1
|
Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
Collapse
Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| |
Collapse
|
2
|
Tl VL, Am CV, I GJ, Mj GG, Cm DM, A GL, G MG, S RR, P ML, A MM. Rubella virus-associated cutaneous granulomatous disease in an immunocompetent woman. Eur J Clin Microbiol Infect Dis 2024; 43:1255-1257. [PMID: 38647845 DOI: 10.1007/s10096-024-04828-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Affiliation(s)
- Vega-López Tl
- Department of Dermatology, University Hospital of Valladolid, Valladolid, Spain.
| | | | - González-Jiménez I
- Department of Dermatology, University Hospital of Valladolid, Valladolid, Spain
| | - García-Gamero Mj
- Department of Dermatology, University Hospital of Valladolid, Valladolid, Spain
| | | | - González-López A
- Department of Dermatology, University Hospital of Valladolid, Valladolid, Spain
| | - Martínez-García G
- Department of Pathology, University Hospital of Valladolid, Valladolid, Spain
| | - Rojo-Rello S
- Department of Microbiology, University Hospital of Valladolid, Valladolid, Spain
| | - Manchado-López P
- Department of Dermatology, University Hospital of Valladolid, Valladolid, Spain
| | - Mateos-Mayo A
- Department of Dermatology, University Hospital of Valladolid, Valladolid, Spain
| |
Collapse
|
3
|
Wang Q, Su H, Han J, Yang J, Lin N. Case report: Rubella virus-associated cutaneous granuloma in an adult with TAP1 deficiency. Front Immunol 2024; 15:1366840. [PMID: 38680488 PMCID: PMC11045939 DOI: 10.3389/fimmu.2024.1366840] [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: 01/11/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024] Open
Abstract
Rubella virus-associated granulomas commonly occur in immunocompromised individuals, exhibiting a diverse range of clinical presentations. These manifestations can vary from predominantly superficial cutaneous plaques or nonulcerative nodules to more severe deep ulcerative lesions, often accompanied by extensive necrosis and significant tissue destruction. TAP1 deficiency, an exceedingly rare primary immune-deficiency disorder, presents with severe chronic sino-pulmonary infection and cutaneous granulomas. This report highlights the occurrence of rubella virus-associated cutaneous granulomas in patients with TAP1 deficiency. Notably, the pathogenic mutation responsible for TAP1 deficiency stems from a novel genetic alteration that has not been previously reported. This novel observation holds potential significance for the field of diagnosis and investigative efforts in the context of immunodeficiency disorders.
Collapse
Affiliation(s)
- Qiaohui Wang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huilin Su
- Department of Dermatology and Venereology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiande Han
- Department of Dermatology and Venereology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Juhua Yang
- Vision Medicals Co., Ltd., Guangzhou, Guangdong, China
| | - Naiyu Lin
- Department of Dermatology and Venereology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
4
|
Kilich G, Perelygina L, Sullivan KE. Rubella virus chronic inflammatory disease and other unusual viral phenotypes in inborn errors of immunity. Immunol Rev 2024; 322:113-137. [PMID: 38009321 DOI: 10.1111/imr.13290] [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: 11/28/2023]
Abstract
Infectious susceptibility is a component of many inborn errors of immunity. Nevertheless, antibiotic use is often used as a surrogate in history taking for infectious susceptibility, thereby disadvantaging patients who present with viral infections as their phenotype. Further complicating clinical evaluations are unusual manifestations of viral infections which may be less familiar that the typical respiratory viral infections. This review covers several unusual viral phenotypes arising in patients with inborn errors of immunity and other settings of immune compromise. In some cases, chronic infections lead to oncogenesis or tumor-like growths and the conditions and mechanisms of viral-induced oncogenesis will be described. This review covers enterovirus, rubella, measles, papillomavirus, and parvovirus B19. It does not cover EBV and hemophagocytic lymphohistiocytosis nor lymphomagenesis related to EBV. EBV susceptibility has been recently reviewed. Our goal is to increase awareness of the unusual manifestations of viral infections in patients with IEI and to describe treatment modalities utilized in this setting. Coincidentally, each of the discussed viral infections can have a cutaneous component and figures will serve as a reminder of the physical features of these viruses. Given the high morbidity and mortality, early recognition can only improve outcomes.
Collapse
Affiliation(s)
- Gonench Kilich
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | |
Collapse
|
5
|
Zhang D, Wanat KA, Perelygina L, Rosenbach M, Haun PL, Drolet BA, Shields BE. Cutaneous granulomas associated with rubella virus: A clinical review. J Am Acad Dermatol 2024; 90:111-121. [PMID: 37271455 DOI: 10.1016/j.jaad.2023.05.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
Since the initial identification of vaccine-derived rubella virus (RuV) in the cutaneous granulomas of pediatric patients with inborn errors of immunity in 2014, more than 80 cases of RuV granulomas have been reported implicating both vaccine-derived and wild type RuV. Previously thought to arise exclusively in patients with significant immunocompromise, the identification of RuV granulomas in clinically immunocompetent patients adds nuance to our understanding of the interplay between host environment, immune dysregulation, and RuV granuloma formation. This review summarizes the literature on RuV granulomas including clinical and histopathologic features, proposed pathomechanisms supporting granuloma development, and potential therapeutic options. There is no standardized algorithm to guide the workup and diagnosis of suspected RuV granulomas. We highlight the importance of contributing RuV granuloma cases to ongoing Centers for Disease Control and Prevention surveillance efforts to monitor wild type and vaccine-derived RuV transmission. Studies advancing our understanding of RuV granulomas may provide insights into the role of viral infectious agents in granulomatous disease pathogenesis and guide the development of improved therapeutic options.
Collapse
Affiliation(s)
- Donglin Zhang
- Department of Dermatology, University of Wisconsin School of Medicine, Madison, Wisconsin
| | - Karolyn A Wanat
- Department of Dermatology and Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Misha Rosenbach
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Paul L Haun
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Beth A Drolet
- Department of Dermatology, University of Wisconsin School of Medicine, Madison, Wisconsin
| | - Bridget E Shields
- Department of Dermatology, University of Wisconsin School of Medicine, Madison, Wisconsin.
| |
Collapse
|
6
|
Patel S, Russo P, M HR, Maurer K, Hao L, Beard RS, Perelygina L, Sullivan KE. Surveillance for rubella virus in samples obtained from non-immunodeficient individuals. Pediatr Allergy Immunol 2024; 35:e14082. [PMID: 38284923 DOI: 10.1111/pai.14082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Affiliation(s)
- Srushti Patel
- Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Pierre Russo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Harris Rebecca M
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly Maurer
- Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - LiJuan Hao
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rachell Suzanne Beard
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kathleen E Sullivan
- Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| |
Collapse
|
7
|
Wang X, Han Y, Li C, Wang M, Yang B, Zhang X, Zhao L. Seroepidemiology study of rubella virus antibodies among neonates and pregnant women at hospitals in Henan province, China. J Med Virol 2023; 95:e29340. [PMID: 38131155 DOI: 10.1002/jmv.29340] [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: 08/07/2023] [Revised: 11/13/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Rubella virus infection can cause vertical transmission to the fetus during pregnancy. In China's Henan province, rubella surveillance needs to be well-established. In this research, a total of 1933 neonates and 2502 pregnant women were enrolled, and their sera for IgG and IgM antibodies against rubella were tested by chemiluminescence assay. Of 1933 neonates' sera tested, the seropositive of rubella IgG was 68.7%. The seroprevalence of rubella IgM in neonates was 0.4%. 30.9% of neonates had negative results for IgG and IgM antibodies. Two thousand five hundred and two pregnant women participated in the serosurvey, and 79.3% were rubella IgG positive. Rubella IgG seropositivity in pregnant women differed by age and number of births. 0.8% of the pregnant women had positive results for IgM against the rubella virus. The seronegative of rubella IgG and IgM antibodies in pregnant women was 19.8%. Due to the negative rubella-specific IgG antibody, many neonates remain at risk of rubella virus infection. Rubella virus continues to spread since some neonates and pregnant women with rubella-specific IgM antibody positive have been detected. Rubella vaccination may be introduced for childbearing-age women to increase immunity levels against rubella with periodic sero-surveillance.
Collapse
Affiliation(s)
- Xiangpeng Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Yu Han
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Changhui Li
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Mengshi Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Beibei Yang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Xiaoqin Zhang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Lijun Zhao
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| |
Collapse
|
8
|
Hönemann M, Scharfenberg E, Dietze N, Claus C, Jochmann C, Liebert UG. Rubella virus-associated uveitis at a tertiary care hospital in Germany between 2013 and 2019. BMC Ophthalmol 2023; 23:447. [PMID: 37932668 PMCID: PMC10629089 DOI: 10.1186/s12886-023-03182-y] [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: 07/23/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
Uveitis is a process of intraocular inflammation that may involve different sections of the uveal tract. Apart from systemic or localized immune-mediated diseases, infections are key players in the etiology of uveitis and entail different treatment strategies. Rubella virus (RuV) is a recognized causative agent for the development of Fuchs uveitis, representing a major cause of virus-associated intraocular inflammation. A cohort of 159 patients diagnosed with different forms of uveitis between 2013 and 2019 was subjected to diagnostic antibody testing of the aqueous or vitreous humor. The diagnostic panel included RuV, cytomegalovirus, herpes simplex virus, varicella-zoster virus, and toxoplasmosis. Within this cohort, 38 RuV-associated uveitis (RAU) patients were identified based on a pathologic Goldman-Witmer coefficient indicative of an underlying RuV infection. With a mean age of 45.9 years, the RAU patients were younger than the non-RAU patients (56.3, p < 0.001). The evaluation of clinical parameters revealed a predominance of anterior uveitis and late sequalae such as cataract and glaucoma among the RAU patients. In 15 of the patients a history of prior RuV infections could be confirmed. The study underlines the importance of long-term surveillance of RuV associated diseases that originate from infections before the introduction of RuV vaccination programs.
Collapse
Affiliation(s)
- Mario Hönemann
- Institute of Medical Microbiology and Virology, Leipzig University, Johannisallee 30, 04103, Leipzig, Germany.
| | - Elizabeth Scharfenberg
- Department of Ophthalmology, University Hospital Leipzig, Leipzig University, Liebigstrasse 21, 04103, Leipzig, Germany
| | - Nadine Dietze
- Institute of Medical Microbiology and Virology, Leipzig University, Johannisallee 30, 04103, Leipzig, Germany
| | - Claudia Claus
- Institute of Medical Microbiology and Virology, Leipzig University, Johannisallee 30, 04103, Leipzig, Germany
| | - Claudia Jochmann
- Department of Ophthalmology, University Hospital Leipzig, Leipzig University, Liebigstrasse 21, 04103, Leipzig, Germany
| | - Uwe Gerd Liebert
- Institute of Medical Microbiology and Virology, Leipzig University, Johannisallee 30, 04103, Leipzig, Germany
| |
Collapse
|
9
|
Pimentel MA, Kim DH, Walker LW, Noelck MB, Perelygina L, Kripps KA, Cartwright VW, Funk T, Green S, Kuo A, Ng J, Ophaug SL, Passo R, Redd T, Small A. Rubella virus-associated necrotizing granulomatous inflammation with extensive eyelid, ocular, and orbital involvement. Pediatr Dermatol 2023; 40:1107-1111. [PMID: 37202834 DOI: 10.1111/pde.15337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 04/15/2023] [Indexed: 05/20/2023]
Abstract
We present a case of cutaneous granulomatous disease associated with rubella virus in a 4-year-old girl without an identifiable immunodeficiency. In this case, a combination of anti-inflammatory, anti-viral, and anti-neutrophil therapies successfully treated vision-threatening eyelid, conjunctival, scleral, and orbital inflammation.
Collapse
Affiliation(s)
- Matthew A Pimentel
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon, USA
| | - Donna H Kim
- Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, USA
| | - Lorne W Walker
- Division of Pediatric Infectious Diseases, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Michelle B Noelck
- Department of Pediatrics, Oregon Health and Science University, Portland, Oregon, USA
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kimberly A Kripps
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
| | - Victoria W Cartwright
- Department of Pediatrics, Division of Rheumatology, Randall Children's Hospital at Legacy Emanuel, Portland, Oregon, USA
| | - Tracy Funk
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon, USA
| | - Sarah Green
- Department of Pediatrics, Pediatric Hospital Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Annie Kuo
- Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, USA
| | - John Ng
- Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, USA
| | - Solveig L Ophaug
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon, USA
| | - Ross Passo
- Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, USA
| | - Travis Redd
- Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, USA
| | - Alison Small
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon, USA
| |
Collapse
|
10
|
Li X, Zhang Y, Wang J, Han J, Shen T. Long-term dynamic shifts in genomic base content and evolutionary trajectories of SARS-CoV-2 variants. J Med Virol 2023; 95:e29128. [PMID: 37772482 DOI: 10.1002/jmv.29128] [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: 05/16/2023] [Revised: 08/30/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023]
Abstract
The rapid spread and remarkable mutations of SARS-CoV-2 variants, particularly Omicron, necessitate an understanding of their evolutionary characteristics. In this study, we analyzed representative high-quality whole-genome sequences of 2008 SARS-CoV-2 variants to explore long-term dynamic changes in genomic base (especially GC) content and variations during viral evolution. Our results demonstrated a highly negative correlation between GC content and variant emergence time (r = -0.765, p < 2.22e-16). Major gene partitions (S, N, ORF1ab) displayed similar trends. Omicron exhibited a significantly lower GC content than non-Omicron variants (p < 2.22e-16). Notably, we observed a robust negative correlation between C and T content (r = -0.778, p < 2.22e-16) and between G and A content (r = -0.773, p < 2.22e-16). Among all strains, Omicron showed the greatest base variation, with C->T mutations being the most frequent (median [interquartile range [IQR]]: 29 (27, 31), 37.67%), succeeded by G->A mutations (11 (9, 13), 14.63%). Over a 3-year span, an annual decline rate of 0.12% in SARS-CoV-2 GC content was observed and could become more pronounced in future emerging variants. These findings provided insights into the evolutionary trajectory of SARS-CoV-2, underscoring the significance of continuous genomic surveillance for effective prediction of and response to future variants.
Collapse
Affiliation(s)
- Xinjie Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuqi Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Jie Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Tao Shen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University, Beijing, China
| |
Collapse
|
11
|
Dittmar M, Whig K, Miller J, Kamalia B, Suppiah S, Perelygina L, Sullivan KE, Schultz DC, Cherry S. Nucleoside analogs NM107 and AT-527 are antiviral against rubella virus. PNAS NEXUS 2023; 2:pgad256. [PMID: 37674858 PMCID: PMC10479830 DOI: 10.1093/pnasnexus/pgad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/21/2023] [Indexed: 09/08/2023]
Abstract
Rubella is a highly contagious viral infection that usually causes a mild disease in children and adults. However, infection during pregnancy can result in a fetal or newborn death or congenital rubella syndrome (CRS), a constellation of permanent birth defects including cataracts, heart defects, and sensorineural deafness. The live-attenuated rubella vaccine has been highly effective, with the Americas declared free of endemic rubella transmission in 2015. However, rubella remains a significant problem worldwide and the leading cause of vaccine-preventable birth defects globally. Thus, elimination of rubella and CRS is a goal of the World Health Organization. No specific therapeutics are approved for the rubella virus. Therefore, we set out to identify whether existing small molecules may be repurposed for use against rubella virus infection. Thus, we performed a high-throughput screen for small molecules active against rubella virus in human respiratory cells and identified two nucleoside analogs, NM107 and AT-527, with potent antiviral activity. Furthermore, we found that combining these nucleoside analogs with inhibitors of host nucleoside biosynthesis had synergistic antiviral activity. These studies open the door to new potential approaches to treat rubella infections.
Collapse
Affiliation(s)
- Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
| | - Kanupriya Whig
- Department of Biochemistry and Biophysics, University of Pennsylvania, 3620 Hamilton Walk Philadelphia, PA 19104, USA
| | - Jesse Miller
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
| | - Brinda Kamalia
- Department of Biochemistry and Biophysics, University of Pennsylvania, 3620 Hamilton Walk Philadelphia, PA 19104, USA
| | - Suganthi Suppiah
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. Atlanta, GA 30329, USA
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. Atlanta, GA 30329, USA
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, 3615 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, 3620 Hamilton Walk Philadelphia, PA 19104, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, 3620 Hamilton Walk Philadelphia, PA 19104, USA
| |
Collapse
|
12
|
Dudley JP. APOBECs: Our fickle friends? PLoS Pathog 2023; 19:e1011364. [PMID: 37200235 DOI: 10.1371/journal.ppat.1011364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Jaquelin P Dudley
- Department of Molecular Biosciences and LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
| |
Collapse
|
13
|
Yonkof JR, Basu A, Redmond MT, Dobbs AK, Perelygina L, Notarangelo LD, Abraham RS, Rangarajan HG. Refractory, fatal autoimmune hemolytic anemia due to ineffective thymic-derived T-cell reconstitution following allogeneic hematopoietic cell transplantation for hypomorphic RAG1 deficiency. Pediatr Blood Cancer 2023; 70:e30183. [PMID: 36583469 PMCID: PMC10038854 DOI: 10.1002/pbc.30183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/31/2022]
Affiliation(s)
- Jennifer R Yonkof
- Department of Pediatrics, Division of Allergy & Immunology, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Amrita Basu
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Margaret T Redmond
- Department of Pediatrics, Division of Allergy & Immunology, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Adam Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland, USA
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland, USA
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Hemalatha G Rangarajan
- Department of Pediatrics, Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, Ohio, USA
| |
Collapse
|
14
|
Keeler EL, Vukmirovic M, Yan X, Gulino K, Ghedin E, Kaminski N, Sullivan KE, Bushman FD, Collman RG, Rosenbach M. Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus. SARCOIDOSIS, VASCULITIS, AND DIFFUSE LUNG DISEASES : OFFICIAL JOURNAL OF WASOG 2022; 39:e2022040. [PMID: 36533601 PMCID: PMC9798337 DOI: 10.36141/svdld.v39i4.13407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/16/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Sarcoidosis is a multisystem granulomatous inflammatory disease of unclear etiology that involves the lung, skin and other organs, with an unknown antigenic trigger. Recently, evidence has been found in both immune deficient and immune competent patients for rubella virus in cutaneous granulomas. These granulomatous lesions share overlapping features with cutaneous sarcoidosis, raising the question of rubella virus in sarcoidosis. OBJECTIVE To investigate the presence of rubella virus in sarcoidosis lung samples. METHODS We employed metagenomic sequencing to interrogate extracellular virome preparations and cellular transcriptomes from bronchoalveolar lavage (BAL) of 209 sarcoidosis patients for rubella virus sequences. RESULTS We found no evidence for rubella virus genomes in acellular fluid or rubella virus gene expression in BAL cells of sarcoidosis patients. CONCLUSIONS These findings argue against rubella virus infection or persistence within the lung at time of sampling as a sarcoidosis trigger.
Collapse
Affiliation(s)
- Emma L Keeler
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
| | - Milica Vukmirovic
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Xiting Yan
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Kristin Gulino
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA and Laboratory of Parasitic Diseases, NIAID, NIH, Washington, DC, USA.
| | - Naftali Kaminski
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Kathleen E Sullivan
- Department of Pediatrics, University of Pennsylvania School of Medicine, and Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
| | - Ronald G Collman
- Departments of Medicine and Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
| | - Misha Rosenbach
- Department of Dermatology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
15
|
Bonner KE, Sukerman E, Liko J, Lanzieri TM, Sutton M, DeBess E, Leesman C, Icenogle J, Hao L, Chen MH, Faisthalab R, Leman RF, Cieslak PR, DeRavin SS, Perelygina L. Case report: Persistent shedding of a live vaccine-derived rubella virus in a young man with severe combined immunodeficiency and cutaneous granuloma. Front Immunol 2022; 13:1075351. [PMID: 36569925 PMCID: PMC9773200 DOI: 10.3389/fimmu.2022.1075351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
A young man with X-linked severe combined immunodeficiency developed a persistent vaccine-derived rubella virus (VDRV) infection, with the emergence of cutaneous granulomas more than fifteen years after receipt of two doses of measles-mumps-rubella (MMR) vaccine. Following nasopharyngeal swab (NP) collection, VDRV was detected by real-time polymerase chain reaction (RT-qPCR) and sequencing, and live, replication-competent VDRV was isolated in cell culture. To assess duration and intensity of viral shedding, sequential respiratory samples, one cerebrospinal fluid sample, and two urine samples were collected over 15 months, and VDRV RNA was detected in all samples by RT-qPCR. Live VDRV was cultured from nine of the eleven respiratory specimens and from one urine specimen. To our knowledge, this was the first reported instance of VDRV cultured from respiratory specimens or from urine. To assess potential transmission to close contacts, NP specimens and sera were collected from all household contacts, all of whom were immunocompetent and previously vaccinated with MMR. VDRV RNA was not detected in any NP swabs from the contacts, nor did serologic investigations suggest VDRV transmission to any contacts. This report highlights the need to understand the prevalence and duration of VDRV shedding in granuloma patients and to estimate the risk of VDRV transmission to immune and non-immune contacts.
Collapse
Affiliation(s)
- Kimberly E. Bonner
- Oregon Health Authority, Public Health Division, Portland, OR, United States,Epidemic Intelligence Service, Center for Surveillance, Epidemiology and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Ellie Sukerman
- Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, United States
| | - Juventila Liko
- Oregon Health Authority, Public Health Division, Portland, OR, United States
| | - Tatiana M. Lanzieri
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Melissa Sutton
- Oregon Health Authority, Public Health Division, Portland, OR, United States
| | - Emilio DeBess
- Oregon Health Authority, Public Health Division, Portland, OR, United States
| | - Christopher Leesman
- Corvallis Family Medicine, Corvallis, OR, United States,Transformative Health and Wellness, Corvallis, OR, United States
| | - Joseph Icenogle
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - LiJuan Hao
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Min-hsin Chen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Raeesa Faisthalab
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Richard F. Leman
- Oregon Health Authority, Public Health Division, Portland, OR, United States
| | - Paul R. Cieslak
- Oregon Health Authority, Public Health Division, Portland, OR, United States
| | - Suk See DeRavin
- Laboratory of Clinical Immunology and Microbiology, The National Institute of Allergy and Infectious Diseases (NIAID), The National Institutes of Health (NIH), Bethesda, MD, United States
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States,*Correspondence: Ludmila Perelygina,
| |
Collapse
|
16
|
Kim K, Calabrese P, Wang S, Qin C, Rao Y, Feng P, Chen XS. The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness. Sci Rep 2022; 12:14972. [PMID: 36100631 PMCID: PMC9470679 DOI: 10.1038/s41598-022-19067-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022] Open
Abstract
During COVID-19 pandemic, mutations of SARS-CoV-2 produce new strains that can be more infectious or evade vaccines. Viral RNA mutations can arise from misincorporation by RNA-polymerases and modification by host factors. Analysis of SARS-CoV-2 sequence from patients showed a strong bias toward C-to-U mutation, suggesting a potential mutational role by host APOBEC cytosine deaminases that possess broad anti-viral activity. We report the first experimental evidence demonstrating that APOBEC3A, APOBEC1, and APOBEC3G can edit on specific sites of SARS-CoV-2 RNA to produce C-to-U mutations. However, SARS-CoV-2 replication and viral progeny production in Caco-2 cells are not inhibited by the expression of these APOBECs. Instead, expression of wild-type APOBEC3 greatly promotes viral replication/propagation, suggesting that SARS-CoV-2 utilizes the APOBEC-mediated mutations for fitness and evolution. Unlike the random mutations, this study suggests the predictability of all possible viral genome mutations by these APOBECs based on the UC/AC motifs and the viral genomic RNA structure.
Collapse
Affiliation(s)
- Kyumin Kim
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peter Calabrese
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shanshan Wang
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chao Qin
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Youliang Rao
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA.
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.
| |
Collapse
|
17
|
Chen MH, Abernathy E, Icenogle JP, Perelygina LM. Improved diagnostic and multiplex RT-qPCR for detecting rubella viral RNA. J Virol Methods 2022; 306:114555. [PMID: 35654258 DOI: 10.1016/j.jviromet.2022.114555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022]
Abstract
An examination of the nucleic acid sequence alignment of 48 full-length rubella virus genomes revealed that the 5' terminus of the genome is more conserved than the commonly used detection windows for rubella virus RNA located in the E1 protein coding region, suggesting that the 5' terminus could be a target for improving detection of all rubella virus genotypes. Two candidate primer sets were tested and the window between nucleotides (nts) 98 and 251 was found to have the greatest analytical sensitivity for detection of different genotypes. The new method had a limit of detection of four copies of rubella RNA per reaction with high specificity. The average coefficient variation of Ct was 2.2%. Concordance between the new method and currently used method, based on testing 251 clinical specimens collected from a rubella outbreak, was 99.4%. The assay was further improved upon by the incorporation of detection of both rubella virus RNA and mRNA from a cellular reference gene in a multiplex format. The multiplex format did not reduce the sensitivity or the reproducibility of rubella RNA detection and, of 60 specimens tested, the concordance between the single target and multiplex assays was 85.0%. To assess the utility of the multiplex assay for molecular surveillance, 62 rubella IgM positive serum samples from a rubella outbreak were tested, and eleven tested positive using the multiplex method while none were positive using the method targeting E1. These results show that the assay based on the new detection window near the 5' terminus of the genome can improve the detection of rubella virus for the purpose of molecular surveillance and case confirmation, with the added benefit of improved efficiency due to multiplexing.
Collapse
Affiliation(s)
- Min-Hsin Chen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Emily Abernathy
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Joseph P Icenogle
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Ludmila M Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| |
Collapse
|
18
|
Ludowyke N, Phumiphanjarphak W, Apiwattanakul N, Manopwisedjaroen S, Pakakasama S, Sensorn I, Pasomsub E, Chantratita W, Hongeng S, Aiewsakun P, Thitithanyanont A. Target Enrichment Metagenomics Reveals Human Pegivirus-1 in Pediatric Hematopoietic Stem Cell Transplantation Recipients. Viruses 2022; 14:v14040796. [PMID: 35458526 PMCID: PMC9025367 DOI: 10.3390/v14040796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Human pegivirus-1 (HPgV-1) is a lymphotropic human virus, typically considered nonpathogenic, but its infection can sometimes cause persistent viremia both in immunocompetent and immunosuppressed individuals. In a viral discovery research program in hematopoietic stem cell transplant (HSCT) pediatric patients, HPgV-1 was detected in 3 out of 14 patients (21.4%) using a target enrichment next-generation sequencing method, and the presence of the viruses was confirmed by agent-specific qRT-PCR assays. For the first time in this patient cohort, complete genomes of HPgV-1 were acquired and characterized. Phylogenetic analyses indicated that two patients had HPgV-1 genotype 2 and one had HPgV-1 genotype 3. Intra-host genomic variations were described and discussed. Our results highlight the necessity to screen HSCT patients and blood and stem cell donors to reduce the potential risk of HPgV-1 transmission.
Collapse
Affiliation(s)
- Natali Ludowyke
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Nopporn Apiwattanakul
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Suwimon Manopwisedjaroen
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
| | - Samart Pakakasama
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Insee Sensorn
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (I.S.); (W.C.)
| | - Ekawat Pasomsub
- Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (I.S.); (W.C.)
| | - Suradej Hongeng
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (P.A.); (A.T.); Tel.: +66-22015676 (P.A.); +66-22015528 (A.T.)
| | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (P.A.); (A.T.); Tel.: +66-22015676 (P.A.); +66-22015528 (A.T.)
| |
Collapse
|
19
|
Notarangelo LD. Rubella Virus-Associated Granulomas in Immunocompetent Adults-Possible Implications. JAMA Dermatol 2022; 158:611-613. [PMID: 35338703 DOI: 10.1001/jamadermatol.2022.0055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
20
|
Wanat KA, Perelygina L, Chen MH, Hao L, Abernathy E, Bender NR, Shields BE, Wilson BD, Crosby D, Routes J, Samimi SS, Haun PL, Sokumbi O, Icenogle JP, Sullivan KE, Rosenbach M, Drolet BA. Association of Persistent Rubella Virus With Idiopathic Skin Granulomas in Clinically Immunocompetent Adults. JAMA Dermatol 2022; 158:626-633. [PMID: 35338705 DOI: 10.1001/jamadermatol.2022.0828] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Importance Vaccine-derived and wild-type rubella virus (RuV) has been identified within granulomas in patients with inborn errors of immunity, but has not been described in granulomas of healthy adults. Objective To determine the association between RuV and atypical granulomatous inflammation in immune-competent adults. Design, Setting, and Participants This case series, conducted in US academic dermatology clinics from January 2019 to January 2021, investigated the presence of RuV in skin specimens using RuV immunofluorescent staining of paraffin-embedded tissue sections, real-time reverse-transcription polymerase chain reaction, whole-genome sequencing with phylogenetic analyses, and cell culture by the US Centers for Disease Control and Prevention. Rubella immunoglobulin G, immunoglobulin M enzyme-linked immunoassay, and viral neutralization assays were performed for the sera of immunocompetent individuals with treatment refractory cutaneous granulomas and histopathology demonstrating atypical palisaded and necrotizing granulomas. Clinical immune evaluation was performed. Main Outcomes and Measures Identification, genotyping, and culture of vaccine-derived and wild-type RuV within granulomatous dermatitis of otherwise clinically immune competent adults. Results Of the 4 total immunocompetent participants, 3 (75%) were women, and the mean (range) age was 61.5 (49.0-73.0) years. The RuV capsid protein was detected by immunohistochemistry in cutaneous granulomas. The presence of RuV RNA was confirmed by real-time reverse-transcription polymerase chain reaction in fresh-frozen skin biopsies and whole-genome sequencing. Phylogenetic analysis of the RuV sequences showed vaccine-derived RuV in 3 cases and wild-type RuV in 1. Live RuV was recovered from the affected skin in 2 participants. Immunology workup results demonstrated no primary immune deficiencies. Conclusions and Relevance The case series study results suggest that RuV (vaccine derived and wild type) can persist for years in cutaneous granulomas in clinically immunocompetent adults and is associated with atypical (palisaded and necrotizing type) chronic cutaneous granulomas. These findings represent a potential paradigm shift in the evaluation, workup, and management of atypical granulomatous dermatitis and raises questions regarding the potential transmissibility of persistent live RuV.
Collapse
Affiliation(s)
| | | | - Min-Hsin Chen
- US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - LiJuan Hao
- US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Emily Abernathy
- US Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Bridget E Shields
- University of Wisconsin, Madison.,Assistant Section Editor, JAMA Dermatology
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Drug Sensitivity of Vaccine-Derived Rubella Viruses and Quasispecies Evolution in Granulomatous Lesions of Two Ataxia-Telangiectasia Patients Treated with Nitazoxanide. Pathogens 2022; 11:pathogens11030338. [PMID: 35335662 PMCID: PMC8955873 DOI: 10.3390/pathogens11030338] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 01/25/2023] Open
Abstract
A strong association between rubella virus (RuV) and chronic granulomas, in individuals with inborn errors of immunity, has been recently established. Both the RA27/3 vaccine and wild-type RuV strains were highly sensitive to a broad-spectrum antiviral drug, nitazoxanide (NTZ), in vitro. However, NTZ treatment, used as a salvage therapy, resulted in little or no improvements of RuV-associated cutaneous granulomas in patients. Here, we report investigations of possible causes of treatment failures in two ataxia-telangiectasia patients. Although a reduction in RuV RNA in skin lesions was detected by real-time RT-PCR, live immunodeficiency-related vaccine-derived rubella viruses (iVDRV) were recovered from granulomas, before and after the treatments. Tizoxanide, an active NTZ metabolite, inhibited replications of all iVDRVs in cultured A549 cells, but the 50% and 90% inhibitory concentrations were 10–40 times higher than those for the RA27/3 strain. There were no substantial differences in iVDRV sensitivities, neither before nor after treatments. Analysis of quasispecies in the E1 gene, a suspected NTZ target, showed no effect of NTZ treatments on quasispecies’ complexity in lesions. Thus, failures of NTZ therapies were likely due to low sensitivities of iVDRVs to the drug, and not related to the emergence of resistance, following long-term NTZ treatments.
Collapse
|
22
|
Perelygina L, Faisthalab R, Abernathy E, Chen MH, Hao L, Bercovitch L, Bayer DK, Noroski LM, Lam MT, Cicalese MP, Al-Herz W, Nanda A, Hajjar J, Vanden Driessche K, Schroven S, Leysen J, Rosenbach M, Peters P, Raedler J, Albert MH, Abraham RS, Rangarjan HG, Buchbinder D, Kobrynski L, Pham-Huy A, Dhossche J, Cunningham Rundles C, Meyer AK, Theos A, Atkinson TP, Musiek A, Adeli M, Derichs U, Walz C, Krüger R, von Bernuth H, Klein C, Icenogle J, Hauck F, Sullivan KE. Rubella Virus Infected Macrophages and Neutrophils Define Patterns of Granulomatous Inflammation in Inborn and Acquired Errors of Immunity. Front Immunol 2022; 12:796065. [PMID: 35003119 PMCID: PMC8728873 DOI: 10.3389/fimmu.2021.796065] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/30/2021] [Indexed: 01/08/2023] Open
Abstract
Rubella virus (RuV) has recently been found in association with granulomatous inflammation of the skin and several internal organs in patients with inborn errors of immunity (IEI). The cellular tropism and molecular mechanisms of RuV persistence and pathogenesis in select immunocompromised hosts are not clear. We provide clinical, immunological, virological, and histological data on a cohort of 28 patients with a broad spectrum of IEI and RuV-associated granulomas in skin and nine extracutaneous tissues to further delineate this relationship. Combined immunodeficiency was the most frequent diagnosis (67.8%) among patients. Patients with previously undocumented conditions, i.e., humoral immunodeficiencies, a secondary immunodeficiency, and a defect of innate immunity were identified as being susceptible to RuV-associated granulomas. Hematopoietic cell transplantation was the most successful treatment in this case series resulting in granuloma resolution; steroids, and TNF-α and IL-1R inhibitors were moderately effective. In addition to M2 macrophages, neutrophils were identified by immunohistochemical analysis as a novel cell type infected with RuV. Four patterns of RuV-associated granulomatous inflammation were classified based on the structural organization of granulomas and identity and location of cell types harboring RuV antigen. Identification of conditions that increase susceptibility to RuV-associated granulomas combined with structural characterization of the granulomas may lead to a better understanding of the pathogenesis of RuV-associated granulomas and discover new targets for therapeutic interventions.
Collapse
Affiliation(s)
- Ludmila Perelygina
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, United States
| | - Raeesa Faisthalab
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, United States
| | - Emily Abernathy
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, United States
| | - Min-Hsin Chen
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, United States
| | - LiJuan Hao
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, United States
| | - Lionel Bercovitch
- Department of Dermatology, Hasbro Children's Hospital and Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Diana K Bayer
- Department of Pediatrics, University of Iowa Stead Family Children's Hospital, Iowa City, IA, United States
| | - Lenora M Noroski
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, United States
| | - Michael T Lam
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, United States
| | - Maria Pia Cicalese
- Pediatric Immunohematology and Bone Marrow Transplantation Unit and San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Istituto di Ricovero e Cura a Carattere Scientifico (National Institute for Research and Treatment) (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Waleed Al-Herz
- Department of Pediatrics, Kuwait University, Kuwait City, Kuwait.,Allergy and Clinical Immunology Unit, Department of Pediatrics, Al-Sabah Hospital, Kuwait City, Kuwait
| | - Arti Nanda
- Pediatric Dermatology Unit, As'ad Al-Hamad Dermatology Center, Al-sabah Hospital, Kuwait City, Kuwait
| | - Joud Hajjar
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, United States
| | - Koen Vanden Driessche
- Department of Pediatrics, Queen Mathilde Mother and Child Centre, Antwerp University Hospital, Antwerp, Belgium
| | - Shari Schroven
- Department of Pediatrics, Queen Mathilde Mother and Child Centre, Antwerp University Hospital, Antwerp, Belgium
| | - Julie Leysen
- Department of Dermatology, Queen Mathilde Mother and Child Centre, Antwerp University Hospital, Antwerp, Belgium
| | - Misha Rosenbach
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Philipp Peters
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Raedler
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael H Albert
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Hemalatha G Rangarjan
- Department of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, United States
| | - David Buchbinder
- Department of Hematology, Children's Hospital of Orange County, Orange, CA, United States.,Department of Pediatrics, University of California at Irvine, Orange, CA, United States
| | - Lisa Kobrynski
- Allergy/Immunology Section, Emory University, Atlanta, GA, United States
| | - Anne Pham-Huy
- Department of Pediatrics, University of Ottawa and Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Julie Dhossche
- Department of Dermatology, Oregon Health and Science University, Portland, OR, United States
| | - Charlotte Cunningham Rundles
- Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Anna K Meyer
- Department of Pediatrics, National Jewish Health, Denver, CO, United States
| | - Amy Theos
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Amy Musiek
- Division of Dermatology, Washington University School of Medicine, St. Louis, MO, United States
| | - Mehdi Adeli
- Division of Immunology and Allergy, Sidra Medicine and Hamad Medical Corporation, Doha, Qatar
| | - Ute Derichs
- Center for Pediatric and Adolescent Medicine, University Medical Hospital Mainz, Mainz, Germany
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Renate Krüger
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Horst von Bernuth
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,Labor Berlin GmbH, Department of Immunology, Berlin, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Joseph Icenogle
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, United States
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| |
Collapse
|
23
|
CD14 Is Involved in the Interferon Response of Human Macrophages to Rubella Virus Infection. Biomedicines 2022; 10:biomedicines10020266. [PMID: 35203475 PMCID: PMC8869353 DOI: 10.3390/biomedicines10020266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Macrophages (MΦ) as specialized immune cells are involved in rubella virus (RuV) pathogenesis and enable the study of its interaction with the innate immune system. A similar replication kinetics of RuV in the two human MΦ types, the pro-inflammatory M1-like (or GM-MΦ) and anti-inflammatory M2-like (M-MΦ), was especially in M-MΦ accompanied by a reduction in the expression of the innate immune receptor CD14. Similar to RuV infection, exogenous interferon (IFN) β induced a loss of glycolytic reserve in M-MΦ, but in contrast to RuV no noticeable influence on CD14 expression was detected. We next tested the contribution of CD14 to the generation of cytokines/chemokines during RuV infection of M-MΦ through the application of anti-CD14 blocking antibodies. Blockage of CD14 prior to RuV infection enhanced generation of virus progeny. In agreement with this observation, the expression of IFNs was significantly reduced in comparison to the isotype control. Additionally, the expression of TNF-α was slightly reduced, whereas the chemokine CXCL10 was not altered. In conclusion, the observed downmodulation of CD14 during RuV infection of M-MΦ appears to contribute to virus-host-adaptation through a reduction of the IFN response.
Collapse
|
24
|
Forni D, Cagliani R, Pontremoli C, Clerici M, Sironi M. The substitution spectra of coronavirus genomes. Brief Bioinform 2022; 23:bbab382. [PMID: 34518866 PMCID: PMC8499949 DOI: 10.1093/bib/bbab382] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/23/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has triggered an unprecedented international effort to sequence complete viral genomes. We leveraged this wealth of information to characterize the substitution spectrum of SARS-CoV-2 and to compare it with those of other human and animal coronaviruses. We show that, once nucleotide composition is taken into account, human and most animal coronaviruses display a mutation spectrum dominated by C to U and G to U substitutions, a feature that is not shared by other positive-sense RNA viruses. However, the proportions of C to U and G to U substitutions tend to decrease as divergence increases, suggesting that, whatever their origin, a proportion of these changes is subsequently eliminated by purifying selection. Analysis of the sequence context of C to U substitutions showed little evidence of apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC)-mediated editing and such contexts were similar for SARS-CoV-2 and Middle East respiratory syndrome coronavirus sampled from different hosts, despite different repertoires of APOBEC3 proteins in distinct species. Conversely, we found evidence that C to U and G to U changes affect CpG dinucleotides at a frequency higher than expected. Whereas this suggests ongoing selective reduction of CpGs, this effect alone cannot account for the substitution spectra. Finally, we show that, during the first months of SARS-CoV-2 pandemic spread, the frequency of both G to U and C to U substitutions increased. Our data suggest that the substitution spectrum of SARS-CoV-2 is determined by an interplay of factors, including intrinsic biases of the replication process, avoidance of CpG dinucleotides and other constraints exerted by the new host.
Collapse
Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Chiara Pontremoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| |
Collapse
|
25
|
Kim K, Calabrese P, Wang S, Qin C, Rao Y, Feng P, Chen XS. The Roles of APOBEC-mediated RNA Editing in SARS-CoV-2 Mutations, Replication and Fitness.. [PMID: 34981048 PMCID: PMC8722585 DOI: 10.1101/2021.12.18.473309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
During COVID-19 pandemic, mutations of SARS-CoV-2 produce new strains that can be more infectious or evade vaccines. Viral RNA mutations can arise from misincorporation by RNA-polymerases and modification by host factors. Analysis of SARS-CoV-2 sequence from patients showed a strong bias toward C-to-U mutation, suggesting a potential mutational role by host APOBEC cytosine deaminases that possess broad anti-viral activity. We report the first experimental evidence demonstrating that APOBEC3A, APOBEC1, and APOBEC3G can edit on specific sites of SARS-CoV-2 RNA to produce C-to-U mutations. However, SARS-CoV-2 replication and viral progeny production in Caco-2 cells are not inhibited by the expression of these APOBECs. Instead, expression of wild-type APOBEC3 greatly promotes viral replication/propagation, suggesting that SARS-CoV-2 utilizes the APOBEC-mediated mutations for fitness and evolution. Unlike the random mutations, this study suggests the predictability of all possible viral genome mutations by these APOBECs based on the UC/AC motifs and the viral genomic RNA structure. Efficient Editing of SARS-CoV-2 genomic RNA by Host APOBEC deaminases and Its Potential Impacts on the Viral Replication and Emergence of New Strains in COVID-19 Pandemic
Collapse
|
26
|
Bansal D, Kamboj M, Anand R, Pandiar D, Narwal A, Sivakumar N, Devi A. Association of childhood vaccination with pediatric lichen planus: A systematic review. Int J Dermatol 2021; 62:22-31. [PMID: 34870853 DOI: 10.1111/ijd.15974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 09/21/2021] [Accepted: 10/23/2021] [Indexed: 12/23/2022]
Abstract
Lichen planus (LP) is a chronic T-cell-mediated mucocutaneous inflammatory disease, largely recognized in adults. It is uncommon in children, and the literature present still lacks comprehensive understanding mainly due to underreporting of such cases. LP shows atypical clinical features, when seen in children, mainly affecting the flexor aspect of the wrists, legs, and the oral and genital mucosae. It is largely considered an autoimmune response of the body with various etiologic factors. Its association with vaccination is still an interesting field for research. The focus of the present systematic review was to discover the link of vaccine in the pathogenesis of juvenile LP. An electronic search was carried out using MEDLINE by PubMed, Google Scholar, and Web of Science databases. Articles that reported LP in children with prior records for vaccination were selected for the present systematic review. Twenty-three published articles in the English language were included for the quantitative and qualitative syntheses. The demographic data, specific vaccine history, and clinical details of the lesions were recorded. The existing evidence supports that vaccines could play an important role in etiopathogenesis of pediatric LP.
Collapse
Affiliation(s)
- Deepty Bansal
- Department of Oral and Maxillofacial Pathology and Microbiology, Post Graduate Institute of Dental Sciences, Pt B.D. Sharma University of Health Sciences, Rohtak, India
| | - Mala Kamboj
- Department of Oral and Maxillofacial Pathology and Microbiology, Post Graduate Institute of Dental Sciences, Pt B.D. Sharma University of Health Sciences, Rohtak, India
| | - Rahul Anand
- Department of Oral and Maxillofacial Pathology and Microbiology, Post Graduate Institute of Dental Sciences, Pt B.D. Sharma University of Health Sciences, Rohtak, India
| | - Deepak Pandiar
- Department of Oral and Maxillofacial Pathology, Saveetha Dental College and Hospitals, Saveetha University (Tamil Nadu), Chennai, India
| | - Anjali Narwal
- Department of Oral and Maxillofacial Pathology and Microbiology, Post Graduate Institute of Dental Sciences, Pt B.D. Sharma University of Health Sciences, Rohtak, India
| | - N Sivakumar
- Department of Oral and Maxillofacial Pathology and Microbiology, Post Graduate Institute of Dental Sciences, Pt B.D. Sharma University of Health Sciences, Rohtak, India
| | - Anju Devi
- Department of Oral and Maxillofacial Pathology and Microbiology, Post Graduate Institute of Dental Sciences, Pt B.D. Sharma University of Health Sciences, Rohtak, India
| |
Collapse
|
27
|
Piontkivska H, Wales-McGrath B, Miyamoto M, Wayne ML. ADAR Editing in Viruses: An Evolutionary Force to Reckon with. Genome Biol Evol 2021; 13:evab240. [PMID: 34694399 PMCID: PMC8586724 DOI: 10.1093/gbe/evab240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 02/06/2023] Open
Abstract
Adenosine Deaminases that Act on RNA (ADARs) are RNA editing enzymes that play a dynamic and nuanced role in regulating transcriptome and proteome diversity. This editing can be highly selective, affecting a specific site within a transcript, or nonselective, resulting in hyperediting. ADAR editing is important for regulating neural functions and autoimmunity, and has a key role in the innate immune response to viral infections, where editing can have a range of pro- or antiviral effects and can contribute to viral evolution. Here we examine the role of ADAR editing across a broad range of viral groups. We propose that the effect of ADAR editing on viral replication, whether pro- or antiviral, is better viewed as an axis rather than a binary, and that the specific position of a given virus on this axis is highly dependent on virus- and host-specific factors, and can change over the course of infection. However, more research needs to be devoted to understanding these dynamic factors and how they affect virus-ADAR interactions and viral evolution. Another area that warrants significant attention is the effect of virus-ADAR interactions on host-ADAR interactions, particularly in light of the crucial role of ADAR in regulating neural functions. Answering these questions will be essential to developing our understanding of the relationship between ADAR editing and viral infection. In turn, this will further our understanding of the effects of viruses such as SARS-CoV-2, as well as many others, and thereby influence our approach to treating these deadly diseases.
Collapse
Affiliation(s)
- Helen Piontkivska
- Department of Biological Sciences, Kent State University, Ohio, USA
- School of Biomedical Sciences, Kent State University, Ohio, USA
- Brain Health Research Institute, Kent State University, Ohio, USA
| | | | - Michael Miyamoto
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Marta L Wayne
- Department of Biology, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
28
|
Plotkin SA. Rubella Eradication: Not Yet Accomplished, but Entirely Feasible. J Infect Dis 2021; 224:S360-S366. [PMID: 34590132 PMCID: PMC8482023 DOI: 10.1093/infdis/jiaa530] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/03/2020] [Indexed: 11/14/2022] Open
Abstract
Rubella virus is the most teratogenic virus known to science and is capable of causing large epidemics. The RA 27/3 rubella vaccine, usually combined with measles vaccine, has eliminated rubella and congenital rubella syndrome from much of the world, notably from the Western Hemisphere. Except in immunosuppressed individuals, it is remarkably safe. Together with rubella vaccine strains used in China and Japan, eradication of the rubella virus is possible, indeed more feasible than eradication of measles or mumps.
Collapse
Affiliation(s)
- Stanley A Plotkin
- Emeritus Professor of Pediatrics, University of Pennsylvania, Vaxconsult, Doylestown, Pennsylvania, USA
| |
Collapse
|
29
|
Domingo E, García-Crespo C, Perales C. Historical Perspective on the Discovery of the Quasispecies Concept. Annu Rev Virol 2021; 8:51-72. [PMID: 34586874 DOI: 10.1146/annurev-virology-091919-105900] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral quasispecies are dynamic distributions of nonidentical but closely related mutant and recombinant viral genomes subjected to a continuous process of genetic variation, competition, and selection that may act as a unit of selection. The quasispecies concept owes its theoretical origins to a model for the origin of life as a collection of mutant RNA replicators. Independently, experimental evidence for the quasispecies concept was obtained from sampling of bacteriophage clones, which revealed that the viral populations consisted of many mutant genomes whose frequency varied with time of replication. Similar findings were made in animal and plant RNA viruses. Quasispecies became a theoretical framework to understand viral population dynamics and adaptability. The evidence came at a time when mutations were considered rare events in genetics, a perception that was to change dramatically in subsequent decades. Indeed, viral quasispecies was the conceptual forefront of a remarkable degree of biological diversity, now evident for cell populations and organisms, not only for viruses. Quasispecies dynamics unveiled complexities in the behavior of viral populations,with consequences for disease mechanisms and control strategies. This review addresses the origin of the quasispecies concept, its major implications on both viral evolution and antiviral strategies, and current and future prospects.
Collapse
Affiliation(s)
- Esteban Domingo
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlos García-Crespo
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
| | - Celia Perales
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain.,Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| |
Collapse
|
30
|
Grammatikos A, Donati M, Johnston SL, Gompels MM. Peripheral B Cell Deficiency and Predisposition to Viral Infections: The Paradigm of Immune Deficiencies. Front Immunol 2021; 12:731643. [PMID: 34527001 PMCID: PMC8435594 DOI: 10.3389/fimmu.2021.731643] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/09/2021] [Indexed: 12/11/2022] Open
Abstract
In the era of COVID-19, understanding how our immune system responds to viral infections is more pertinent than ever. Immunodeficiencies with very low or absent B cells offer a valuable model to study the role of humoral immunity against these types of infection. This review looks at the available evidence on viral infections in patients with B cell alymphocytosis, in particular those with X-linked agammaglobulinemia (XLA), Good’s syndrome, post monoclonal-antibody therapy and certain patients with Common Variable Immune Deficiency (CVID). Viral infections are not as infrequent as previously thought in these conditions and individuals with very low circulating B cells seem to be predisposed to an adverse outcome. Particularly in the case of SARS-CoV2 infection, mounting evidence suggests that peripheral B cell alymphocytosis is linked to a poor prognosis.
Collapse
Affiliation(s)
- Alexandros Grammatikos
- Department of Immunology, Southmead Hospital, North Bristol National Health Service (NHS) Trust, Bristol, United Kingdom
| | - Matthew Donati
- Severn Infection Sciences and Public Health England National Infection Service South West, Department of Virology, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
| | - Sarah L Johnston
- Department of Immunology, Southmead Hospital, North Bristol National Health Service (NHS) Trust, Bristol, United Kingdom
| | - Mark M Gompels
- Department of Immunology, Southmead Hospital, North Bristol National Health Service (NHS) Trust, Bristol, United Kingdom
| |
Collapse
|
31
|
Kitamura K, Shimizu H. The Molecular Evolution of Type 2 Vaccine-Derived Polioviruses in Individuals with Primary Immunodeficiency Diseases. Viruses 2021; 13:v13071407. [PMID: 34372613 PMCID: PMC8310373 DOI: 10.3390/v13071407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/17/2021] [Accepted: 07/17/2021] [Indexed: 12/28/2022] Open
Abstract
The oral poliovirus vaccine (OPV), which prevents person-to-person transmission of poliovirus by inducing robust intestinal immunity, has been a crucial tool for global polio eradication. However, polio outbreaks, mainly caused by type 2 circulating vaccine-derived poliovirus (cVDPV2), are increasing worldwide. Meanwhile, immunodeficiency-associated vaccine-derived poliovirus (iVDPV) is considered another risk factor during the final stage of global polio eradication. Patients with primary immunodeficiency diseases are associated with higher risks for long-term iVDPV infections. Although a limited number of chronic iVDPV excretors were reported, the recent identification of a chronic type 2 iVDPV (iVDPV2) excretor in the Philippines highlights the potential risk of inapparent iVDPV infection for expanding cVDPV outbreaks. Further research on the genetic characterizations and molecular evolution of iVDPV2, based on comprehensive iVDPV surveillance, will be critical for elucidating the remaining risk of iVDPV2 during the post-OPV era.
Collapse
|
32
|
Haralambieva IH, Eberhard KG, Ovsyannikova IG, Grill DE, Schaid DJ, Kennedy RB, Poland GA. Transcriptional signatures associated with rubella virus-specific humoral immunity after a third dose of MMR vaccine in women of childbearing age. Eur J Immunol 2021; 51:1824-1838. [PMID: 33818775 PMCID: PMC9841595 DOI: 10.1002/eji.202049054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/03/2021] [Accepted: 12/17/2020] [Indexed: 01/19/2023]
Abstract
Multiple factors linked to host genetics/inherent biology play a role in interindividual variability in immune response outcomes after rubella vaccination. In order to identify these factors, we conducted a study of rubella-specific humoral immunity before (Baseline) and after (Day 28) a third dose of MMR-II vaccine in a cohort of 109 women of childbearing age. We performed mRNA-Seq profiling of PBMCs after rubella virus in vitro stimulation to delineate genes associated with post-vaccination rubella humoral immunity and to define genes mediating the association between prior immune response status (high or low antibody) and subsequent immune response outcome. Our study identified novel genes that mediated the association between prior immune response and neutralizing antibody titer after a third MMR vaccine dose. These genes included the following: CDC34; CSNK1D; APOBEC3F; RAD18; AAAS; SLC37A1; FAS; and JAK2. The encoded proteins are involved in innate antiviral response, IFN/cytokine signaling, B cell repertoire generation, the clonal selection of B lymphocytes in germinal centers, and somatic hypermutation/antibody affinity maturation to promote optimal antigen-specific B cell immune function. These data advance our understanding of how subjects' prior immune status and/or genetic propensity to respond to rubella/MMR vaccination ultimately affects innate immunity and humoral immune outcomes after vaccination.
Collapse
Affiliation(s)
| | | | | | - Diane E. Grill
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel J. Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
33
|
Shields BE, Perelygina L, Samimi S, Haun P, Leung T, Abernathy E, Chen MH, Hao L, Icenogle J, Drolet B, Wilson B, Bryer JS, England R, Blumberg E, Wanat KA, Sullivan K, Rosenbach M. Granulomatous Dermatitis Associated With Rubella Virus Infection in an Adult With Immunodeficiency. JAMA Dermatol 2021; 157:842-847. [PMID: 34037685 DOI: 10.1001/jamadermatol.2021.1577] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Importance Immunodeficiency-related, vaccine-derived rubella virus (RuV) as an antigenic trigger of cutaneous and visceral granulomas is a rare, recently described phenomenon in children and young adults treated with immunosuppressant agents. Objective To perform a comprehensive clinical, histologic, immunologic, molecular, and genomic evaluation to elucidate the potential cause of an adult patient's atypical cutaneous granulomas. Design, Setting, and Participants A prospective evaluation of skin biopsies, nasopharyngeal swabs, and serum samples submitted to the Centers for Disease Control and Prevention was conducted to assess for RuV using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) and viral genomic sequencing. The samples were obtained from a man in his 70s with extensive cutaneous granulomas mimicking both cutaneous sarcoidosis (clinically) and CD8+ granulomatous cutaneous T-cell lymphoma (histopathologically). The study was conducted from September 2019 to February 2021. Main Outcomes and Measures Identification and genotyping of a novel immunodeficiency-related RuV-associated granulomatous dermatitis. Results Immunohistochemistry for RuV capsid protein and RT-PCR testing for RuV RNA revealed RuV in 4 discrete skin biopsies from different body sites. In addition, RuV RNA was detected in the patient's nasopharyngeal swabs by RT-PCR. The full viral genome was sequenced from the patient's skin biopsy (RVs/Philadelphia.PA.USA/46.19/GR, GenBank Accession #MT249313). The patient was ultimately diagnosed with a novel RuV-associated granulomatous dermatitis. Conclusions and Relevance The findings of this study suggest that clinicians and pathologists may consider RuV-associated granulomatous dermatitis during evaluation of a patient because it might have implications for the diagnosis of cutaneous sarcoidosis, with RuV serving as a potential antigenic trigger, and for the diagnosis of granulomatous cutaneous T-cell lymphoma, with histopathologic features that may prompt an evaluation for immunodeficiency and/or RuV.
Collapse
Affiliation(s)
- Bridget E Shields
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison.,Assistant Section Editor, JAMA Dermatology
| | - Ludmila Perelygina
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, Georgia
| | - Sara Samimi
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Paul Haun
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Thomas Leung
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Emily Abernathy
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, Georgia
| | - Min-Hsin Chen
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, Georgia
| | - LiJuan Hao
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, Georgia
| | - Joseph Icenogle
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, Georgia
| | - Beth Drolet
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison
| | - Barbara Wilson
- Department of Dermatology, Medical College of Wisconsin, Milwaukee
| | - Joshua S Bryer
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Ross England
- Division of Infectious Diseases, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Emily Blumberg
- Division of Infectious Diseases, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Karolyn A Wanat
- Department of Dermatology, Medical College of Wisconsin, Milwaukee.,Section Editor, JAMA Dermatology
| | - Kathleen Sullivan
- Division of Allergy and Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Allergy and Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Misha Rosenbach
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| |
Collapse
|
34
|
Kockler ZW, Gordenin DA. From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution. Cells 2021; 10:1557. [PMID: 34202997 PMCID: PMC8234929 DOI: 10.3390/cells10061557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
The current SARS-CoV-2 pandemic underscores the importance of understanding the evolution of RNA genomes. While RNA is subject to the formation of similar lesions as DNA, the evolutionary and physiological impacts RNA lesions have on viral genomes are yet to be characterized. Lesions that may drive the evolution of RNA genomes can induce breaks that are repaired by recombination or can cause base substitution mutagenesis, also known as base editing. Over the past decade or so, base editing mutagenesis of DNA genomes has been subject to many studies, revealing that exposure of ssDNA is subject to hypermutation that is involved in the etiology of cancer. However, base editing of RNA genomes has not been studied to the same extent. Recently hypermutation of single-stranded RNA viral genomes have also been documented though its role in evolution and population dynamics. Here, we will summarize the current knowledge of key mechanisms and causes of RNA genome instability covering areas from the RNA world theory to the SARS-CoV-2 pandemic of today. We will also highlight the key questions that remain as it pertains to RNA genome instability, mutations accumulation, and experimental strategies for addressing these questions.
Collapse
Affiliation(s)
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA;
| |
Collapse
|
35
|
Abstract
Evaluation of antibodies produced after immunization is central to immune deficiency diagnosis. This includes assessment of responses to routine immunizations as well as to vaccines administered specifically for diagnosis. Here, we present the basic concepts of the humoral immune response and their relevance for vaccine composition and diagnosis of immune deficiency. Current vaccines are discussed, including nonviable protein and glycoprotein vaccines, pure polysaccharide vaccines, polysaccharide-protein conjugate vaccines, and live agent vaccines. Diagnostic and therapeutic applications of vaccine antibody measurement are discussed in depth. Important adverse effects of vaccines are also presented.
Collapse
|
36
|
Simmonds P, Ansari MA. Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA. PLoS Pathog 2021; 17:e1009596. [PMID: 34061905 PMCID: PMC8195396 DOI: 10.1371/journal.ppat.1009596] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/11/2021] [Accepted: 04/29/2021] [Indexed: 11/18/2022] Open
Abstract
The rapid evolution of RNA viruses has been long considered to result from a combination of high copying error frequencies during RNA replication, short generation times and the consequent extensive fixation of neutral or adaptive changes over short periods. While both the identities and sites of mutations are typically modelled as being random, recent investigations of sequence diversity of SARS coronavirus 2 (SARS-CoV-2) have identified a preponderance of C->U transitions, proposed to be driven by an APOBEC-like RNA editing process. The current study investigated whether this phenomenon could be observed in datasets of other RNA viruses. Using a 5% divergence filter to infer directionality, 18 from 36 datasets of aligned coding region sequences from a diverse range of mammalian RNA viruses (including Picornaviridae, Flaviviridae, Matonaviridae, Caliciviridae and Coronaviridae) showed a >2-fold base composition normalised excess of C->U transitions compared to U->C (range 2.1x-7.5x), with a consistently observed favoured 5' U upstream context. The presence of genome scale RNA secondary structure (GORS) was the only other genomic or structural parameter significantly associated with C->U/U->C transition asymmetries by multivariable analysis (ANOVA), potentially reflecting RNA structure dependence of sites targeted for C->U mutations. Using the association index metric, C->U changes were specifically over-represented at phylogenetically uninformative sites, potentially paralleling extensive homoplasy of this transition reported in SARS-CoV-2. Although mechanisms remain to be functionally characterised, excess C->U substitutions accounted for 11-14% of standing sequence variability of structured viruses and may therefore represent a potent driver of their sequence diversification and longer-term evolution.
Collapse
Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - M. Azim Ansari
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
37
|
Groß M, Speckmann C, May A, Gajardo-Carrasco T, Wustrau K, Maier SL, Panning M, Huzly D, Agaimy A, Bryceson YT, Choo S, Chow CW, Dückers G, Fasth A, Fraitag S, Gräwe K, Haxelmans S, Holzinger D, Hudowenz O, Hübschen JM, Khurana C, Kienle K, Klifa R, Korn K, Kutzner H, Lämmermann T, Ledig S, Lipsker D, Meeths M, Naumann-Bartsch N, Rascon J, Schänzer A, Seidl M, Tesi B, Vauloup-Fellous C, Vollmer-Kary B, Warnatz K, Wehr C, Neven B, Vargas P, Sepulveda FE, Lehmberg K, Schmitt-Graeff A, Ehl S. Rubella vaccine-induced granulomas are a novel phenotype with incomplete penetrance of genetic defects in cytotoxicity. J Allergy Clin Immunol 2021; 149:388-399.e4. [PMID: 34033843 DOI: 10.1016/j.jaci.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/19/2021] [Accepted: 05/05/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Rubella virus-induced granulomas have been described in patients with various inborn errors of immunity. Most defects impair T-cell immunity, suggesting a critical role of T cells in rubella elimination. However, the molecular mechanism of virus control remains elusive. OBJECTIVE This study sought to understand the defective effector mechanism allowing rubella vaccine virus persistence in granulomas. METHODS Starting from an index case with Griscelli syndrome type 2 and rubella skin granulomas, this study combined an international survey with a literature search to identify patients with cytotoxicity defects and granuloma. The investigators performed rubella virus immunohistochemistry and PCR and T-cell migration assays. RESULTS This study identified 21 patients with various genetically confirmed cytotoxicity defects, who presented with skin and visceral granulomas. Rubella virus was demonstrated in all 12 accessible biopsies. Granuloma onset was typically before 2 years of age and lesions persisted from months to years. Granulomas were particularly frequent in MUNC13-4 and RAB27A deficiency, where 50% of patients at risk were affected. Although these proteins have also been implicated in lymphocyte migration, 3-dimensional migration assays revealed no evidence of impaired migration of patient T cells. Notably, patients showed no evidence of reduced control of concomitantly given measles, mumps, or varicella live-attenuated vaccine or severe infections with other viruses. CONCLUSIONS This study identified lymphocyte cytotoxicity as a key effector mechanism for control of rubella vaccine virus, without evidence for its need in control of live measles, mumps, or varicella vaccines. Rubella vaccine-induced granulomas are a novel phenotype with incomplete penetrance of genetic disorders of cytotoxicity.
Collapse
Affiliation(s)
- Miriam Groß
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Annette May
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Tania Gajardo-Carrasco
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM), Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris, Paris, France
| | - Katharina Wustrau
- Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Lena Maier
- Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Panning
- Institute of Virology, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Daniela Huzly
- Institute of Virology, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Yenan T Bryceson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Broegelmann Research Laboratory, Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Sharon Choo
- Department of Allergy and Immunology, The Royal Children's Hospital, Melbourne, Australia
| | - C W Chow
- Department of Anatomical Pathology, The Royal Children's Hospital, Melbourne, Australia
| | - Gregor Dückers
- Helios Klinikum Krefeld, Zentrum für Kinder- und Jugendmedizin, Krefeld, Germany
| | - Anders Fasth
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy University of Gothenburg, Gothenburg, Sweden
| | - Sylvie Fraitag
- Department of Pathology, Necker-Enfants Malades Hospital, Paris, France
| | - Katja Gräwe
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | | | - Dirk Holzinger
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Ole Hudowenz
- Department of Rheumatology, Immunology, Osteology, and Physical Medicine, Campus Kerckhoff of Justus-Liebig-University Gießen, Bad Nauheim, Germany
| | - Judith M Hübschen
- World Health Organization European Regional Reference Laboratory for Measles and Rubella, Luxembourg Institute of Health, Department of Infection and Immunity, Esch-sur-Alzette, Luxembourg
| | - Claudia Khurana
- Department of Pediatric Hematology and Oncology, Children's Center Bethel, University Hospital Ostwestfalen-Lippe (OWL)/University Bielefeld, Bielefeld, Germany
| | - Korbinian Kienle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Roman Klifa
- Immunology and Pediatric Hematology Department, Assistance Publique-Hôpitaux de Paris (AH-PH), Paris, France
| | - Klaus Korn
- Institute of Virology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | | | - Tim Lämmermann
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Svea Ledig
- Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dan Lipsker
- Faculté de Médecine, Université de Strasbourg and Clinique Dermatologique, Hôpitaux Universitaires, Strasbourg, France
| | - Marie Meeths
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Theme of Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Nora Naumann-Bartsch
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Jelena Rascon
- Center for Pediatric Oncology and Hematology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania; Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Anne Schänzer
- Institute of Neuropathology, Justus Liebig University Gießen, Gießen, Germany
| | - Maximilian Seidl
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany; Institute of Pathology, Heinrich Heine University and University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Christelle Vauloup-Fellous
- AP-HP, Hôpital Paul-Brousse, Department of Virology, World Health Organization Rubella National Reference Laboratory, Groupe de Recherche sur les Infections pendant la Grossesse, University Paris Saclay, INSERM U1193, Villejuif, France
| | - Beate Vollmer-Kary
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Claudia Wehr
- Center for Chronic Immunodeficiency, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany; Department of Medicine I, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Bénédicte Neven
- Imagine Institute, Université de Paris, Paris, France; Pediatric Hematology-Immunology and Rheumatology Department, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; Laboratory of Immunogenetics of Pediatric Autoimmunity, INSERM UMR 1163, Imagine Institute, Université de Paris, Paris, France
| | - Pablo Vargas
- Institut Curie, Centre National de la Recherche Scientifique (CNRS) UMR 144 and Institut Pierre-Gilles de Gennes, and INSERM U932 Immunité et Cancer, Institut Curie, Paris Sciences et Lettres Research University, Paris, France
| | - Fernando E Sepulveda
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM), Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris, Paris, France; Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Kai Lehmberg
- Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annette Schmitt-Graeff
- Center for Chronic Immunodeficiency, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany.
| |
Collapse
|
38
|
Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution. Virology 2021; 556:62-72. [PMID: 33545556 PMCID: PMC7831814 DOI: 10.1016/j.virol.2020.12.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Members of the APOBEC family of cytidine deaminases show antiviral activities in mammalian cells through lethal editing in the genomes of small DNA viruses, herpesviruses and retroviruses, and potentially those of RNA viruses such as coronaviruses. Consistent with the latter, APOBEC-like directional C→U transitions of genomic plus-strand RNA are greatly overrepresented in SARS-CoV-2 genome sequences of variants emerging during the COVID-19 pandemic. A C→U mutational process may leave evolutionary imprints on coronavirus genomes, including extensive homoplasy from editing and reversion at targeted sites and the occurrence of driven amino acid sequence changes in viral proteins. If sustained over longer periods, this process may account for the previously reported marked global depletion of C and excess of U bases in human seasonal coronavirus genomes. This review synthesizes the current knowledge on APOBEC evolution and function and the evidence of their role in APOBEC-mediated genome editing of SARS-CoV-2 and other coronaviruses. SARS-CoV-2 sequence variants contain an overabundance of C- > U transitions C- > U transitions are the hallmark of the activity of APOBEC cytosine deaminases Further work is needed to determine APOBEC's role in coronavirus evolution
Collapse
|
39
|
Gotesman R, Ramien M, Armour CM, Pham-Huy A, Kirshen C. Cutaneous granulomas as the presenting manifestation of Griscelli syndrome type 2. Pediatr Dermatol 2021; 38:194-197. [PMID: 32965739 DOI: 10.1111/pde.14370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/19/2020] [Accepted: 08/22/2020] [Indexed: 01/16/2023]
Abstract
Griscelli syndrome type 2 is a rare autosomal recessive disorder characterized by hypopigmentation, silvery hair, and immunological dysfunction with no primary neurological impairment. We report an 18-month-old girl with Griscelli syndrome type 2 who presented to the dermatology department for cutaneous granulomas that developed following live-attenuated vaccination. Two compound heterozygous variants in the RAB27A gene were subsequently identified. She developed hemophagocytic lymphohistiocytosis, the key immunological concern, at age 5 years.
Collapse
Affiliation(s)
- Ryan Gotesman
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Michele Ramien
- Division of Community Pediatrics, Department of Pediatrics, Alberta Children's Hospital, Calgary, AB, Canada
| | - Christine M Armour
- Regional Genetics Program, Children's Hospital of Eastern Ontario, and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Anne Pham-Huy
- Division of Infectious Diseases, Immunology and Allergy, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Carly Kirshen
- Division of Dermatology, Department of Medicine, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
40
|
Khatami M. Deceptology in cancer and vaccine sciences: Seeds of immune destruction-mini electric shocks in mitochondria: Neuroplasticity-electrobiology of response profiles and increased induced diseases in four generations - A hypothesis. Clin Transl Med 2020; 10:e215. [PMID: 33377661 PMCID: PMC7749544 DOI: 10.1002/ctm2.215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
From Rockefeller's support of patent medicine to Gates' patent vaccines, medical establishment invested a great deal in intellectual ignorance. Through the control over medical education and research it has created a public illusion to prop up corporate profit and encouraged the lust for money and power. An overview of data on cancer and vaccine sciences, the status of Americans' health, a survey of repeated failed projects, economic toxicity, and heavy drug consumption or addiction among young and old provide compelling evidence that in the twentieth century nearly all classic disease categories (congenital, inheritance, neonatal, or induced) shifted to increase induced diseases. Examples of this deceptology in ignoring or minimizing, and mocking fundamental discoveries and theories in cancer and vaccine sciences are attacks on research showing that (a), effective immunity is responsible for defending and killing pathogens and defective cancerous cells, correcting and repairing genetic mutations; (b) viruses cause cancer; and (c), abnormal gene mutations are often the consequences of (and secondary to) disturbances in effective immunity. The outcomes of cancer reductionist approaches to therapies reveal failure rates of 90% (+/-5) for solid tumors; loss of over 50 million lives and waste of $30-50 trillions on too many worthless, out-of-focus, and irresponsible projects. Current emphasis on vaccination of public with pathogen-specific vaccines and ingredients seems new terms for drugging young and old. Cumulative exposures to low level carcinogens and environmental hazards or high energy electronic devices (EMF; 5G) are additional triggers to vaccine toxicities (antigen-mitochondrial overload) or "seeds of immune destruction" that create mini electrical shocks (molecular sinks holes) in highly synchronized and regulated immune network that retard time-energy-dependent biorhythms in organs resulting in causes, exacerbations or consequences of mild, moderate or severe immune disorders. Four generations of drug-dependent Americans strongly suggest that medical establishment has practiced decades of intellectual deception through its claims on "war on cancer"; that cancer is 100, 200, or 1000 diseases; identification of "individual" genetic mutations to cure diseases; "vaccines are safe". Such immoral and unethical practices, along with intellectual harassment and bullying, censoring or silencing of independent and competent professionals ("Intellectual Me Too") present grave concerns, far greater compared with the sexual harassment of 'Me Too' movement that was recently spearheaded by NIH. The principal driving forces behind conducting deceptive and illogical medical/cancer and vaccine projects seem to be; (a) huge return of investment and corporate profit for selling drugs and vaccines; (b) maintenance of abusive power over public health; (c) global control of population growth via increased induction of diseases, infertility, decline in life-span, and death. An overview of accidental discoveries that we established and extended since 1980s, on models of acute and chronic ocular inflammatory diseases, provides series of the first evidence for a direct link between inflammation and multistep immune dysfunction in tumorigenesis and angiogenesis. Results are relevant to demonstrate that current emphasis on vaccinating the unborn, newborn, or infant would induce immediate or long-term immune disorders (eg, low birth weight, preterm birth, fatigue, autism, epilepsy/seizures, BBB leakage, autoimmune, neurodegenerative or digestive diseases, obesity, diabetes, cardiovascular problems, or cancers). Vaccination of the unborn is likely to disturb trophoblast-embryo-fetus-placenta biology and orderly growth of embryo-fetus, alter epithelial-mesenchymal transition or constituent-inducible receptors, damage mitochondria, and diverse function of histamine-histidine pathways. Significant increased in childhood illnesses are likely due to toxicities of vaccine and incipient (eg, metals [Al, Hg], detergents, fetal tissue, DNA/RNA) that retard bioenergetics of mitochondria, alter polarization-depolarization balance of tumoricidal (Yin) and tumorigenic (Yang) properties of immunity. Captivated by complex electobiology of immunity, this multidisciplinary perspective is an attempt to initiate identifying bases for increased induction of immune disorders in three to four generations in America. We hypothesize that (a) gene-environment-immune biorhythms parallel neuronal function (brain neuroplasticity) with super-packages of inducible (adaptive or horizontal) electronic signals and (b) autonomic sympathetic and parasympathetic circuitry that shape immunity (Yin-Yang) cannot be explained by limited genomics (innate, perpendicular) that conventionally explain certain inherited diseases (eg, sickle cell anemia, progeria). Future studies should focus on deep learning of complex electrobiology of immunity that requires differential bioenergetics from mitochondria and cytoplasm. Approaches to limit or control excessive activation of gene-environment-immunity are keys to assess accurate disease risk formulations, prevent inducible diseases, and develop universal safe vaccines that promote health, the most basic human right.
Collapse
Affiliation(s)
- Mahin Khatami
- Inflammation, Aging and Cancer, National Cancer Institute (NCI)the National Institutes of Health (NIH) (Retired)BethesdaMarylandUSA
| |
Collapse
|
41
|
Point mutation bias in SARS-CoV-2 variants results in increased ability to stimulate inflammatory responses. Sci Rep 2020; 10:17766. [PMID: 33082451 PMCID: PMC7575582 DOI: 10.1038/s41598-020-74843-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/08/2020] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection induces severe pneumonia and is the cause of a worldwide pandemic. Coronaviruses, including SARS-CoV-2, have RNA proofreading enzymes in their genomes, resulting in fewer gene mutations than other RNA viruses. Nevertheless, variants of SARS-CoV-2 exist and may induce different symptoms; however, the factors and the impacts of these mutations are not well understood. We found that there is a bias to the mutations occurring in SARS-CoV-2 variants, with disproportionate mutation to uracil (U). These point mutations to U are mainly derived from cytosine (C), which is consistent with the substrate specificity of host RNA editing enzymes, APOBECs. We also found the point mutations which are consistent with other RNA editing enzymes, ADARs. For the C-to-U mutations, the context of the upstream uracil and downstream guanine from mutated position was found to be most prevalent. Further, the degree of increase of U in SARS-CoV-2 variants correlates with enhanced production of cytokines, such as TNF-α and IL-6, in cell lines when compared with stimulation by the ssRNA sequence of the isolated virus in Wuhan. Therefore, RNA editing is a factor for mutation bias in SARS-CoV-2 variants, which affects host inflammatory cytokines production.
Collapse
|
42
|
Rubella virus-associated chronic inflammation in primary immunodeficiency diseases. Curr Opin Allergy Clin Immunol 2020; 20:574-581. [PMID: 33044342 DOI: 10.1097/aci.0000000000000694] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF THE REVIEW The aim of this article is to summarize recent data on rubella virus (RuV) vaccine in chronic inflammation focusing on granulomas in individuals with primary immunodeficiencies (PIDs). RECENT FINDINGS The live attenuated RuV vaccine has been recently associated with cutaneous and visceral granulomas in children with various PIDs. RuV vaccine strain can persist for decades subclinically in currently unknown body site(s) before emerging in granulomas. Histologically, RuV is predominately localized in M2 macrophages in the granuloma centers. Multiple mutations accumulate during persistence resulting in emergence of immunodeficiency-related vaccine-derived rubella viruses (iVDRVs) with altered immunological, replication, and persistence properties. Viral RNA was detected in granuloma biopsies and nasopharyngeal secretions and infectious virus were isolated from the granuloma lesions. The risk of iVDRV transmissibility to contacts needs to be evaluated. Several broad-spectrum antiviral drugs have been tested recently but did not provide significant clinical improvement. Hematopoietic stem cell transplantation remains the only reliable option for curing chronic RuV-associated granulomas in PIDs. SUMMARY Persistence of vaccine-derived RuVs appears to be a crucial factor in a significant proportion of granulomatous disease in PIDs. RuV testing of granulomas in PID individuals might help with case management.
Collapse
|
43
|
Klimczak LJ, Randall TA, Saini N, Li JL, Gordenin DA. Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic. PLoS One 2020; 15:e0237689. [PMID: 33006981 PMCID: PMC7531822 DOI: 10.1371/journal.pone.0237689] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
Genomes of tens of thousands of SARS-CoV2 isolates have been sequenced across the world and the total number of changes (predominantly single base substitutions) in these isolates exceeds ten thousand. We compared the mutational spectrum in the new SARS-CoV-2 mutation dataset with the previously published mutation spectrum in hypermutated genomes of rubella-another positive single stranded (ss) RNA virus. Each of the rubella virus isolates arose by accumulation of hundreds of mutations during propagation in a single subject, while SARS-CoV-2 mutation spectrum represents a collection events in multiple virus isolates from individuals across the world. We found a clear similarity between the spectra of single base substitutions in rubella and in SARS-CoV-2, with C to U as well as A to G and U to C being the most prominent in plus strand genomic RNA of each virus. Of those, U to C changes universally showed preference for loops versus stems in predicted RNA secondary structure. Similarly, to what was previously reported for rubella virus, C to U changes showed enrichment in the uCn motif, which suggested a subclass of APOBEC cytidine deaminase being a source of these substitutions. We also found enrichment of several other trinucleotide-centered mutation motifs only in SARS-CoV-2-likely indicative of a mutation process characteristic to this virus. Altogether, the results of this analysis suggest that the mutation mechanisms that lead to hypermutation of the rubella vaccine virus in a rare pathological condition may also operate in the background of the SARS-CoV-2 viruses currently propagating in the human population.
Collapse
Affiliation(s)
- Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Durham, North Carolina, United State of America
| | - Thomas A. Randall
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Durham, North Carolina, United State of America
| | - Natalie Saini
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, NIH, Durham, North Carolina, United State of America
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Durham, North Carolina, United State of America
| | - Dmitry A. Gordenin
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, NIH, Durham, North Carolina, United State of America
- * E-mail:
| |
Collapse
|
44
|
Bennett AJ, Paskey AC, Ebinger A, Pfaff F, Priemer G, Höper D, Breithaupt A, Heuser E, Ulrich RG, Kuhn JH, Bishop-Lilly KA, Beer M, Goldberg TL. Relatives of rubella virus in diverse mammals. Nature 2020; 586:424-428. [PMID: 33029010 PMCID: PMC7572621 DOI: 10.1038/s41586-020-2812-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 07/17/2020] [Indexed: 12/17/2022]
Abstract
Since 1814, when rubella was first described, the origins of the disease and its causative agent, rubella virus (Matonaviridae: Rubivirus), have remained unclear1. Here we describe ruhugu virus and rustrela virus in Africa and Europe, respectively, which are, to our knowledge, the first known relatives of rubella virus. Ruhugu virus, which is the closest relative of rubella virus, was found in apparently healthy cyclops leaf-nosed bats (Hipposideros cyclops) in Uganda. Rustrela virus, which is an outgroup to the clade that comprises rubella and ruhugu viruses, was found in acutely encephalitic placental and marsupial animals at a zoo in Germany and in wild yellow-necked field mice (Apodemus flavicollis) at and near the zoo. Ruhugu and rustrela viruses share an identical genomic architecture with rubella virus2,3. The amino acid sequences of four putative B cell epitopes in the fusion (E1) protein of the rubella, ruhugu and rustrela viruses and two putative T cell epitopes in the capsid protein of the rubella and ruhugu viruses are moderately to highly conserved4-6. Modelling of E1 homotrimers in the post-fusion state predicts that ruhugu and rubella viruses have a similar capacity for fusion with the host-cell membrane5. Together, these findings show that some members of the family Matonaviridae can cross substantial barriers between host species and that rubella virus probably has a zoonotic origin. Our findings raise concerns about future zoonotic transmission of rubella-like viruses, but will facilitate comparative studies and animal models of rubella and congenital rubella syndrome.
Collapse
Affiliation(s)
- Andrew J Bennett
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Leidos, Reston, VA, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Arnt Ebinger
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Grit Priemer
- State Office for Agriculture, Food Safety and Fisheries, Rostock, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Elisa Heuser
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Kimberly A Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Global Health Institute, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
45
|
Matsumoto K, Hoshino A, Nishimura A, Kato T, Mori Y, Shimomura M, Naito C, Watanabe K, Hamazaki M, Mitsuiki N, Takagi M, Imai K, Nonoyama S, Kanegane H, Morio T. DNA Ligase IV Deficiency Identified by Chance Following Vaccine-Derived Rubella Virus Infection. J Clin Immunol 2020; 40:1187-1190. [PMID: 32914283 DOI: 10.1007/s10875-020-00831-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Kazuaki Matsumoto
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akihiro Hoshino
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akira Nishimura
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tamaki Kato
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
| | - Yoshio Mori
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masaki Shimomura
- Department of Allergy and Clinical Immunology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Chie Naito
- Department of Allergy and Clinical Immunology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Kenichiro Watanabe
- Department of Hematology and Oncology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Minoru Hamazaki
- Department of Pathology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Noriko Mitsuiki
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kohsuke Imai
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| |
Collapse
|
46
|
Klimczak LJ, Randall TA, Saini N, Li JL, Gordenin DA. Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.03.234005. [PMID: 32793907 PMCID: PMC7418721 DOI: 10.1101/2020.08.03.234005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Genomes of tens of thousands of SARS-CoV2 isolates have been sequenced across the world and the total number of changes (predominantly single base substitutions) in these isolates exceeds ten thousand. We compared the mutational spectrum in the new SARS-CoV-2 mutation dataset with the previously published mutation spectrum in hypermutated genomes of rubella - another positive single stranded (ss) RNA virus. Each of the rubella isolates arose by accumulation of hundreds of mutations during propagation in a single subject, while SARS-CoV-2 mutation spectrum represents a collection events in multiple virus isolates from individuals across the world. We found a clear similarity between the spectra of single base substitutions in rubella and in SARS-CoV-2, with C to U as well as A to G and U to C being the most prominent in plus strand genomic RNA of each virus. Of those, U to C changes universally showed preference for loops versus stems in predicted RNA secondary structure. Similarly, to what was previously reported for rubella, C to U changes showed enrichment in the uCn motif, which suggested a subclass of APOBEC cytidine deaminase being a source of these substitutions. We also found enrichment of several other trinucleotide-centered mutation motifs only in SARS-CoV-2 - likely indicative of a mutation process characteristic to this virus. Altogether, the results of this analysis suggest that the mutation mechanisms that lead to hypermutation of the rubella vaccine virus in a rare pathological condition may also operate in the background of the SARS-CoV-2 viruses currently propagating in the human population.
Collapse
|
47
|
Poulain F, Lejeune N, Willemart K, Gillet NA. Footprint of the host restriction factors APOBEC3 on the genome of human viruses. PLoS Pathog 2020; 16:e1008718. [PMID: 32797103 PMCID: PMC7449416 DOI: 10.1371/journal.ppat.1008718] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/26/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5'TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint. The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The papillomaviridae and polyomaviridae are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the parvoviridae family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic coronaviridae as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the gamma-herpesviridae and adenoviridae where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses. Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses.
Collapse
Affiliation(s)
- Florian Poulain
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Noémie Lejeune
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Kévin Willemart
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Nicolas A. Gillet
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| |
Collapse
|
48
|
Saini N, Gordenin DA. Hypermutation in single-stranded DNA. DNA Repair (Amst) 2020; 91-92:102868. [PMID: 32438271 PMCID: PMC7234795 DOI: 10.1016/j.dnarep.2020.102868] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
Regions of genomic DNA can become single-stranded in the course of normal replication and transcription as well as during DNA repair. Abnormal repair and replication intermediates can contain large stretches of persistent single-stranded DNA, which is extremely vulnerable to DNA damaging agents and hypermutation. Since such single-stranded DNA spans only a fraction of the genome at a given instance, hypermutation in these regions leads to tightly-spaced mutation clusters. This phenomenon of hypermutation in single-stranded DNA has been documented in several experimental models as well as in cancer genomes. Recently, hypermutated single-stranded RNA viral genomes also have been documented. Moreover, indications of hypermutation in single-stranded DNA may also be found in the human germline. This review will summarize key current knowledge and the recent developments in understanding the diverse mechanisms and sources of ssDNA hypermutation.
Collapse
Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.
| |
Collapse
|
49
|
Di Giorgio S, Martignano F, Torcia MG, Mattiuz G, Conticello SG. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2. SCIENCE ADVANCES 2020; 6:eabb5813. [PMID: 32596474 PMCID: PMC7299625 DOI: 10.1126/sciadv.abb5813] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/05/2020] [Indexed: 05/13/2023]
Abstract
The COVID-19 outbreak has become a global health risk, and understanding the response of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host deaminases is an innate restriction process to counter virus infection, but it is not yet known whether this process operates against coronaviruses. Here, we analyze RNA sequences from bronchoalveolar lavage fluids obtained from coronavirus-infected patients. We identify nucleotide changes that may be signatures of RNA editing: adenosine-to-inosine changes from ADAR deaminases and cytosine-to-uracil changes from APOBEC deaminases. Mutational analysis of genomes from different strains of Coronaviridae from human hosts reveals mutational patterns consistent with those observed in the transcriptomic data. However, the reduced ADAR signature in these data raises the possibility that ADARs might be more effective than APOBECs in restricting viral propagation. Our results thus suggest that both APOBECs and ADARs are involved in coronavirus genome editing, a process that may shape the fate of both virus and patient.
Collapse
Affiliation(s)
- Salvatore Di Giorgio
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Filippo Martignano
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Maria Gabriella Torcia
- Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy
| | - Giorgio Mattiuz
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy
| | - Silvestro G. Conticello
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| |
Collapse
|
50
|
Bartholomeus E, De Neuter N, Suls A, Elias G, van der Heijden S, Keersmaekers N, Jansens H, Van Tendeloo V, Beutels P, Laukens K, Ogunjimi B, Mortier G, Meysman P, Van Damme P. Transcriptomic profiling of different responder types in adults after a Priorix® vaccination. Vaccine 2020; 38:3218-3226. [PMID: 32165045 DOI: 10.1016/j.vaccine.2020.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the recommendation of a combined Measles/Mumps/Rubella (MMR) vaccine, like Priorix®, these childhood diseases are less common now. This is beneficial to limit the spread of these diseases and work towards their elimination. However, the measles, mumps and rubella antibody titers show a large variability in short- and long-term immunity. The recent outbreaks worldwide of measles and mumps and previous studies, which mostly focused on only one of the three virus responses, illustrate that there is a clear need for better understanding the immune responses after vaccination. Our healthy cohort was already primed with the MMR antigens in their childhood. In this study, the adult volunteers received one Priorix® vaccine dose at day 0. First, we defined 4 different groups of responders, based on their antibody titers' evolution over 4 time points (Day 0, 21, 150 and 365). This showed a high variability within and between individuals. Second, we determined transcriptome profiles using 3'mRNA sequencing at day 0, 3 and 7. Using two analytical approaches, "one response group per time point" and "a time comparison per response group", we correlated the short-term gene expression profiles to the different response groups. In general, the list of differentially expressed genes is limited, however, most of them are clearly immune-related and upregulated at day 3 and 7, compared to the baseline day 0. Depending on the specific response group there are overlapping signatures for two of the three viruses. Antibody titers and transcriptomics data showed that an additional Priorix vaccination does not facilitate an equal immune response against the 3 viruses or among different vaccine recipients.
Collapse
Affiliation(s)
- Esther Bartholomeus
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
| | - Nicolas De Neuter
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - George Elias
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Sanne van der Heijden
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Nina Keersmaekers
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Viggo Van Tendeloo
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium.
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| |
Collapse
|