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Hong JJ, Zhang RT, Ma CL, Hu QY. Pulmonary microbial spectrum in late-stage SARS-CoV-2 infection: a case series. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04897-6. [PMID: 39031269 DOI: 10.1007/s10096-024-04897-6] [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: 04/04/2024] [Accepted: 07/08/2024] [Indexed: 07/22/2024]
Abstract
Coronavirus disease 2019 (COVID-19), a kind of respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), primarily spreads through the respiratory tract from human to human. Its extensive and rapid spread has led to a global pandemic, causing great harm to human health and economic development all over the world. Current known evidence indicates that SARS-CoV-2 has evolved accumulating multiple mutations, with altered infectivity and viral replication capacity. A better understanding of the complications of COVID-19 and its relationship with underlying diseases is crucial for the prevention and treatment of SARS-CoV-2. This case series reviewed case data of our 4 recent patients with severe or critical COVID-19, including treatment plan, status of pulmonary infection and their microbiology workup with metagenomic next-generation sequencing with bronchoalveolar lavage fluid. This report shed light on the significance of rapid and accurate clinical diagnosis and treatment on COVID-19.
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Affiliation(s)
- Jin-Jing Hong
- School of Medicine, The First People's Hospital of Wenling (Taizhou University Affiliated Wenling Hospital), Taizhou University, 1139 Shifu Blvd, Jiaojiang District, Taizhou, Zhejiang, 318000, China
| | - Ren-Tao Zhang
- School of Medicine, The First People's Hospital of Wenling (Taizhou University Affiliated Wenling Hospital), Taizhou University, 1139 Shifu Blvd, Jiaojiang District, Taizhou, Zhejiang, 318000, China
| | - Chun-Lian Ma
- School of Medicine, The First People's Hospital of Wenling (Taizhou University Affiliated Wenling Hospital), Taizhou University, 1139 Shifu Blvd, Jiaojiang District, Taizhou, Zhejiang, 318000, China.
| | - Qiong-Ying Hu
- School of Medicine, The First People's Hospital of Wenling (Taizhou University Affiliated Wenling Hospital), Taizhou University, 1139 Shifu Blvd, Jiaojiang District, Taizhou, Zhejiang, 318000, China.
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2
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Sun R, Zhang X, Hou J, Jia W, Li P, Song C. Development and validation of nomogram for predicting the risk of transferring to the ICU for children with influenza. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04898-5. [PMID: 39002105 DOI: 10.1007/s10096-024-04898-5] [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: 05/16/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
OBJECTIVE Development of a nomogram model for predicting the magnitude of risk of transferring hospitalized children with influenza to the ICU. METHODS In a single-center retrospective study, 318 children with influenza who were hospitalized in our hospital from January 2018 to August 2023 were collected as study subjects. Children with influenza were randomly assigned to the training set and validation set in a ratio of 4:1. In the training set, risk factors were identified using univariate and multivariate logistic regression analyses, and a nomogram model was created on this basis. The validation set was used to evaluate the predictive power of the model. RESULTS Multifactorial logistic regression analysis revealed six independent risk factors for transfer to the ICU in hospitalized children with influenza, including elevated peripheral white blood cell counts, elevated large platelet ratios, reduced mean platelet width, reduced complement C3, elevated serum globulin levels, and reduced total immunoglobulin M levels. Using these six metrics as predictors to construct a nomogram graphical model, the C-index was 0.970 (95% Cl: 0.953-0.988). The areas under the curve for the training and validation sets were 0.966 (95%Cl 0.947-0.985) and 0.919 (95%Cl 0.851-0.986), respectively. CONCLUSION A nomogram for predicting the risk of transferring to the ICU for children with influenza was developed and validated, which demonstrates good calibration and clinical benefits.
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Affiliation(s)
- Ruiyang Sun
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450052, China
| | - Xue Zhang
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450052, China
| | - Jiapu Hou
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450052, China
| | - Wanyu Jia
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450052, China
| | - Peng Li
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450052, China
| | - Chunlan Song
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450052, China.
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3
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Liu Y, Wu D, Zhang K, Ren R, Liu Y, Zhang S, Zhang X, Cheng J, Chen L, Huang J. Detection technology and clinical applications of serum viral products of hepatitis B virus infection. Front Cell Infect Microbiol 2024; 14:1402001. [PMID: 39035352 PMCID: PMC11257880 DOI: 10.3389/fcimb.2024.1402001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/12/2024] [Indexed: 07/23/2024] Open
Abstract
Viral hepatitis, caused by its etiology, hepatitis virus, is a public health problem globally. Among all infections caused by hepatitis-associated viruses, hepatitis B virus (HBV) infection remains the most serious medical concern. HBV infection particularly affects people in East Asia and Africa, the Mediterranean region, and Eastern Europe, with a prevalence rate of > 2%. Currently, approximately 1 billion people worldwide are infected with HBV, and nearly 30% of them experience chronic infection. Chronic HBV infection can lead to chronic hepatitis B (CHB), liver cirrhosis, and hepatocellular carcinoma (HCC), resulting in the related death of approximately 1 million people annually. Although preventative vaccines and antiviral therapies are currently available, there is no cure for this infection. Clinical testing is not only the gateway for diagnosis of HBV infection, but also crucial for judging the timing of medication, evaluating the effect of antiviral therapy, and predicting the risk of relapse after drug withdrawal in the whole follow-up management of hepatitis B infected persons. With advances in detection technology, it is now possible to measure various viral components in the blood to assess the clinical status of HBV infection. Serum viral products of HBV infection, such as HBV DNA, HBV RNA, hepatitis B surface antigen, hepatitis B e-antigen, and hepatitis B core-related antigen, are non-invasive indicators that are critical for the rapid diagnosis and management of related diseases. Improving the sensitivity of monitoring of these products is essential, and the development of corresponding detection technologies is pivotal in achieving this goal. This review aims to offer valuable insights into CHB infection and references for its effective treatment. We provide a comprehensive and systematic overview of classical and novel methods for detecting HBV serum viral products and discusses their clinical applications, along with the latest research progress in this field.
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Affiliation(s)
- Ying Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Di Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Kui Zhang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Rongrong Ren
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Yuxuan Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuya Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xuanyu Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jilin Cheng
- Department of Gastroenterology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Liping Chen
- Department of Gastroenterology, Shanghai Geriatric Medical Center, Shanghai, China
| | - Jun Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
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4
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Ferreira Menoni SM, Leon LL, de Lima RG, Lutaif ACGDB, Prates LC, Palma LMP, Costa SCB, Belangero VMS, Bonon SHA. Characterization of Herpesviridae Family Members, BK Virus, and Adenovirus in Children and Adolescents with Nephrotic Syndrome. Viruses 2024; 16:1017. [PMID: 39066180 PMCID: PMC11281385 DOI: 10.3390/v16071017] [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: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 07/28/2024] Open
Abstract
Since the significance of viral infections in children and adolescents with nephrotic syndrome (NS) is yet to be defined, this study intended to estimate the occurrence, pattern, and outcomes of some DNA viral infections in children with NS. METHODS A prospective study was conducted to determine the genome identification of the viruses Epstein-Barr (EBV), human cytomegalovirus (HCMV), human herpesvirus 6 (HHV-6 type A and type B) and 7 (HHV-7), polyomavirus (BKV), and human adenovirus (HAdV) in plasma and urine samples of pediatric patients with NS. RESULTS A total of 35 patients aged 1 to 18 years with NS and under immunosuppressant drugs participated in the study. Plasma and urine samples were collected at regular intervals during a median follow-up of 266 days (range 133-595), and DNA was analyzed to detect the selected DNA viruses. Eleven patients (31.4%) had active virus infections, and patterns were classified as coinfection, recurrent, and consecutive. Of these, six patients (54.5%) presented viral coinfection, six (54.5%) viral recurrence, and seven patients (63.3%) had viral consecutive infection. Ten of the eleven patients with active infection had a proteinuria relapse (91%) and eight (72.7%) were hospitalized (p = 0.0022). Active HCMV infection was the most frequent infection and was observed in six patients (54.5%), three of the eleven patients (27.2%) had suspected HCMV disease in the gastrointestinal tract, and one had HHV-7 coinfection. The frequency of other infections was: 9% for HHV-6, 45.5% for BKV, 27.3% for HHV-7, 18.2% for EBV, and 18.2% for HAdV. CONCLUSION viral infections, especially HCMV, can be an important cause of morbidity and nephrotic syndrome relapse in children.
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Affiliation(s)
- Silvia Mendonça Ferreira Menoni
- Laboratory of Virology, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (S.M.F.M.); (L.L.L.); (R.G.d.L.); (S.C.B.C.)
| | - Lucas Lopes Leon
- Laboratory of Virology, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (S.M.F.M.); (L.L.L.); (R.G.d.L.); (S.C.B.C.)
| | - Rodrigo Gonçalves de Lima
- Laboratory of Virology, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (S.M.F.M.); (L.L.L.); (R.G.d.L.); (S.C.B.C.)
| | - Anna Cristina Gervásio de Brito Lutaif
- Integrated Nephrology Center Unit, Pediatric Nephrology, Department of Pediatrics, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (A.C.G.d.B.L.); (L.C.P.); (L.M.P.P.); (V.M.S.B.)
| | - Liliane Cury Prates
- Integrated Nephrology Center Unit, Pediatric Nephrology, Department of Pediatrics, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (A.C.G.d.B.L.); (L.C.P.); (L.M.P.P.); (V.M.S.B.)
| | - Lilian Monteiro Pereira Palma
- Integrated Nephrology Center Unit, Pediatric Nephrology, Department of Pediatrics, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (A.C.G.d.B.L.); (L.C.P.); (L.M.P.P.); (V.M.S.B.)
| | - Sandra Cecília Botelho Costa
- Laboratory of Virology, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (S.M.F.M.); (L.L.L.); (R.G.d.L.); (S.C.B.C.)
| | - Vera Maria Santoro Belangero
- Integrated Nephrology Center Unit, Pediatric Nephrology, Department of Pediatrics, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (A.C.G.d.B.L.); (L.C.P.); (L.M.P.P.); (V.M.S.B.)
| | - Sandra Helena Alves Bonon
- Laboratory of Virology, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-887, Brazil; (S.M.F.M.); (L.L.L.); (R.G.d.L.); (S.C.B.C.)
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Pastor F, Charles E, Belmudes L, Chabrolles H, Cescato M, Rivoire M, Burger T, Passot G, Durantel D, Lucifora J, Couté Y, Salvetti A. Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes. Front Microbiol 2024; 15:1415449. [PMID: 38841065 PMCID: PMC11150682 DOI: 10.3389/fmicb.2024.1415449] [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: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Phosphorylation is a major post-translation modification (PTM) of proteins which is finely tuned by the activity of several hundred kinases and phosphatases. It controls most if not all cellular pathways including anti-viral responses. Accordingly, viruses often induce important changes in the phosphorylation of host factors that can either promote or counteract viral replication. Among more than 500 kinases constituting the human kinome only few have been described as important for the hepatitis B virus (HBV) infectious cycle, and most of them intervene during early or late infectious steps by phosphorylating the viral Core (HBc) protein. In addition, little is known on the consequences of HBV infection on the activity of cellular kinases. The objective of this study was to investigate the global impact of HBV infection on the cellular phosphorylation landscape early after infection. For this, primary human hepatocytes (PHHs) were challenged or not with HBV, and a mass spectrometry (MS)-based quantitative phosphoproteomic analysis was conducted 2- and 7-days post-infection. The results indicated that while, as expected, HBV infection only minimally modified the cell proteome, significant changes were observed in the phosphorylation state of several host proteins at both time points. Gene enrichment and ontology analyses of up- and down-phosphorylated proteins revealed common and distinct signatures induced by infection. In particular, HBV infection resulted in up-phosphorylation of proteins involved in DNA damage signaling and repair, RNA metabolism, in particular splicing, and cytoplasmic cell-signaling. Down-phosphorylated proteins were mostly involved in cell signaling and communication. Validation studies carried out on selected up-phosphorylated proteins, revealed that HBV infection induced a DNA damage response characterized by the appearance of 53BP1 foci, the inactivation of which by siRNA increased cccDNA levels. In addition, among up-phosphorylated RNA binding proteins (RBPs), SRRM2, a major scaffold of nuclear speckles behaved as an antiviral factor. In accordance with these findings, kinase prediction analysis indicated that HBV infection upregulates the activity of major kinases involved in DNA repair. These results strongly suggest that HBV infection triggers an intrinsic anti-viral response involving DNA repair factors and RBPs that contribute to reduce HBV replication in cell culture models.
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Affiliation(s)
- Florentin Pastor
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Emilie Charles
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Lucid Belmudes
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Hélène Chabrolles
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Marion Cescato
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | | | - Thomas Burger
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Guillaume Passot
- Service de Chirurgie Générale et Oncologique, Hôpital Lyon Sud, Hospices Civils de Lyon Et CICLY, EA3738, Université Claude Bernard Lyon, Lyon, France
| | - David Durantel
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Julie Lucifora
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Anna Salvetti
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
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6
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Liu BM, Rakhmanina NY, Yang Z, Bukrinsky MI. Mpox (Monkeypox) Virus and Its Co-Infection with HIV, Sexually Transmitted Infections, or Bacterial Superinfections: Double Whammy or a New Prime Culprit? Viruses 2024; 16:784. [PMID: 38793665 PMCID: PMC11125633 DOI: 10.3390/v16050784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Epidemiologic studies have established that mpox (formerly known as monkeypox) outbreaks worldwide in 2022-2023, due to Clade IIb mpox virus (MPXV), disproportionately affected gay, bisexual, and other men who have sex with men. More than 35% and 40% of the mpox cases suffer from co-infection with HIV and sexually transmitted infections (STIs) (e.g., Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, and herpes simplex virus), respectively. Bacterial superinfection can also occur. Co-infection of MPXV and other infectious agents may enhance disease severity, deteriorate outcomes, elongate the recovery process, and potentially contribute to the morbidity and mortality of the ensuing diseases. However, the interplays between MPXV and HIV, bacteria, other STI pathogens and host cells are poorly studied. There are many open questions regarding the impact of co-infections with HIV, STIs, or bacterial superinfections on the diagnosis and treatment of MPXV infections, including clinical and laboratory-confirmed mpox diagnosis, suboptimal treatment effectiveness, and induction of antiviral drug resistance. In this review article, we will discuss the progress and knowledge gaps in MPXV biology, antiviral therapy, pathogenesis of human MPXV and its co-infection with HIV, STIs, or bacterial superinfections, and the impact of the co-infections on the diagnosis and treatment of mpox disease. This review not only sheds light on the MPXV infection and co-infection of other etiologies but also calls for more research on MPXV life cycles and the molecular mechanisms of pathogenesis of co-infection of MPXV and other infectious agents, as well as research and development of a novel multiplex molecular testing panel for the detection of MPXV and other STI co-infections.
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Affiliation(s)
- Benjamin M. Liu
- Division of Pathology and Laboratory Medicine, Children’s National Hospital, Washington, DC 20010, USA
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA;
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
- Department of Microbiology, Immunology & Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA;
- Children’s National Research Institute, Washington, DC 20012, USA
- The District of Columbia Center for AIDS Research, Washington, DC 20052, USA
| | - Natella Y. Rakhmanina
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA;
- The District of Columbia Center for AIDS Research, Washington, DC 20052, USA
- Division of Infectious Diseases, Children’s National Hospital, Washington, DC 20010, USA
- Elizabeth Glaser Pediatric AIDS Foundation, Washington, DC 20005, USA
| | - Zhilong Yang
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Michael I. Bukrinsky
- Department of Microbiology, Immunology & Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA;
- The District of Columbia Center for AIDS Research, Washington, DC 20052, USA
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7
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Liu BM, Li NL, Wang R, Li X, Li ZA, Marion TN, Li K. Key roles for phosphorylation and the Coiled-coil domain in TRIM56-mediated positive regulation of TLR3-TRIF-dependent innate immunity. J Biol Chem 2024; 300:107249. [PMID: 38556084 PMCID: PMC11067339 DOI: 10.1016/j.jbc.2024.107249] [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: 01/25/2024] [Revised: 02/28/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024] Open
Abstract
Tripartite-motif protein-56 (TRIM56) positively regulates the induction of type I interferon response via the TLR3 pathway by enhancing IRF3 activation and depends on its C-terminal residues 621-750 for interacting with the adaptor TRIF. However, the precise underlying mechanism and detailed TRIM56 determinants remain unclear. Herein, we show ectopic expression of murine TRIM56 also enhances TLR3-dependent interferon-β promoter activation, suggesting functional conservation. We found that endogenous TRIM56 and TRIF formed a complex early (0.5-2 h) after poly-I:C stimulation and that TRIM56 overexpression also promoted activation of NF-κB by poly-I:C but not that by TNF-α or IL-1β, consistent with a specific effect on TRIF prior to the bifurcation of NF-κB and IRF3. Using transient transfection and Tet-regulated cell lines expressing various TRIM56 mutants, we demonstrated the Coiled-coil domain and a segment spanning residues ∼434-610, but not the B-box or residues 355-433, were required for TRIM56 augmentation of TLR3 signaling. Moreover, alanine substitution at each putative phosphorylation site, Ser471, Ser475, and Ser710, abrogated TRIM56 function. Concordantly, mutants bearing Ser471Ala, Ser475Ala, or Ser710Ala, or lacking the Coiled-coil domain, all lost the capacity to enhance poly-I:C-induced establishment of an antiviral state. Furthermore, the Ser710Ala mutation disrupted the TRIM56-TRIF association. Using phospho-specific antibodies, we detected biphasic phosphorylation of TRIM56 at Ser471 and Ser475 following TLR3 stimulation, with the early phase occurring at ∼0.5 to 1 h, prior to IRF3 phosphorylation. Together, these data reveal novel molecular details critical for the TRIM56 augmentation of TLR3-dependent antiviral response and highlight important roles for TRIM56 scaffolding and phosphorylation.
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Affiliation(s)
- Benjamin M Liu
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA; Divisions of Pathology and Laboratory Medicine, Children's National Hospital, Washington, District of Columbia, USA; Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA; Department of Pathology, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA; Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA; Children's National Research Institute, Washington, District of Columbia, USA; The District of Columbia Center for AIDS Research, Washington, District of Columbia, USA
| | - Nan L Li
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Ruixue Wang
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Xiaofan Li
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Z Alex Li
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Tony N Marion
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Kui Li
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
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8
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Duchen D, Clipman SJ, Vergara C, Thio CL, Thomas DL, Duggal P, Wojcik GL. A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction. PLoS One 2024; 19:e0301069. [PMID: 38669259 PMCID: PMC11051683 DOI: 10.1371/journal.pone.0301069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/09/2024] [Indexed: 04/28/2024] Open
Abstract
Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Center for Biomedical Data Science, Yale School of Medicine, New Haven, CT, United States of America
| | - Steven J. Clipman
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Chloe L. Thio
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David L. Thomas
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
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9
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Gao Y, Wang M, Liu X. Noninvasive serum markers for predicting significant liver histopathology in HBeAg-negative chronic HBV-infected patients with normal alanine aminotransferase. Microbiol Spectr 2024; 12:e0394123. [PMID: 38426768 PMCID: PMC11325860 DOI: 10.1128/spectrum.03941-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/16/2023] [Indexed: 03/02/2024] Open
Abstract
This study is to explore the proportion of significant liver histopathology in hepatitis B e antigen (HBeAg)-negative chronic hepatitis B virus (HBV)-infected patients with normal alanine aminotransferase (ALT) and investigate noninvasive indicators for predicting significant liver histopathology. A total of 201 HBeAg-negative chronic HBV-infected patients with normal ALT who underwent liver biopsy were involved in this study. Significant liver histological changes were defined as necroinflammation grade ≥2 (G ≥ 2) and/or fibrosis stage ≥2 (S ≥ 2). The results showed that 42.3% (85/201) and 45.8% (92/201) of the HBeAg-negative patients with normal ALT have significant liver necroinflammation (G ≥ 2) and fibrosis (S ≥ 2), respectively. High normal ALT (>22 U/L), high level of serum HBV DNA (>3.42 log IU/mL), and low level of prealbumin (PA) (<170 mg/L) were independent predictors for significant liver necroinflammation, and the predictive value of the combined indicators was 0.750 (P < 0.001), while high normal ALT (>24 U/L) and high level of FIB-4 (>1.53) were independent predictors for significant liver fibrosis, and the predictive value of the combined indicators was 0.740 (P < 0.001). In conclusion, more than 40% of HBeAg-negative patients with normal ALT have significant liver histopathology and require immediate antiviral treatment. ALT, PA, HBV DNA, and FIB-4 can independently predict significant liver inflammation and fibrosis for HBeAg-negative patients with normal ALT. Lowering the treatment threshold of ALT may benefit the HBeAg-negative chronic HBV-infected patients. IMPORTANCE Hepatitis B e antigen (HBeAg)-negative chronic hepatitis B virus (HBV)-infected patients with normal alanine aminotransferase (ALT) were supposed to have a low risk of progression to cirrhosis or hepatocellular carcinoma, and it was recommended to regularly follow up or undergo liver biopsy to assess liver histopathology according to the major international guidelines. However, this study indicates that a considerable number of HBeAg-negative chronic HBV-infected patients with normal ALT have significant liver histopathology and require immediate antiviral treatment. Besides, several clinical commonly used noninvasive indicators were found that can be used to predict significant liver histopathology; thereby liver biopsy might be avoided for HBeAg-negative chronic HBV-infected patients with normal ALT.
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Affiliation(s)
- Yuhua Gao
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, Henan, China
| | - Mingyang Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, Henan, China
| | - Xia'nan Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, Henan, China
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10
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Quarton S, McGee K, Cumley N, Behruznia M, Jeff C, Belchamber K, Cox M, Thickett D, Scott A, Parekh D, McNally A, Sapey E. Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. PLoS One 2024; 19:e0298425. [PMID: 38551904 PMCID: PMC10980213 DOI: 10.1371/journal.pone.0298425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/24/2024] [Indexed: 04/01/2024] Open
Abstract
INTRODUCTION Infection causes a vast burden of disease, with significant mortality, morbidity and costs to health-care systems. However, identifying the pathogen causative infection can be challenging, resulting in high use of broad-spectrum antibiotics, much of which may be inappropriate. Novel metagenomic methods have potential to rapidly identify pathogens, however their clinical utility for many infections is currently unclear. Outcome from infection is also impacted by the effectiveness of immune responses, which can be impaired by age, co-morbidity and the infection itself. The aims of this study are twofold: To compare diversity of organisms identified and time-to-result using metagenomic methods versus traditional culture -based techniques, to explore the potential clinical role of metagenomic approaches to pathogen identification in a range of infections.To characterise the ex vivo function of immune cells from patients with acute infection, exploring host and pathogen-specific factors which may affect immune function and overall outcomes. METHODS This is a prospective observational study of patients with acute infection. Patients with symptoms suggestive of an acute infection will be recruited, and blood and bodily fluid relevant to the site of infection collected (for example, sputum and naso-oropharyngeal swabs for respiratory tract infections, or urine for a suspected urinary tract infection). Metagenomic analysis of samples will be compared to traditional microbiology, alongside the antimicrobials received. Blood and respiratory samples such as bronchoalveolar lavage will be used to isolate immune cells and interrogate immune cell function. Where possible, similar samples will be collected from matched participants without a suspected infection to determine the impact of infection on both microbiome and immune cell function.
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Affiliation(s)
- Samuel Quarton
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kirsty McGee
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nicola Cumley
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mahboobeh Behruznia
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Charlotte Jeff
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Kylie Belchamber
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Cox
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - David Thickett
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Aaron Scott
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dhruv Parekh
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alan McNally
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Elizabeth Sapey
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Director of PIONEER: Health Data Research UK (HDRUK) Health Data Research Hub for Acute Care, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- Patient Safety Research Collaborative, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
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11
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Tepjanta P, Fujiyama K, Misaki R, Kimkong I. The N-linked glycosylation modifications in the hepatitis B surface protein impact cellular autophagy, HBV replication, and HBV secretion. PLoS One 2024; 19:e0299403. [PMID: 38489292 PMCID: PMC10942060 DOI: 10.1371/journal.pone.0299403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
N-linked glycosylation is a pivotal post-translational modification that significantly influences various aspects of protein biology. Autophagy, a critical cellular process, is instrumental in cell survival and maintenance. The hepatitis B virus (HBV) has evolved mechanisms to manipulate this process to ensure its survival within host cells. Significantly, post-translational N-linked glycosylation in the large surface protein of HBV (LHBs) influences virion assembly, infectivity, and immune evasion. This study investigated the role of N-linked glycosylation of LHBs in autophagy, and its subsequent effects on HBV replication and secretion. LHBs plasmids were constructed by incorporating single-, double-, and triple-mutated N-linked glycosylation sites through amino acid substitutions at N4, N112, and N309. In comparison to the wild-type LHBs, N-glycan mutants, including N309Q, N4-309Q, N112-309Q, and N4-112-309Q, induced autophagy gene expression and led to autophagosome accumulation in hepatoma cells. Acridine orange staining of cells expressing LHBs mutations revealed impaired lysosomal acidification, suggesting potential blockage of autophagic flux at later stages. Furthermore, N-glycan mutants increased the mRNA expression of HBV surface antigen (HBsAg). Notably, N309Q significantly elevated HBx oncogene level. The LHBs mutants, particularly N309Q and N112-309Q, significantly enhanced HBV replication, whereas N309Q, N4-309Q, and N4-112-309Q markedly increased HBV progeny secretion. Remarkably, our findings demonstrated that autophagy is indispensable for the impact of N-linked glycosylation mutations in LHBs on HBV secretion, as evidenced by experiments with a 3-methyladenine (3-MA) inhibitor. Our study provides pioneering insights into the interplay between N-linked glycosylation mutations in LHBs, host autophagy, and the HBV life cycle. Additionally, we offer a new clue for further investigation into carcinogenesis of hepatocellular carcinoma (HCC). These findings underscore the potential of targeting either N-linked glycosylation modifications or the autophagic pathway for the development of innovative therapies against HBV and/or HCC.
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Affiliation(s)
- Patcharin Tepjanta
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Kazuhito Fujiyama
- International Center for Biotechnology (ICBiotech), Osaka University, Osaka, Japan
| | - Ryo Misaki
- International Center for Biotechnology (ICBiotech), Osaka University, Osaka, Japan
| | - Ingorn Kimkong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University – Kasetsart University, Bangkok, Thailand
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12
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Li Y, Lv S, Zeng Y, Chen Z, Xia F, Zhang H, Dan D, Hu C, Tang Y, Yang Q, Ji Y, Lu J, Wang Z. Evaluation of Stability, Inactivation, and Disinfection Effectiveness of Mpox Virus. Viruses 2024; 16:104. [PMID: 38257804 PMCID: PMC10820592 DOI: 10.3390/v16010104] [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: 12/02/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Mpox virus (MPXV) infections have increased in many countries since May 2022, increasing demand for diagnostic tests and research on the virus. To ensure personnel safety, appropriate and reliable measures are needed to disinfect and inactivate infectious samples; Methods: We evaluated the stability of infectious MPXV cultures stored at different temperatures and through freeze-thaw cycles. Heat physical treatment (56 °C, 70 °C, 95 °C), chemical treatment (beta-propiolactone (BPL)) and two commercialized disinfectants (Micro-Chem Plus (MCP) and ethanol) were tested against infectious MPXV cultures; Results: The results indicated that MPXV stability increases with lower temperatures. The MPXV titer was stable within three freeze-thaw cycles and only decreased by 1.04 log10 (lg) 50% cell culture infective dose (CCID50) per milliliter (12.44%) after twelve cycles. MPXV could be effectively inactivated at 56 °C for 40 min, 70 °C for 10 min, and 95 °C for 5 min. For BPL inactivation, a 1:1000 volume ratio (BPL:virus) could also effectively inactivate MPXV. A total of 2% or 5% MCP and 75% ethanol treated with MPXV for at least 1 min could reduce >4.25 lg; Conclusions: MPXV shows high stability to temperature and freeze-thaw. Heat and BPL treatments are effective for the inactivation of MPXV, while MCP and ethanol are effective for disinfection, which could help laboratory staff operate the MPXV under safer conditions and improve operational protocols.
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Affiliation(s)
- Yuwei Li
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Shiyun Lv
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Yan Zeng
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Zhuo Chen
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Fei Xia
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Hao Zhang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Demiao Dan
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Chunxia Hu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Yi Tang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Qiao Yang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
| | - Yaqi Ji
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
| | - Jia Lu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
| | - Zejun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430200, China; (Y.L.); (S.L.); (Y.Z.); (Z.C.); (F.X.); (H.Z.); (D.D.); (C.H.); (Y.T.); (Q.Y.); (Y.J.)
- State Key Laboratory for Novel Vaccines Research and Development of Emerging Infectious Diseases, Wuhan 430200, China
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13
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Duchen D, Clipman S, Vergara C, Thio CL, Thomas DL, Duggal P, Wojcik GL. A hepatitis B virus (HBV) sequence variation graph improves sequence alignment and sample-specific consensus sequence construction for genetic analysis of HBV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523611. [PMID: 36711598 PMCID: PMC9882026 DOI: 10.1101/2023.01.11.523611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Hepatitis B virus (HBV) remains a global public health concern, with over 250 million individuals living with chronic HBV infection (CHB) and no curative therapy currently available. Viral diversity is associated with CHB pathogenesis and immunological control of infection. Improved methods to characterize the viral genome at both the population and intra-host level could aid drug development efforts. Conventionally, HBV sequencing data are aligned to a linear reference genome and only sequences capable of aligning to the reference are captured for analysis. Reference selection has additional consequences, including sample-specific 'consensus' sequence construction. It remains unclear how to select a reference from available sequences and whether a single reference is sufficient for genetic analyses. Using simulated short-read sequencing data generated from full-length publicly available HBV genome sequences and HBV sequencing data from a longitudinally sampled individual with CHB, we investigate alternative graph-based alignment approaches. We demonstrate that using a phylogenetically representative 'genome graph' for alignment, rather than linear reference sequences, avoids issues of reference ambiguity, improves alignment, and facilitates the construction of sample-specific consensus sequences genetically similar to an individual's infection. Graph-based methods can therefore improve efforts to characterize the genetics of viral pathogens, including HBV, and may have broad implications in host pathogen research.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Steven Clipman
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Chloe L Thio
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - David L Thomas
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
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14
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Liu B, Totten M, Nematollahi S, Datta K, Memon W, Marimuthu S, Wolf LA, Carroll KC, Zhang SX. Development and Evaluation of a Fully Automated Molecular Assay Targeting the Mitochondrial Small Subunit rRNA Gene for the Detection of Pneumocystis jirovecii in Bronchoalveolar Lavage Fluid Specimens. J Mol Diagn 2020; 22:1482-1493. [PMID: 33069878 DOI: 10.1016/j.jmoldx.2020.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/10/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
The fungal pathogen Pneumocystis jirovecii causes Pneumocystis pneumonia. Although the mitochondrial large subunit rRNA gene (mtLSU) is commonly used as a PCR target, a mitochondrial small subunit rRNA gene (mtSSU)-targeted MultiCode PCR assay was developed on the fully automated ARIES platform for detection of P. jirovecii in bronchoalveolar lavage fluid specimens in 2.5 hours. The assay showed a limit of detection of 800 copies/mL (approximately equal to 22 organisms/mL), with no cross-reactivity with other respiratory pathogens. Compared with the reference Pneumocystis-specific direct fluorescent antibody assay (DFA) and mtLSU-targeted PCR assay, the new assay demonstrated sensitivity of 96.9% (31/32) and specificity of 94.6% (139/147) in detecting P. jirovecii in 180 clinical bronchoalveolar lavage fluid specimens. This assay was concordant with all DFA-positive samples and all but one mtLSU PCR-positive sample, and detected eight positive samples that were negative by DFA and mtLSU PCR. Receiver operating characteristic curve analysis revealed an area under the curve of 0.98 and a threshold cycle (CT) cutoff of 39.1 with sensitivity of 90.9% and specificity of 99.3%. The detection of 39.1 <CT < 40.0 indicates the presence of a low load of the organism and needs further determination of either colonization or probable/possible Pneumocystis pneumonia. Overall, the new assay demonstrates excellent analytical and clinical performance and may be more sensitive than mtLSU PCR target for the detection of P. jirovecii.
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Affiliation(s)
- Baoming Liu
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marissa Totten
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Saman Nematollahi
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kausik Datta
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Warda Memon
- Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland
| | - Subathra Marimuthu
- Division of Infectious Diseases, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Leslie A Wolf
- Division of Infectious Diseases, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland
| | - Sean X Zhang
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland.
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15
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Ren CC, Chen QY, Wang XY, Harrison TJ, Yang QL, Hu LP, Liu HB, He X, Jia HH, Fang ZL. Novel subgenotype D11 of hepatitis B virus in NaPo County, Guangxi, bordering Vietnam. J Gen Virol 2019; 100:828-837. [PMID: 30990399 DOI: 10.1099/jgv.0.001257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus has been classified into 10 genotypes and 48 subgenotypes worldwide. We found previously, through polymerase chain reaction (PCR) amplification of a sample collected in 2011, that an HBsAg carrier was infected with two genotypes (B and D) of HBV. We carried out cloning, sequencing and phylogenetic analysis of the complete genomes and, for confirmation, analysed a sample collected from the same individual in 2018. Fifteen complete sequences were obtained from each sample. The carrier was infected in 2011 by genotypes B and D and by various recombinants, but only genotype D was present in 2018. The major and minor parents of the recombinants are genotypes B and D, respectively, although the recombination breakpoints vary among them. All 23 genotype D isolates form a cluster, branching out from other subgenotype D sequences and supported by a 100 % bootstrap value. Based on complete genome sequences, almost all of the estimated intragroup nucleotide divergence values between our isolates and HBV subgenotypes D1-D10 exceed 4 %. Compared to the other subgenotypes (D1-D10), 35 unique amino acids were present in our isolates. Our data provide evidence for a novel subgenotype, provisionally designated HBV subgenotype D11.
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Affiliation(s)
- Chuang-Chuang Ren
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China.,2School of Preclinical Medicine, Guangxi Medical University, UCL Medical School, 22 ShuangYong Road Nanning, Guangxi 530021, PR China
| | - Qin-Yan Chen
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
| | - Xue-Yan Wang
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
| | | | - Qing-Li Yang
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
| | - Li-Ping Hu
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
| | - Hua-Bing Liu
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China.,2School of Preclinical Medicine, Guangxi Medical University, UCL Medical School, 22 ShuangYong Road Nanning, Guangxi 530021, PR China
| | - Xiang He
- 4Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, PR China
| | - Hui-Hua Jia
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China.,2School of Preclinical Medicine, Guangxi Medical University, UCL Medical School, 22 ShuangYong Road Nanning, Guangxi 530021, PR China
| | - Zhong-Liao Fang
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
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16
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Choi YM, Lee SY, Kim BJ. Naturally occurring hepatitis B virus reverse transcriptase mutations related to potential antiviral drug resistance and liver disease progression. World J Gastroenterol 2018; 24:1708-1724. [PMID: 29713126 PMCID: PMC5922991 DOI: 10.3748/wjg.v24.i16.1708] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/10/2018] [Accepted: 04/15/2018] [Indexed: 02/06/2023] Open
Abstract
The annual number of deaths caused by hepatitis B virus (HBV)-related disease, including cirrhosis and hepatocellular carcinoma (HCC), is estimated as 887000. The reported prevalence of HBV reverse transcriptase (RT) mutation prior to treatment is varied and the impact of preexisting mutations on the treatment of naïve patients remains controversial, and primarily depends on geographic factors, HBV genotypes, HBeAg serostatus, HBV viral loads, disease progression, intergenotypic recombination and co-infection with HIV. Different sensitivity of detection methodology used could also affect their prevalence results. Several genotype-dependent HBV RT positions that can affect the emergence of drug resistance have also been reported. Eight mutations in RT (rtL80I, rtD134N, rtN139K/T/H, rtY141F, rtM204I/V, rtF221Y, rtI224V, and rtM309K) are significantly associated with HCC progression. HBeAg-negative status, low viral load, and genotype C infection are significantly related to a higher frequency and prevalence of preexisting RT mutations. Preexisting mutations are most frequently found in the A-B interdomain of RT which overlaps with the HBsAg “a” determinant region, mutations of which can lead to simultaneous viral immune escape. In conclusion, the presence of baseline RT mutations can affect drug treatment outcomes and disease progression in HBV-infected populations via modulation of viral fitness and host-immune responses.
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Affiliation(s)
- Yu-Min Choi
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
| | - So-Young Lee
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
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Characterization of Serum HBV RNA in Patients with Untreated HBeAg-Positive and -Negative Chronic Hepatitis B Infection. HEPATITIS MONTHLY 2018. [DOI: 10.5812/hepatmon.62079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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