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Yin Q, Liu W, Jiang Y, Feng Q, Wang X, Dou H, Liu Z, He F, Fan Y, Jiao B, Jiao B. Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022. BMC Genomics 2024; 25:378. [PMID: 38632523 PMCID: PMC11022347 DOI: 10.1186/s12864-024-10246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. METHODS Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. RESULTS All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites. CONCLUSION SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.
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Affiliation(s)
- Qiang Yin
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Wei Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Yajuan Jiang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Qiang Feng
- Department of Laboratory, Rencheng Center for Disease Control and Prevention, Jining, China
| | - Xiaoyu Wang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Huixin Dou
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Zanzan Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Feifei He
- Computer Information Technology, Northern Arizona University, Arizona, USA
| | - Yingying Fan
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
| | - Baihai Jiao
- Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| | - Boyan Jiao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
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Li L, Liu T, Wang Q, Ding Y, Jiang Y, Wu Z, Wang X, Dou H, Jia Y, Jiao B. Genetic characterization and whole-genome sequencing-based genetic analysis of influenza virus in Jining City during 2021-2022. Front Microbiol 2023; 14:1196451. [PMID: 37426015 PMCID: PMC10324579 DOI: 10.3389/fmicb.2023.1196451] [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: 03/29/2023] [Accepted: 05/02/2023] [Indexed: 07/11/2023] Open
Abstract
Background The influenza virus poses a significant threat to global public health due to its high mutation rate. Continuous surveillance, development of new vaccines, and public health measures are crucial in managing and mitigating the impact of influenza outbreaks. Methods Nasal swabs were collected from individuals with influenza-like symptoms in Jining City during 2021-2022. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect influenza A viruses, followed by isolation using MDCK cells. Additionally, nucleic acid detection was performed to identify influenza A H1N1, seasonal H3N2, B/Victoria, and B/Yamagata strains. Whole-genome sequencing was conducted on 24 influenza virus strains, and subsequent analyses included characterization, phylogenetic construction, mutation analysis, and assessment of nucleotide diversity. Results A total of 1,543 throat swab samples were collected. The study revealed the dominance of the B/Victoria influenza virus in Jining during 2021-2022. Whole-genome sequencing showed co-prevalence of B/Victoria influenza viruses in the branches of Victoria clade 1A.3a.1 and Victoria clade 1A.3a.2, with a higher incidence observed in winter and spring. Comparative analysis demonstrated lower similarity in the HA, MP, and PB2 gene segments of the 24 sequenced influenza virus strains compared to the Northern Hemisphere vaccine strain B/Washington/02/2019. Mutations were identified in all antigenic epitopes of the HA protein at R133G, N150K, and N197D, and the 17-sequence antigenic epitopes exhibited more than 4 amino acid variation sites, resulting in antigenic drift. Moreover, one sequence had a D197N mutation in the NA protein, while seven sequences had a K338R mutation in the PA protein. Conclusion This study highlights the predominant presence of B/Victoria influenza strain in Jining from 2021 to 2022. The analysis also identified amino acid site variations in the antigenic epitopes, contributing to antigenic drift.
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Affiliation(s)
- Libo Li
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Tiantian Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Qingchuan Wang
- Department of Medicine, Jining Municipal Government Hospital, Jining, China
| | - Yi Ding
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Yajuan Jiang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Zengding Wu
- Department of AI and Bioinformatics, Nanjing Chengshi BioTech (TheraRNA) Co., Ltd., Nanjing, China
| | - Xiaoyu Wang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Huixin Dou
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Yongjian Jia
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Boyan Jiao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
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Qu L, Jiao B. The Interplay between Immune and Metabolic Pathways in Kidney Disease. Cells 2023; 12:1584. [PMID: 37371054 DOI: 10.3390/cells12121584] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Kidney disease is a significant health problem worldwide, affecting an estimated 10% of the global population. Kidney disease encompasses a diverse group of disorders that vary in their underlying pathophysiology, clinical presentation, and outcomes. These disorders include acute kidney injury (AKI), chronic kidney disease (CKD), glomerulonephritis, nephrotic syndrome, polycystic kidney disease, diabetic kidney disease, and many others. Despite their distinct etiologies, these disorders share a common feature of immune system dysregulation and metabolic disturbances. The immune system and metabolic pathways are intimately connected and interact to modulate the pathogenesis of kidney diseases. The dysregulation of immune responses in kidney diseases includes a complex interplay between various immune cell types, including resident and infiltrating immune cells, cytokines, chemokines, and complement factors. These immune factors can trigger and perpetuate kidney inflammation, causing renal tissue injury and progressive fibrosis. In addition, metabolic pathways play critical roles in the pathogenesis of kidney diseases, including glucose and lipid metabolism, oxidative stress, mitochondrial dysfunction, and altered nutrient sensing. Dysregulation of these metabolic pathways contributes to the progression of kidney disease by inducing renal tubular injury, apoptosis, and fibrosis. Recent studies have provided insights into the intricate interplay between immune and metabolic pathways in kidney diseases, revealing novel therapeutic targets for the prevention and treatment of kidney diseases. Potential therapeutic strategies include modulating immune responses through targeting key immune factors or inhibiting pro-inflammatory signaling pathways, improving mitochondrial function, and targeting nutrient-sensing pathways, such as mTOR, AMPK, and SIRT1. This review highlights the importance of the interplay between immune and metabolic pathways in kidney diseases and the potential therapeutic implications of targeting these pathways.
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Affiliation(s)
- Lili Qu
- Division of Nephrology, Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT 06030-1405, USA
| | - Baihai Jiao
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT 06030-1405, USA
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Yuan Y, Jiao B, Qu L, Yang D, Liu R. The development of COVID-19 treatment. Front Immunol 2023; 14:1125246. [PMID: 36776881 PMCID: PMC9909293 DOI: 10.3389/fimmu.2023.1125246] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic named coronavirus disease 2019 (COVID-19) that has become the greatest worldwide public health threat of this century. Recent studies have unraveled numerous mysteries of SARS-CoV-2 pathogenesis and thus largely improved the studies of COVID-19 vaccines and therapeutic strategies. However, important questions remain regarding its therapy. In this review, the recent research advances on COVID-19 mechanism are quickly summarized. We mainly discuss current therapy strategies for COVID-19, with an emphasis on antiviral agents, neutralizing antibody therapies, Janus kinase inhibitors, and steroids. When necessary, specific mechanisms and the history of therapy are present, and representative strategies are described in detail. Finally, we discuss key outstanding questions regarding future directions of the development of COVID-19 treatment.
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Affiliation(s)
- Yongliang Yuan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Baihai Jiao
- Division of Nephrology, Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Lili Qu
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Duomeng Yang
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States,*Correspondence: Ruijuan Liu, ; Duomeng Yang,
| | - Ruijuan Liu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China,*Correspondence: Ruijuan Liu, ; Duomeng Yang,
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Analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling in the activation of neural stem progenitor cells. NPJ Regen Med 2021; 6:68. [PMID: 34686684 PMCID: PMC8536777 DOI: 10.1038/s41536-021-00179-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
Xenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPCs). Here we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, aiming to identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC-specific ribosome biogenesis factors, and genes involved in stem cell proliferation. Western blot and immunofluorescence analysis showed that mTORC1 is rapidly and transiently activated after SCI, and its pharmacological inhibition impairs spinal cord regeneration and proliferation of NSPC through the downregulation of genes involved in the G1/S transition of cell cycle, with a strong effect on PCNA. We propose that the mTOR signaling pathway is a key player in the activation of NPSCs during the early steps of spinal cord regeneration.
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Cao Y, Fang T, Fan M, Wang L, Lv C, Jin P, Ma F. Functional characterization of STATa/b genes encoding transcription factors from Branchiostoma belcheri. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103838. [PMID: 32846160 DOI: 10.1016/j.dci.2020.103838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
The signal transducer and activator of transcription (STAT), as an important transcription factor of the Janus kinase (JAK)-STAT signaling pathway, is pivotal for development and immunity and well documented in vertebrates. However, the STAT gene has not been reported in chordate amphioxus (Branchiostoma belcheri). In this study, we firstly identify and characterize two STAT genes from Branchiostoma belcheri (designed as AmphiSTATa and AmphiSTATb). Secondly, our results reveal that AmphiSTATa is clustered with vertebrate STAT1, STAT2, STAT3 and STAT4, whereas AmphiSTATb is grouped with STAT5 and STAT6 based on phylogenetic analysis. Thirdly, AmphiSTATa and AmphiSTATb are found to widely express in five representative tissues of amphioxus (gill, hepatic cecum, intestine, muscle and notochord) by RT-qPCR analysis. Importantly, both AmphiSTATa and AmphiSTATb can be involved in innate immune responses to LPS stimulation. Fourthly, we demonstrate that AmphiSTATa and AmphiSTATb can form homodimers or heterodimers by Co-IP and Native-PAGE assay, and that AmphiSTATa and AmphiSTATb proteins can also distribute in cytoplasm and nucleus by the subcellular localization. Taken together, our findings not only reveal the roles of AmphiSTATa and AmphiSTATb in amphioxus innate immune responses to LPS stimulation, but provide a new insight into further elucidating the evolution and function of STATs in animals.
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Affiliation(s)
- Yunpeng Cao
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Tao Fang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Mingli Fan
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Lei Wang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Caiyun Lv
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
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Dagenais-Lussier X, Loucif H, Cadorel H, Blumberger J, Isnard S, Bego MG, Cohen ÉA, Routy JP, van Grevenynghe J. USP18 is a significant driver of memory CD4 T-cell reduced viability caused by type I IFN signaling during primary HIV-1 infection. PLoS Pathog 2019; 15:e1008060. [PMID: 31658294 PMCID: PMC6837632 DOI: 10.1371/journal.ppat.1008060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 11/07/2019] [Accepted: 08/31/2019] [Indexed: 02/07/2023] Open
Abstract
The loss of Memory CD4 T-cells (Mem) is a major hallmark of HIV-1 immuno-pathogenesis and occurs early during the first months of primary infection. A lot of effort has been put into understanding the molecular mechanisms behind this loss, yet they still have not been fully identified. In this study, we unveil the unreported role of USP18 in the deleterious effects of sustained type I IFN signaling on Mem, including HIV-1-specific CD4 T-cells. We find that interfering with IFN-I signaling pathway in infected patients, notably by targeting the interferon-stimulated gene USP18, resulted in reduced PTEN expression similar to those observed in uninfected control donors. We show that AKT activation in response to cytokine treatment, T-cell receptor (TcR) triggering, as well as HIV-1 Gag stimulation was significantly improved in infected patients when PTEN or USP18 were inhibited. Finally, our data demonstrate that higher USP18 in Mem from infected patients prevent proper cell survival and long-lasting maintenance in an AKT-dependent manner. Altogether, we establish a direct role for type I IFN/USP18 signaling in the maintenance of total and virus-specific Mem and provide a new mechanism for the reduced survival of these populations during primary HIV-1 infection. In this study, we expend our knowledge of how type I interferons (IFN-I) leads to memory CD4 T-cell defective survival by unveiling the molecular mechanism behind such impairments, placing USP18 at its center. Our data further deciphers the specific USP18-related mechanism that is responsible for such impairments by implicating AKT inhibition in a PTEN-dependent manner. Our findings also point to a potential use of neutralizing anti-interferon α/β receptor antibodies to rescue the defective memory CD4 T-cell survival during HIV-1 infection, even in HIV-1 specific CD4 T-cell. To conclude, our findings provide the characterization of the molecular pathway leading to disturbances caused by sustained IFN-I signaling which occurs early during primary HIV-1 infection, complementing current knowledge which placed sustained IFN-I signaling as detrimental to the host during this infection.
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Affiliation(s)
- Xavier Dagenais-Lussier
- Institut national de la recherche scientifique (INRS)-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, Canada
| | - Hamza Loucif
- Institut national de la recherche scientifique (INRS)-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, Canada
| | - Hugo Cadorel
- Institut national de la recherche scientifique (INRS)-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, Canada
| | - Juliette Blumberger
- Institut national de la recherche scientifique (INRS)-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, Canada
| | - Stéphane Isnard
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Glen site, Montréal, Québec, Canada
| | - Mariana Gé Bego
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Éric A. Cohen
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Glen site, Montréal, Québec, Canada
| | - Julien van Grevenynghe
- Institut national de la recherche scientifique (INRS)-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, Canada
- * E-mail:
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Liao X, Wang Y, Ye H, Li S, Chen L, Duan X. Role of interferon-stimulated genes in regulation of HCV infection and type I interferon anti-HCV activity. Future Virol 2018. [DOI: 10.2217/fvl-2017-0160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
HCV chronically infects over 71 million people worldwide and is one of the leading causes of advanced liver diseases. Type I interferons (IFN-α/β) play critical role in host antiviral innate immunity. IFN-α/β exerts its anti-HCV effects through the activation of the JAK/STAT signaling pathway leading to the induction of a few hundred interferon-stimulated genes (ISGs). The interplay between ISG and HCV infection remains partially understood. In this review, we summarized the role of ISGs in HCV infection and interferon anti-HCV activity.
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Affiliation(s)
- Xinzhong Liao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, 610052 Chengdu, PR China
| | - Yancui Wang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, 610052 Chengdu, PR China
| | - Haiyan Ye
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, 610052 Chengdu, PR China
| | - Shilin Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, 610052 Chengdu, PR China
| | - Limin Chen
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, 610052 Chengdu, PR China
| | - Xiaoqiong Duan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, 610052 Chengdu, PR China
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