1007/s12551-023-01153-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of biological macromolecules has expanded. Significant progress in the development of structural biology methods has been largely achieved through the use of synchrotron radiation. Modern sources of synchrotron radiation allow to conduct high-performance structural studies with high temporal and spatial resolution. Thus, modern techniques make it possible to obtain not only static structures, but also to study dynamic processes, which play a key role in understanding biological mechanisms. One of the key directions in the development of structural research is the drug design based on the structures of biomolecules. Synchrotron radiation offers insights into the three-dimensional time-resolved structure of individual viral proteins and their complexes at atomic resolution. The rapid and accurate determination of protein structures is crucial for understanding viral pathogenicity and designing targeted therapeutics. Through the application of experimental techniques, including X-ray crystallography and small-angle X-ray scattering (SAXS), it is possible to elucidate the structural details of SARS-CoV-2 virion containing 4 structural, 16 nonstructural proteins (nsp), and several accessory proteins. The most studied potential targets for vaccines and drugs are the structural spike (S) protein, which is responsible for entering the host cell, as well as nonstructural proteins essential for replication and transcription, such as main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp). This article provides a brief overview of structural analysis techniques, with focus on synchrotron radiation-based methods applied to the analysis of SARS-CoV-2 proteins.
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Affiliation(s)
- Maksim Kosenko
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Galina Onkhonova
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Ivan Susloparov
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Alexander Ryzhikov
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
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Afrin SZ, Sathi FA, Nooruzzaman M, Parvin R. Molecular insights into the SARS-CoV-2 Omicron variant from Bangladesh suggest diverse and continuous evolution. Virology 2023; 587:109882. [PMID: 37757731 DOI: 10.1016/j.virol.2023.109882] [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: 05/27/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
The study analyzed the molecular dynamics of the circulating SARS-CoV-2 Omicron variant from its identification in November 2021 to January 2023. The SARS-CoV-2 sequences from Bangladesh revealed three distinct waves of the Omicron variant. More than 50 sub-lineages of Omicron variant were introduced into the country, with the majority belonging to the major lineages of BA.1-like (24.91%), BA.2-like (43.35%), BA.5-like (5.76%), XBB (10.47%), and "Others and Unassigned" (18.64%). Furthermore, the relative frequencies over time revealed that Omicron lineages existed for a short period of time before being replaced by other sub-lineages. Many potential mutations were found in the receptor binding domain of the Spike protein including G339D/H, S371 L/F, K417 N, T478K, E484A, Q493R, Q498R, and N501Y. In conclusion, the SARS-CoV-2 Omicron variant from Bangladesh showed diverse genetic features and continuous evolution. Therefore, the choice of vaccine and monitoring of hospitalized patients is important alongside genetic characterization of the circulating SARS-CoV-2.
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Affiliation(s)
| | - Fardousi Akter Sathi
- Department of Microbiology, Mymensingh Medical College, Mymensingh 2200, Bangladesh
| | - Mohammed Nooruzzaman
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Rokshana Parvin
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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Mikhailov M, Budde K, Halleck F, Eleftheriadis G, Naik MG, Schrezenmeier E, Bachmann F, Choi M, Duettmann W, von Hoerschelmann E, Koch N, Liefeldt L, Lücht C, Straub-Hohenbleicher H, Waiser J, Weber U, Zukunft B, Osmanodja B. COVID-19 Outcomes in Kidney Transplant Recipients in a German Transplant Center. J Clin Med 2023; 12:6103. [PMID: 37763043 PMCID: PMC10531713 DOI: 10.3390/jcm12186103] [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: 08/10/2023] [Revised: 09/02/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Kidney transplant recipients (KTRs) show higher morbidity and mortality from COVID-19 than the general population and have an impaired response to vaccination. We analyzed COVID-19 incidence and clinical outcomes in a single-center cohort of approximately 2500 KTRs. Between 1 February 2020 and 1 July 2022, 578 KTRs were infected with SARS-CoV-2, with 25 (4%) recurrent infections. In total, 208 KTRs (36%) were hospitalized, and 39 (7%) died. Among vaccinated patients, infection with the Omicron variant had a mortality of 2%. Unvaccinated patients infected with the Omicron variant showed mortality (9% vs. 11%) and morbidity (hospitalization 52% vs. 54%, ICU admission 12% vs. 18%) comparable to the pre-Omicron era. Multivariable analysis revealed that being unvaccinated (OR = 2.15, 95% CI [1.38, 3.35]), infection in the pre-Omicron era (OR = 3.06, 95% CI [1.92, 4.87]), and higher patient age (OR = 1.04, 95% CI [1.03, 1.06]) are independent risk factors for COVID-19 hospitalization, whereas a steroid-free immunosuppressive regimen was found to reduce the risk of COVID-19 hospitalization (OR = 0.51, 95% CI [0.33, 0.79]). This suggests that both virological changes in the Omicron variant and vaccination reduce the risk for morbidity and mortality from COVID-19 in KTRs. Our data extend the knowledge from the general population to KTRs and provide important insights into outcomes during the Omicron era.
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Affiliation(s)
- Michael Mikhailov
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
- Clinic for Anaesthesiology and Intensive Care Medicine, Charité–Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Klemens Budde
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Fabian Halleck
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Georgios Eleftheriadis
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Marcel G. Naik
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Eva Schrezenmeier
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Friederike Bachmann
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Mira Choi
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Wiebke Duettmann
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Ellen von Hoerschelmann
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Nadine Koch
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Lutz Liefeldt
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Christian Lücht
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Henriette Straub-Hohenbleicher
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Johannes Waiser
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Ulrike Weber
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Bianca Zukunft
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
| | - Bilgin Osmanodja
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (K.B.); (F.H.); (G.E.); (M.G.N.); (E.S.); (F.B.); (M.C.); (W.D.); (E.v.H.); (N.K.); (L.L.); (C.L.); (H.S.-H.); (J.W.); (U.W.); (B.Z.); (B.O.)
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Lim HGM, Fann YC, Lee YCG. COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2. Brief Bioinform 2023; 24:bbad280. [PMID: 37738400 PMCID: PMC10516370 DOI: 10.1093/bib/bbad280] [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: 12/30/2022] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 09/24/2023] Open
Abstract
Implementing a specific cloud resource to analyze extensive genomic data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a challenge when resources are limited. To overcome this, we repurposed a cloud platform initially designed for use in research on cancer genomics (https://cgc.sbgenomics.com) to enable its use in research on SARS-CoV-2 to build Cloud Workflow for Viral and Variant Identification (COWID). COWID is a workflow based on the Common Workflow Language that realizes the full potential of sequencing technology for use in reliable SARS-CoV-2 identification and leverages cloud computing to achieve efficient parallelization. COWID outperformed other contemporary methods for identification by offering scalable identification and reliable variant findings with no false-positive results. COWID typically processed each sample of raw sequencing data within 5 min at a cost of only US$0.01. The COWID source code is publicly available (https://github.com/hendrick0403/COWID) and can be accessed on any computer with Internet access. COWID is designed to be user-friendly; it can be implemented without prior programming knowledge. Therefore, COWID is a time-efficient tool that can be used during a pandemic.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
- Department of Medical Research, Tzu Chi Hospital Indonesia, Pantai Indah Kapuk, Greater Jakarta, Indonesia 14470
| | - Yang C Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
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Wang R, Huang H, Yu C, Sun C, Ma J, Kong D, Lin Y, Zhao D, Zhou S, Lu J, Cao S, Zhang Y, Luo C, Li X, Wang Y, Xie L. A spike-trimer protein-based tetravalent COVID-19 vaccine elicits enhanced breadth of neutralization against SARS-CoV-2 Omicron subvariants and other variants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1818-1830. [PMID: 36598621 PMCID: PMC9811042 DOI: 10.1007/s11427-022-2207-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/17/2022] [Indexed: 01/05/2023]
Abstract
Multivalent vaccines combining crucial mutations from phylogenetically divergent variants could be an effective approach to defend against existing and future SARS-CoV-2 variants. In this study, we developed a tetravalent COVID-19 vaccine SCTV01E, based on the trimeric Spike protein of SARS-CoV-2 variants Alpha, Beta, Delta, and Omicron BA.1, with a squalene-based oil-in-water adjuvant SCT-VA02B. In the immunogenicity studies in naïve BALB/c and C57BL/6J mice, SCTV01E exhibited the most favorable immunogenic characteristics to induce balanced and broad-spectrum neutralizing potencies against pre-Omicron variants (D614G, Alpha, Beta, and Delta) and newly emerging Omicron subvariants (BA.1, BA.1.1, BA.2, BA.3, and BA.4/5). Booster studies in C57BL/6J mice previously immunized with D614G monovalent vaccine demonstrated superior neutralizing capacities of SCTV01E against Omicron subvariants, compared with the D614G booster regimen. Furthermore, SCTV01E vaccination elicited naïve and central memory T cell responses to SARS-CoV-2 ancestral strain and Omicron spike peptides. Together, our comprehensive immunogenicity evaluation results indicate that SCTV01E could become an important COVID-19 vaccine platform to combat surging infections caused by the highly immune evasive BA.4/5 variants. SCTV01E is currently being studied in a head-to-head immunogenicity comparison phase 3 clinical study with inactivated and mRNA vaccines (NCT05323461).
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Affiliation(s)
- Rui Wang
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Hongpeng Huang
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Chulin Yu
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Chunyun Sun
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Juan Ma
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Desheng Kong
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Yalong Lin
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Dandan Zhao
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Shaozheng Zhou
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Jianbo Lu
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Sai Cao
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Yanjing Zhang
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Chunxia Luo
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Xuefeng Li
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Yang Wang
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China
| | - Liangzhi Xie
- Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing, 100176, China.
- Cell Culture Engineering Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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44
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Chernyaeva EN, Ayginin AA, Kosenkov AV, Romanova SV, Tsypkina AV, Luparev AR, Stetsenko IF, Gnusareva NI, Matsvay AD, Savochkina YA, Shipulin GA. SARS-CoV-2 Recombination and Coinfection Events Identified in Clinical Samples in Russia. Viruses 2023; 15:1660. [PMID: 37632003 PMCID: PMC10458065 DOI: 10.3390/v15081660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Recombination is one of the mechanisms of SARS-CoV-2 evolution along with the occurrence of point mutations, insertions, and deletions. Recently, recombinant variants of SARS-CoV-2 have been registered in different countries, and some of them have become circulating forms. In this work, we performed screening of SARS-CoV-2 genomic sequences to identify recombination events and co-infections with various strains of the SARS-CoV-2 virus detected in Russia from February 2020 to March 2022. The study included 9336 genomes of the COVID-19 pathogen obtained as a result of high-throughput sequencing on the Illumina platform. For data analysis, we used an algorithm developed by our group that can identify viral recombination variants and cases of co-infections by estimating the frequencies of characteristic substitutions in raw read alignment files and VCF files. The detected cases of recombination were confirmed by alternative sequencing methods, principal component analysis, and phylogenetic analysis. The suggested approach allowed for the identification of recombinant variants of strains BA.1 and BA.2, among which a new recombinant variant was identified, as well as a previously discovered one. The results obtained are the first evidence of the spread of recombinant variants of SARS-CoV-2 in Russia. In addition to cases of recombination we identified cases of coinfection: eight of them contained the genome of the Omicron line as one of the variants, six of them the genome of the Delta line, and two with the genome of the Alpha line.
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Fang L, Xu J, Zhao Y, Fan J, Shen J, Liu W, Cao G. The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2. Front Microbiol 2023; 14:1228128. [PMID: 37560529 PMCID: PMC10409611 DOI: 10.3389/fmicb.2023.1228128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.
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Affiliation(s)
- Letian Fang
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jie Xu
- Department of Foreign Languages, International Exchange Center for Military Medicine, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jiaying Shen
- School of Medicine, Tongji University, Shanghai, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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Szekely J, Swangphon P, Nanakorn N, Chaimuti P, Nualnoi T, Wongwitwichot P, Somapa N, Somapa D, Pengsakul T. Breakthrough SARS-CoV-2 Omicron Variant in Individuals Primed with Heterologous Vaccines Enhances Inhibition Performance of Neutralizing Antibody to BA.2 Parental Lineage. Vaccines (Basel) 2023; 11:1230. [PMID: 37515045 PMCID: PMC10383937 DOI: 10.3390/vaccines11071230] [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: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
This study aims to analyze the neutralization ability against Omicron parental variants in five clusters of individuals with different Coronavirus disease (COVID-19) immunity backgrounds, including individuals receiving a homologous or heterologous vaccine without prior infection, recovered patients with homologous or heterologous vaccination, and recovery patients without vaccination. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surrogate virus neutralization assay was performed on serum samples. Spearman correlation analysis showed that the percent inhibition against Omicron B.1.1.529 and BA.2 was significantly related to the period of serum collection (r = 0.730 and 0.787, p < 0.001, respectively). Very strong correlation between percent inhibition of neutralizing antibody against Omicron B.1.1.529 and BA.2 variants (rs = 0.973, p < 0.001) was also observed. The neutralizing activity of the sera from recovery patients receiving homologous and heterologous vaccine against the wild-type, B.1.1.529, and BA.2 Omicron variants was significantly higher (p < 0.001) than that of recovery patients without vaccination. This study robustly showed that the breakthrough SARS-CoV-2 Omicron variant in individuals who received homologous and heterologous vaccines had a high level of neutralizing activity against B.1.1.529 and BA.2 parental lineage of XBB subvariants. Therefore, the next-generation COVID-19 vaccine against emerging variants is needed to improve resilience against ongoing variants, particularly for persons who have never been infected.
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Affiliation(s)
- Jidapa Szekely
- Faculty of Medical Technology, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Piyawut Swangphon
- Faculty of Medical Technology, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Natthaphon Nanakorn
- Faculty of Medical Technology, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Panuttha Chaimuti
- Immunology and Virology Unit, Department of Medical Technology and Clinical Pathology, Hat Yai Hospital, Hat Yai 90110, Thailand
| | - Teerapat Nualnoi
- Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Paweena Wongwitwichot
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Namchoke Somapa
- Master Labs Incorporation Co., Ltd., Bangkok 10510, Thailand
| | - Denpong Somapa
- Master Labs Incorporation Co., Ltd., Bangkok 10510, Thailand
| | - Theerakamol Pengsakul
- Faculty of Environmental Management, Prince of Songkla University, Hat Yai 90110, Thailand
- Health and Environmental Research Center, Faculty of Environmental Management, Prince of Songkla University, Hat Yai 90110, Thailand
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Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023; 41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Universidade Federal do Triângulo Mineiro, Hospital de Clínicas, Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, PR China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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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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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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Escaffre O, Szaniszlo P, Törő G, Vilas CL, Servantes BJ, Lopez E, Juelich TL, Levine CB, McLellan SLF, Cardenas JC, Freiberg AN, Módis K. Hydrogen Sulfide Ameliorates SARS-CoV-2-Associated Lung Endothelial Barrier Disruption. Biomedicines 2023; 11:1790. [PMID: 37509430 PMCID: PMC10376201 DOI: 10.3390/biomedicines11071790] [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: 05/18/2023] [Revised: 06/14/2023] [Accepted: 06/17/2023] [Indexed: 07/30/2023] Open
Abstract
Recent studies have confirmed that lung microvascular endothelial injury plays a critical role in the pathophysiology of COVID-19. Our group and others have demonstrated the beneficial effects of H2S in several pathological processes and provided a rationale for considering the therapeutic implications of H2S in COVID-19 therapy. Here, we evaluated the effect of the slow-releasing H2S donor, GYY4137, on the barrier function of a lung endothelial cell monolayer in vitro, after challenging the cells with plasma samples from COVID-19 patients or inactivated SARS-CoV-2 virus. We also assessed how the cytokine/chemokine profile of patients' plasma, endothelial barrier permeability, and disease severity correlated with each other. Alterations in barrier permeability after treatments with patient plasma, inactivated virus, and GYY4137 were monitored and assessed by electrical impedance measurements in real time. We present evidence that GYY4137 treatment reduced endothelial barrier permeability after plasma challenge and completely reversed the endothelial barrier disruption caused by inactivated SARS-CoV-2 virus. We also showed that disease severity correlated with the cytokine/chemokine profile of the plasma but not with barrier permeability changes in our assay. Overall, these data demonstrate that treatment with H2S-releasing compounds has the potential to ameliorate SARS-CoV-2-associated lung endothelial barrier disruption.
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Affiliation(s)
- Olivier Escaffre
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections & Immunity, Sealy & Smith Foundation, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Peter Szaniszlo
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gabor Törő
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Caitlyn L. Vilas
- John Sealy School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Brenna J. Servantes
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ernesto Lopez
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Terry L. Juelich
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Corri B. Levine
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Susan L. F. McLellan
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jessica C. Cardenas
- The Center for Translational Injury Research, Department of Surgery, UTHealth McGovern Medical School, Houston, TX 77030, USA
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections & Immunity, Sealy & Smith Foundation, University of Texas Medical Branch, Galveston, TX 77555, USA
- The Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Katalin Módis
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
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