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Fan T, Li C, Liu X, Xu H, Li W, Wang M, Mei X, Li D. Development of practical techniques for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. ANAL SCI 2023; 39:1839-1856. [PMID: 37517003 DOI: 10.1007/s44211-023-00396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Countless individuals have fallen victim to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have generated antibodies, reducing the risk of secondary infection in the short term. However, with the emergence of mutated strains, the probability of subsequent infections remains high. Consequently, the demand for simple and accessible methods for distinguishing between different variants is soaring. Although monitoring viral gene sequencing is an effective approach for differentiating between various types of SARS-CoV-2 variants, it may not be easily accessible to the general public. In this article, we provide an overview of the reported techniques that use combined approaches and adaptable testing methods that use editable recognition receptors for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. These techniques employ straightforward detection strategies, including tests capable of simultaneously identifying and differentiating between different variants. Furthermore, we recommend advancing the development of uncomplicated protocols for distinguishing between current and emerging variants. Additionally, we propose further development of facile protocols for the differentiation of existing and emerging variants.
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Affiliation(s)
- Tuocen Fan
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Chengjie Li
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Xinlei Liu
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Hongda Xu
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Wenhao Li
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Minghao Wang
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Jinzhou Medical University, Jinzhou, 121000, China.
| | - Dan Li
- Jinzhou Medical University, Jinzhou, 121000, China.
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
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Yang PP, Zeng ZD, Hou Y, Chen AM, Xu J, Zhao LQ, Liu XY. Rapid authentication of variants of Gastrodia elata Blume using near-infrared spectroscopy combined with chemometric methods. J Pharm Biomed Anal 2023; 235:115592. [PMID: 37499425 DOI: 10.1016/j.jpba.2023.115592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/05/2023] [Accepted: 07/16/2023] [Indexed: 07/29/2023]
Abstract
The variety is one of the most important factors to generate difference of chemical compositions, which unavoidably influences the quality of natural medicine. Thus, simple and rapid authentication of different variants has great academic and practical significance. In this study, the goal was achieved with the help of near infrared spectroscopy (NIR) and chemometrics by using Gastrodia elata Blume as an example. A total of 540 samples including two classes of variants and their forms were investigated as a whole. The mean spectra of samples of each class and their 2-D synchronous correlation spectra were simultaneously applied to discover the difference of chemical characteristics. After hybrid pre-processing of the first and second derivative combined with Savitzky-Golay and Norris filtering, partial least squares discrimination analysis (PLS-DA) on the basis of latent variable projection was used to assess the feasibility for classification. The results show higher prediction accuracy in both internal test set and external prediction set. In order to further improve the robustness for modeling, three methods for wavelength selection were comprehensively compared to optimize PLS-DA models, including variable importance in the projection (VIP), random frog (RF), and Monte Carlo uninformative variable elimination (MC-UVE). The prediction accuracy of combination of the 2nd derivative, Norris, MC-UVE and PLS-DA achieved to 99.11% and 98.89% corresponding to the internal test set and external prediction set, respectively. The strategies proposed in this work perform effectiveness for rapid and accurate authentication of variants of plants with high chemical complexity.
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Affiliation(s)
- Pan-Pan Yang
- Gastrodia elata Research Institute, Southwest Forestry University, Kunming 650224, China
| | - Zhong-da Zeng
- College of Environmental and Chemical Engineering, Dalian University, Dalian 116622, China.
| | - Ying Hou
- Gastrodia elata Research Institute, Southwest Forestry University, Kunming 650224, China
| | - Ai-Ming Chen
- Dalian ChemDataSolution Information Technology Co., Ltd., Dalian 116086, China
| | - Juan Xu
- Gastrodia elata Research Institute, Southwest Forestry University, Kunming 650224, China
| | - Long-Qing Zhao
- Gastrodia elata Research Institute, Southwest Forestry University, Kunming 650224, China.
| | - Xiang-Yi Liu
- Gastrodia elata Research Institute, Southwest Forestry University, Kunming 650224, China.
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Zhang Y, Pang D, Wang Z, Ma L, Chen Y, Yang L, Xiao W, Yuan H, Chang F, Ouyang H. An integrative analysis of genotype-phenotype correlation in Charcot Marie Tooth type 2A disease with MFN2 variants: A case and systematic review. Gene 2023; 883:147684. [PMID: 37536398 DOI: 10.1016/j.gene.2023.147684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/24/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Dominant genetic variants in the mitofusin 2 (MFN2) gene lead to Charcot-Marie-Tooth type 2A (CMT2A), a neurodegenerative disease caused by genetic defects that directly damage axons. In this study, we reported a proband with a pathogenic variant in the GTPase domain of MFN2, c.494A > G (p.His165Arg). To date, at least 184 distinct MFN2 variants identified in 944 independent probands have been reported in 131 references. However, the field of medical genetics has long been challenged by how genetic variation in the MFN2 gene is associated with disease phenotypes. Here, by collating the MFN2 variant data and patient clinical information from Leiden Open Variant Database 3.0, NCBI clinvar database, and available related references in PubMed, we determined the mutation frequency, age of onset, sex ratio, and geographical distribution. Furthermore, the results of an analysis examining the relationship between variants and phenotypes from multiple genetic perspectives indicated that insertion and deletions (indels), copy number variants (CNVs), duplication variants, and nonsense mutations in single nucleotide variants (SNVs) tend to be pathogenic, and the results emphasized the importance of the GTPase domain to the structure and function of MFN2. Overall, three reliable classification methods of MFN2 genotype-phenotype associations provide insights into the prediction of CMT2A disease severity. Of course, there are still many MFN2 variants that have not been given clear clinical significance, which requires clinicians to make more accurate clinical diagnoses.
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Affiliation(s)
- Yuanzhu Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China.
| | - Daxin Pang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401120, China; Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401120, China.
| | - Ziru Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China.
| | - Lerong Ma
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China.
| | - Yiwu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China.
| | - Lin Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China.
| | - Wenyu Xiao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China.
| | - Hongming Yuan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401120, China.
| | - Fei Chang
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130022, China.
| | - Hongsheng Ouyang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401120, China; Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401120, China.
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Aaron R, Premkumar K, Chapla A, Vijayalekshmi B, Zachariah U, Elias E, Kodiatte TA, Daniel D, Jude J, Balasubramanian KA, Nair SC, Thomas N, Ramakrishna B, Eapen CE, Goel A. Focused panel sequencing points to genetic predisposition in non-cirrhotic intrahepatic portal hypertension patients in India. Indian J Gastroenterol 2023:10.1007/s12664-023-01454-5. [PMID: 37796423 DOI: 10.1007/s12664-023-01454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/22/2023] [Indexed: 10/06/2023]
Abstract
OBJECTIVE Non-cirrhotic intrahepatic portal hypertension (NCIPH), a portal microangiopathy affecting small portal vein radicles, is a disease of Indian sub-continent. NCIPH appears to be a complex disease with interactions between inherited and acquired factors, though the exact pathophysiological mechanism is unknown. We aimed at investigating the genetic variants that might contribute to susceptibility to NCIPH. METHODS In this case-control study, we analyzed genes associated with microangiopathy-VWF-ADAMTS13 (von Willebrand factor and its cleavase enzyme - a disintegrin and matrix metalloprotease with thrombospondin type-1 motifs member 13) and alternative complement system vitamin B12 metabolism and with familial NCIPH. RESULT Eighty-four Indian patients with liver biopsy-proven NCIPH (cases) and 103 healthy controls (matched for residential region of India) were included in the study. Targeted next-generation sequencing (NGS) panel, comprising 11 genes of interest, was done on 54 cases. Genotyping of selected variants was performed in 84 cases and 103 healthy controls. We identified variants in MBL2, CD46 and VWF genes either associated or predisposing to NCIPH. We also identified a single case with a novel compound heterozygous mutation in MBL2 gene, possibly contributing to development of NCIPH. CONCLUSION In this first of a kind comprehensive gene panel study, multiple variants of significance have been noted, especially in ADAMTS13-VWF and complement pathways in NCIPH patients in India. Functional significance of these variants needs to be further studied.
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Affiliation(s)
- Rekha Aaron
- Wellcome Trust Research Laboratory, Division of GI Sciences, Christian Medical College, Vellore, 632 004, India
| | - Kalpana Premkumar
- Wellcome Trust Research Laboratory, Division of GI Sciences, Christian Medical College, Vellore, 632 004, India
| | - Aaron Chapla
- Department of Endocrinology, Christian Medical College, Vellore, 632 004, India
| | - B Vijayalekshmi
- Wellcome Trust Research Laboratory, Division of GI Sciences, Christian Medical College, Vellore, 632 004, India
| | - Uday Zachariah
- Department of Hepatology, Christian Medical College, Vellore, 632 004, India
| | - Elwyn Elias
- Department of Hepatology, Christian Medical College, Vellore, 632 004, India
| | | | - Dolly Daniel
- Department of Transfusion Medicine and Immuno-Haematology, Christian Medical College, Vellore, 632 004, India
| | - John Jude
- Department of Transfusion Medicine and Immuno-Haematology, Christian Medical College, Vellore, 632 004, India
- Department of Microbiology, Christian Medical College, Vellore, 632 004, India
| | - K A Balasubramanian
- Wellcome Trust Research Laboratory, Division of GI Sciences, Christian Medical College, Vellore, 632 004, India
| | - Sukesh C Nair
- Department of Pathology, Christian Medical College, Vellore, 632 004, India
| | - Nihal Thomas
- Department of Endocrinology, Christian Medical College, Vellore, 632 004, India
| | - Banumathi Ramakrishna
- Department of Pathology, Christian Medical College, Vellore, 632 004, India
- Department of Pathology, SRM Institutes for Medical Science, Chennai, 600 083, India
| | - C E Eapen
- Department of Hepatology, Christian Medical College, Vellore, 632 004, India
| | - Ashish Goel
- Department of Hepatology, Christian Medical College, Vellore, 632 004, India.
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Grigalionienė K, Burnytė B, Ambrozaitytė L, Utkus A. Wide diagnostic and genotypic spectrum in patients with suspected mitochondrial disease. Orphanet J Rare Dis 2023; 18:307. [PMID: 37784170 PMCID: PMC10544509 DOI: 10.1186/s13023-023-02921-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Mitochondrial Diseases (MDs) are a diverse group of neurometabolic disorders characterized by impaired mitochondrial oxidative phosphorylation and caused by pathogenic variants in more than 400 genes. The implementation of next-generation sequencing (NGS) technologies helps to increase the understanding of molecular basis and diagnostic yield of these conditions. The purpose of the study was to investigate diagnostic and genotypic spectrum in patients with suspected MD. The comprehensive analysis of mtDNA variants using Sanger sequencing was performed in the group of 83 unrelated individuals with clinically suspected mitochondrial disease. Additionally, targeted next generation sequencing or whole exome sequencing (WES) was performed for 30 patients of the study group. RESULTS The overall diagnostic rate was 21.7% for the patients with suspected MD, increasing to 36.7% in the group of patients where NGS methods were applied. Mitochondrial disease was confirmed in 11 patients (13.3%), including few classical mitochondrial syndromes (MELAS, MERRF, Leigh and Kearns-Sayre syndrome) caused by pathogenic mtDNA variants (8.4%) and MDs caused by pathogenic variants in five nDNA genes. Other neuromuscular diseases caused by pathogenic variants in seven nDNA genes, were confirmed in seven patients (23.3%). CONCLUSION The wide spectrum of identified rare mitochondrial or neurodevelopmental diseases proves that MD suspected patients would mostly benefit from an extensive genetic profiling allowing rapid diagnostics and improving the care of these patients.
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Affiliation(s)
- Kristina Grigalionienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania.
| | - Birutė Burnytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
| | - Laima Ambrozaitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
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Li C, Ma L, Zou D, Zhang R, Bai X, Li L, Wu G, Huang T, Zhao W, Jin E, Bao Y, Song S. RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning. Genomics Proteomics Bioinformatics 2023; 21:1066-1079. [PMID: 37898309 PMCID: PMC10928372 DOI: 10.1016/j.gpb.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
The Resource for Coronavirus 2019 (RCoV19) is an open-access information resource dedicated to providing valuable data on the genomes, mutations, and variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This model now features an automated integration pipeline and optimized curation rules, enabling efficient daily updates of data in RCoV19. Secondly, we have developed a global and regional lineage evolution monitoring platform, alongside an outbreak risk pre-warning system. These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns, enabling better preparedness and response strategies. Thirdly, we have developed a powerful interactive mutation spectrum comparison module. This module allows users to compare and analyze mutation patterns, assisting in the detection of potential new lineages. Furthermore, we have incorporated a comprehensive knowledgebase on mutation effects. This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations. In summary, RCoV19 serves as a vital scientific resource, providing access to valuable data, relevant information, and technical support in the global fight against COVID-19. The complete contents of RCoV19 are available to the public at https://ngdc.cncb.ac.cn/ncov/.
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Affiliation(s)
- Cuiping Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lina Ma
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Rongqin Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Bai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lun Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Gangao Wu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianhao Huang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enhui Jin
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuhui Song
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
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Ashrafi M, Kameli R, Hosseinpour S, Razmara E, Zamani Z, Rezaei Z, Mashayekhi R, Pak N, Barzegar M, Azizimalamiri R, Kashani MR, Khosroshahi N, Rasulinezhad M, Heidari M, Amanat M, Abdi A, Mohammadi B, Mohammadi M, Zamani GR, Badv RS, Omrani A, Nikbakht S, Bereshneh AH, Movahedinia M, Moghaddam HF, Ardakani HS, Akbari MG, Tousi MB, Shahi MV, Hosseini F, Amouzadeh MH, Hosseini SA, Nikkhah A, Khajeh A, Alizadeh H, Yarali B, Rohani M, Karimi P, Elahi HML, Hosseiny SMM, Sadeghzadeh MS, Mohebbi H, Moghadam MH, Aryan H, Vahidnezhad H, Soveizi M, Rabbani B, Rabbani A, Mahdieh N, Garshasbi M, Tavasoli AR. High genetic heterogeneity of leukodystrophies in Iranian children: the first report of Iranian Leukodystrophy Registry. Neurogenetics 2023; 24:279-289. [PMID: 37597066 DOI: 10.1007/s10048-023-00730-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
Leukodystrophies (LDs) are a heterogeneous group of progressive neurological disorders and characterized by primary involvement of white matter of the central nervous system (CNS). This is the first report of the Iranian LD Registry database to describe the clinical, radiological, and genomic data of Persian patients with leukodystrophies. From 2016 to 2019, patients suspicious of LDs were examined followed by a brain magnetic resonance imaging (MRI). A single gene testing or whole-exome sequencing (WES) was used depending on the neuroradiologic phenotypes. In a few cases, the diagnosis was made by metabolic studies. Based on the MRI pattern, diagnosed patients were divided into cohorts A (hypomyelinating LDs) versus cohort B (Other LDs). The most recent LD classification was utilized for classification of diagnosed patients. For novel variants, in silico analyses were performed to verify their pathogenicity. Out of 680 registered patients, 342 completed the diagnostic evaluations. In total, 245 patients met a diagnosis which in turn 24.5% were categorized in cohort A and the remaining in cohort B. Genetic tests revealed causal variants in 228 patients consisting of 213 variants in 110 genes with 78 novel variants. WES and single gene testing identified a causal variant in 65.5% and 34.5% cases, respectively. The total diagnostic rate of WES was 60.7%. Lysosomal disorders (27.3%; GM2-gangliosidosis-9.8%, MLD-6.1%, KD-4.5%), amino and organic acid disorders (17.15%; Canavan disease-4.5%, L-2-HGA-3.6%), mitochondrial leukodystrophies (12.6%), ion and water homeostasis disorders (7.3%; MLC-4.5%), peroxisomal disorders (6.5%; X-ALD-3.6%), and myelin protein disorders (3.6%; PMLD-3.6%) were the most commonly diagnosed disorders. Thirty-seven percent of cases had a pathogenic variant in nine genes (ARSA, HEXA, ASPA, MLC1, GALC, GJC2, ABCD1, L2HGDH, GCDH). This study highlights the most common types as well as the genetic heterogeneity of LDs in Iranian children.
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Affiliation(s)
- Mahmoudreza Ashrafi
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Reyhaneh Kameli
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Sareh Hosseinpour
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Ehsan Razmara
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Zahra Zamani
- MD, MPH, Community Medicine Specialist, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Rezaei
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Raziyeh Mashayekhi
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Neda Pak
- Department of Radiology, Children's Hospital Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Barzegar
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Nahideh Khosroshahi
- Department of Pediatric Neurology, Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Rasulinezhad
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Morteza Heidari
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Man Amanat
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Alireza Abdi
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Bahram Mohammadi
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Mahmoud Mohammadi
- Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholam Reza Zamani
- Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shervin Badv
- Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Abdolmajid Omrani
- Division of Clinical Studies, The Persian Gulf Nuclear Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Sedigheh Nikbakht
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Ali Hosseini Bereshneh
- Prenatal Diagnosis and Genetic Research Center, Dastgheib Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mojtaba Movahedinia
- Department of Pediatric, Growth Disorders of Children Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Masood Ghahvechi Akbari
- Department of Physical Medicine and Rehabilitation, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehran Beiraghi Tousi
- Pediatric Ward, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Vafaee Shahi
- Pediatric Growth and Development Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Firouzeh Hosseini
- Department of Pediatric Neurology, Hamedan University of Medical Sciences, Hamedan, Iran
| | | | - Seyed Ahmad Hosseini
- Department of Pediatric Neurology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ali Nikkhah
- Department of Pediatric Neurology, Mofid Children Hospital, Shahid Beheshti University of Medical, Tehran, Iran
| | - Ali Khajeh
- Children and Adolescence Research Center, Zahedan University of Medical Sciences, Zahedan, 000000321469345, Iran
| | - Hooman Alizadeh
- Department of Radiology, Children's Hospital Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Yarali
- Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Rohani
- Department of Neurology, Hazrat-E-Rasool Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Parviz Karimi
- Department of Pediatric Neurology, Ilam University of Medical Sciences, Ilam, Iran
| | - Hadi Montazer Lotf Elahi
- Department of Pediatric Neurology, Imam Ali Hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Seyyed Mohamad Mahdi Hosseiny
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Masoumeh Sadat Sadeghzadeh
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran
| | - Hossein Mohebbi
- Department of Pediatric Neurology, AJA University of Medical Sciences, Tehran, Iran
| | - Maryam Hosseini Moghadam
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hajar Aryan
- Farhud Medical Genetic Laboratory, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Vahidnezhad
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Mahdieh Soveizi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Bahareh Rabbani
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Rabbani
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nejat Mahdieh
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalal-Al Ahmad Hwy, Tehran, Iran.
| | - Ali Reza Tavasoli
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, No. 61, Gharib Street, Keshavarz Blvd, Tehran, 1419733151, Iran.
- Pediatric Headache Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA.
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Waryah YM, Khidri FF, Nigar R, Devrajani T, Rajput AR, Waryah AM, Ujjan ID. Impact of ACE2 gene variations on COVID-19 pathogenicity in Pakistani patients. Saudi J Biol Sci 2023; 30:103813. [PMID: 37811480 PMCID: PMC10550763 DOI: 10.1016/j.sjbs.2023.103813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/24/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Background COVID-19, caused by the SARS-CoV-2 virus, swiftly disseminated and was declared a pandemic. Variations in the ACE2 gene can impact the virus's ability to bind to ACE2 receptor, potentially influencing an individual's susceptibility and its association with COVID-19 severity across various populations. Methods In total, 200 individuals were sequenced for the ACE2 gene and potential impact of the found variants on the ACE2 protein was assessed using in-silico tools. Results Eight variations in the ACE2 gene were identified in 27 COVID-19 patients, of which four were missense and four were intronic variants. Three variants had a MAF of < 0.01 (c.251C > T, p.Pro86Leu; 15C > G, p.S5S; and c. 91 A > G, p.Lys31Glu). A missense variant, p.Pro86Leu, C > T, TT genotype, was found in 9 out of 200 individuals with an allele frequency of 0.045 and showed a significant association with COVID-19 (P = 0.003). The heterozygous allele of 15C > G, p.S5S, was found with a frequency of 0.02 (8/400) in eight patients, and its CG genotype showed a significant association with COVID-19 (P = 0.0068). The remaining identified variants were not associated with COVID-19 susceptibility. Conclusion The ACE2 gene sequence in Pakistani individuals exhibited a low frequency of identified variants in COVID-19 patients. Overall, only two variants were associated with susceptibility to the disease, possibly contributing to Pakistan's lower COVID-19 mortality and infection rates. However, individuals carrying the mutant variant experienced more severe symptoms.
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Affiliation(s)
- Yar Muhammad Waryah
- Scientific Ophthalmic and Research Laboratory, Sindh Institute of Ophthalmology and Visual Sciences, Hyderabad 71500, Pakistan
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Feriha Fatima Khidri
- Department of Biochemistry, Bilawal Medical College, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
- Department of Molecular Biology and Genetics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Roohi Nigar
- Department of Gynecology, Bilawal Medical College, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Tarachand Devrajani
- Department of Medicine, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ali Raza Rajput
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
- Department of Molecular Biology and Genetics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ali Muhammad Waryah
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
- Department of Molecular Biology and Genetics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ikram Din Ujjan
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
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59
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Sperotto F, Gutiérrez-Sacristán A, Makwana S, Li X, Rofeberg VN, Cai T, Bourgeois FT, Omenn GS, Hanauer DA, Sáez C, Bonzel CL, Bucholz E, Dionne A, Elias MD, García-Barrio N, González TG, Issitt RW, Kernan KF, Laird-Gion J, Maidlow SE, Mandl KD, Ahooyi TM, Moraleda C, Morris M, Moshal KL, Pedrera-Jiménez M, Shah MA, South AM, Spiridou A, Taylor DM, Verdy G, Visweswaran S, Wang X, Xia Z, Zachariasse JM, Newburger JW, Avillach P. Clinical phenotypes and outcomes in children with multisystem inflammatory syndrome across SARS-CoV-2 variant eras: a multinational study from the 4CE consortium. EClinicalMedicine 2023; 64:102212. [PMID: 37745025 PMCID: PMC10511777 DOI: 10.1016/j.eclinm.2023.102212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
Background Multisystem inflammatory syndrome in children (MIS-C) is a severe complication of SARS-CoV-2 infection. It remains unclear how MIS-C phenotypes vary across SARS-CoV-2 variants. We aimed to investigate clinical characteristics and outcomes of MIS-C across SARS-CoV-2 eras. Methods We performed a multicentre observational retrospective study including seven paediatric hospitals in four countries (France, Spain, U.K., and U.S.). All consecutive confirmed patients with MIS-C hospitalised between February 1st, 2020, and May 31st, 2022, were included. Electronic Health Records (EHR) data were used to calculate pooled risk differences (RD) and effect sizes (ES) at site level, using Alpha as reference. Meta-analysis was used to pool data across sites. Findings Of 598 patients with MIS-C (61% male, 39% female; mean age 9.7 years [SD 4.5]), 383 (64%) were admitted in the Alpha era, 111 (19%) in the Delta era, and 104 (17%) in the Omicron era. Compared with patients admitted in the Alpha era, those admitted in the Delta era were younger (ES -1.18 years [95% CI -2.05, -0.32]), had fewer respiratory symptoms (RD -0.15 [95% CI -0.33, -0.04]), less frequent non-cardiogenic shock or systemic inflammatory response syndrome (SIRS) (RD -0.35 [95% CI -0.64, -0.07]), lower lymphocyte count (ES -0.16 × 109/uL [95% CI -0.30, -0.01]), lower C-reactive protein (ES -28.5 mg/L [95% CI -46.3, -10.7]), and lower troponin (ES -0.14 ng/mL [95% CI -0.26, -0.03]). Patients admitted in the Omicron versus Alpha eras were younger (ES -1.6 years [95% CI -2.5, -0.8]), had less frequent SIRS (RD -0.18 [95% CI -0.30, -0.05]), lower lymphocyte count (ES -0.39 × 109/uL [95% CI -0.52, -0.25]), lower troponin (ES -0.16 ng/mL [95% CI -0.30, -0.01]) and less frequently received anticoagulation therapy (RD -0.19 [95% CI -0.37, -0.04]). Length of hospitalization was shorter in the Delta versus Alpha eras (-1.3 days [95% CI -2.3, -0.4]). Interpretation Our study suggested that MIS-C clinical phenotypes varied across SARS-CoV-2 eras, with patients in Delta and Omicron eras being younger and less sick. EHR data can be effectively leveraged to identify rare complications of pandemic diseases and their variation over time. Funding None.
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Affiliation(s)
- Francesca Sperotto
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, United States
| | - Alba Gutiérrez-Sacristán
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, United States
| | - Simran Makwana
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, United States
| | - Xiudi Li
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Ave, Boston, MA 02115, United States
| | - Valerie N. Rofeberg
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, United States
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, United States
| | - Florence T. Bourgeois
- Department of Pediatrics, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, United States
| | - Gilbert S. Omenn
- Dept of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, & Public Health, University of Michigan, 2017 Palmer Commons, Ann Arbor, MI 48109-2218, United States
| | - David A. Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, 100-107 NCRC, 2800 Plymouth Road, Ann Arbor, MI 48109, United States
| | - Carlos Sáez
- Biomedical Data Science Lab, Instituto Universitario de Tecnologías de la Información y Comunicaciones, Universitat Politécnica de Valéncia, Camino de Vera S/N, Valencia 46022, Spain
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, United States
| | - Emily Bucholz
- Department of Cardiology, Children's Hospital Colorado, University of Colorado Anschutz, 13123 E. 16th Ave, Aurora, CO 80045, United States
| | - Audrey Dionne
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, United States
| | - Matthew D. Elias
- Division of Cardiology, The Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, United States
| | - Noelia García-Barrio
- Health Informatics, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n, Madrid 28041, Spain
| | - Tomás González González
- Health Informatics, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n, Madrid 28041, Spain
| | - Richard W. Issitt
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, Great Ormond Street, London WC1N 3JH, United Kingdom
| | - Kate F. Kernan
- Department of Critical Care Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15213, United States
| | - Jessica Laird-Gion
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, United States
| | - Sarah E. Maidlow
- Michigan Institute for Clinical and Health Research (MICHR) Informatics, University of Michigan, NCRC Bldg 400, 2800 Plymouth Road, Ann Arbor, MI 48109, United States
| | - Kenneth D. Mandl
- Computational Health Informatics Program, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, United States
| | - Taha Mohseni Ahooyi
- Department of Biomedical Health Informatics, The Children's Hospital of Philadelphia, Roberts Building, 734 Schuylkill Ave, Philadelphia, PA 19146, United States
| | - Cinta Moraleda
- Pediatric Infectious Disease Department, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n, Madrid 28041, Spain
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Pittsburgh, PA 15206, United States
| | - Karyn L. Moshal
- Department of Infectious Diseases, Great Ormond Street Hospital for Children, Great Ormond Street, London WC1N 3JH, United Kingdom
| | - Miguel Pedrera-Jiménez
- Health Informatics, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n, Madrid 28041, Spain
| | - Mohsin A. Shah
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, DRIVE, 40 Bernard St, London WC1N 1LE, United Kingdom
| | - Andrew M. South
- Department of Pediatrics-Section of Nephrology, Brenner Children’s, Wake Forest University School of Medicine, Medical Center Boulevard, Winston Salem, NC 27157, United States
| | - Anastasia Spiridou
- Data Research, Innovation and Virtual Environments, Great Ormond Street Hospital for Children, DRIVE, 40 Bernard St, London WC1N 1LE, United Kingdom
| | - Deanne M. Taylor
- Department of Biomedical Health Informatics, The Children's Hospital of Philadelphia, United States
- The Department of Pediatrics, University of Pennsylvania Perelman Medical School, 3601 Civic Center Blvd, 6032 Colket, Philadelphia, PA 19104, United States
| | - Guillaume Verdy
- IAM Unit, Bordeaux University Hospital, Place amélie rabat Léon, Bordeaux 33076, France
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Pittsburgh, PA 15206, United States
| | - Xuan Wang
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, United States
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, 3501 5th Avenue, BST-3 Suite 7014, Pittsburgh, PA 15260, United States
| | - Joany M. Zachariasse
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, United States
| | - Jane W. Newburger
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, United States
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, United States
- Computational Health Informatics Program, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, United States
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Davidson AL, Dressel U, Norris S, Canson DM, Glubb DM, Fortuno C, Hollway GE, Parsons MT, Vidgen ME, Holmes O, Koufariotis LT, Lakis V, Leonard C, Wood S, Xu Q, McCart Reed AE, Pickett HA, Al-Shinnag MK, Austin RL, Burke J, Cops EJ, Nichols CB, Goodwin A, Harris MT, Higgins MJ, Ip EL, Kiraly-Borri C, Lau C, Mansour JL, Millward MW, Monnik MJ, Pachter NS, Ragunathan A, Susman RD, Townshend SL, Trainer AH, Troth SL, Tucker KM, Wallis MJ, Walsh M, Williams RA, Winship IM, Newell F, Tudini E, Pearson JV, Poplawski NK, Mar Fan HG, James PA, Spurdle AB, Waddell N, Ward RL. The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants-a multi-site prospective cohort study. Genome Med 2023; 15:74. [PMID: 37723522 PMCID: PMC10507925 DOI: 10.1186/s13073-023-01223-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/18/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer. METHODS This multi-centre prospective study recruited 195 cancer-affected participants suspected to have a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing (WGS) and a comprehensive cancer virtual gene panel analysis were undertaken. RESULTS Pathogenic variants consistent with the presenting cancer(s) were identified in 5.1% (10/195) of participants and pathogenic variants considered secondary findings with potential risk management implications were identified in another 9.7% (19/195) of participants. Health economic analysis estimated the marginal cost per case with an actionable variant was significantly lower for upfront WGS with virtual panel ($8744AUD) compared to standard testing followed by WGS ($24,894AUD). Financial analysis suggests that national adoption of diagnostic WGS testing would require a ninefold increase in government annual expenditure compared to conventional testing. CONCLUSIONS These findings make a case for replacing conventional testing with WGS to deliver clinically important benefits for cancer patients and families. The uptake of such an approach will depend on the perspectives of different payers on affordability.
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Affiliation(s)
- Aimee L Davidson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Uwe Dressel
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Sarah Norris
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia
| | - Daffodil M Canson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Dylan M Glubb
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Cristina Fortuno
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Georgina E Hollway
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Michael T Parsons
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Miranda E Vidgen
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Amy E McCart Reed
- Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Mohammad K Al-Shinnag
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel L Austin
- Australian Genomics, Melbourne, VIC, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Elisa J Cops
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Cassandra B Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Marion T Harris
- Monash Health Familial Cancer, Monash Health, Melbourne, VIC, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Megan J Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Emilia L Ip
- Cancer Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | | | - Chiyan Lau
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genomics, Pathology Queensland, Brisbane, QLD, Australia
| | - Julia L Mansour
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Michael W Millward
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Melissa J Monnik
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia
| | - Abiramy Ragunathan
- Familial Cancer Services, The Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, NSW, Australia
| | - Rachel D Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Sharron L Townshend
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Alison H Trainer
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Simon L Troth
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Katherine M Tucker
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Mathew J Wallis
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Maie Walsh
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Rachel A Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ingrid M Winship
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
- Genomic Medicine and Familial Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Emma Tudini
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Nicola K Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Helen G Mar Fan
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Robyn L Ward
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia.
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Lamb MM, DeHority K, Russel SM, Kim S, Stack T, Mohammad I, Zeatoun A, Klatt-Cromwell C, Ebert CS, Baratta JM, Senior BA, Kimple AJ. Characteristics of olfactory dysfunction in patients with long-haul covid-19. Rhinol Online 2023; 6:30-37. [PMID: 37711977 PMCID: PMC10501207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023] Open
Abstract
Background A subset of individuals suffering from Coronavirus Disease 2019 (COVID-19) will experience ongoing symptoms that last longer than three months (i.e., long-haul COVID). This includes olfactory dysfunction (OD), which is currently estimated to occur in 1-63.5% of patients at one-year post-infection. However, OD in individuals with long-haul COVID-19 is poorly understood, and there is little information regarding how initial SARS-CoV-2 variants correlate with long-haul symptoms. In this study, we investigated the prevalence and severity of OD in patients with long-haul COVID-19 and investigated how OD severity varied with SARS-CoV-2 variants. Methods Patients were recruited from the University of North Carolina-Chapel Hill COVID Recovery Clinic. Each patient completed the University of Pennsylvania Smell Identification Test (UPSIT). The dominant strain at the time of infection was determined using the date of COVID-19 diagnosis, and Centers for Disease Control and Prevention, World Health Organization, and North Carolina Department of Health and Human Services databases. Results Nearly 85% of patients with long-haul COVID-19 reported some degree of OD, which persisted in some patients for two or more years from the date of the initial infection. There was no association between the time since COVID-19 infection and severity of OD. No difference was detected between OD in patients with long-haul COVID-19 based on the dominant variant at the time of infection (p=0.0959). Conclusion A vast majority of patients with long-haul COVID-19 had some degree of ongoing olfactory complications, although the severity of symptoms was not dependent on the dominant SARS-CoV-2 variant at the time of infection.
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Affiliation(s)
- Meredith M. Lamb
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - Kaitlyn DeHority
- Department Physical Medicine & Rehabilitation, The University of North Carolina, Chapel Hill, NC
| | - Sarah M. Russel
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - Sulgi Kim
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - Taylor Stack
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - Ibtisam Mohammad
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - Abdullah Zeatoun
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - Cristine Klatt-Cromwell
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - Charles S. Ebert
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - John M. Baratta
- Department Physical Medicine & Rehabilitation, The University of North Carolina, Chapel Hill, NC
| | - Brent A. Senior
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
| | - Adam J. Kimple
- Department of Otolaryngology – Head and Neck Surgery, The University of North Carolina, Chapel Hill, NC
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Zhan Q, Solo-Gabriele HM, Sharkey ME, Amirali A, Beaver CC, Boone MM, Comerford S, Cooper D, Cortizas EM, Cosculluela GA, Currall BB, Grills GS, Kobetz E, Kumar N, Laine J, Lamar WE, Lyu J, Mason CE, Reding BD, Roca MA, Schürer SC, Shukla BS, Solle NS, Suarez MM, Stevenson M, Tallon JJ, Thomas C, Vidović D, Williams SL, Yin X, Zarnegarnia Y, Babler KM. Correlative analysis of wastewater trends with clinical cases and hospitalizations through five dominant variant waves of COVID-19. ACS ES T Water 2023; 3:2849-2862. [PMID: 38487696 PMCID: PMC10936583 DOI: 10.1021/acsestwater.3c00032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Wastewater-based epidemiology (WBE) has been utilized to track community infections of Coronavirus Disease 2019 (COVID-19) by detecting RNA of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), within samples collected from wastewater. The correlations between community infections and wastewater measurements of the RNA can potentially change as SARS-CoV-2 evolves into new variations by mutating. This study analyzed SARS-CoV-2 RNA, and indicators of human waste in wastewater from two sewersheds of different scales (University of Miami (UM) campus and Miami-Dade County Central District wastewater treatment plant (CDWWTP)) during five internally defined COVID-19 variant dominant periods (Initial, Pre-Delta, Delta, Omicron and Post-Omicron wave). SARS-CoV-2 RNA quantities were compared against COVID-19 clinical cases and hospitalizations to evaluate correlations with wastewater SARS-CoV-2 RNA. Although correlations between documented clinical cases and hospitalizations were high, prevalence for a given wastewater SARS-CoV-2 level varied depending upon the variant analyzed. The correlative relationship was significantly steeper (more cases per level found in wastewater) for the Omicron-dominated period. For hospitalization, the relationships were steepest for the Initial wave, followed by the Delta wave with flatter slopes during all other waves. Overall results were interpreted in the context of SARS-CoV-2 virulence and vaccination rates among the community.
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Affiliation(s)
- Qingyu Zhan
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Helena Maria Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Mark E. Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Cynthia C. Beaver
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | | | - Elena M. Cortizas
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Gabriella A. Cosculluela
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Benjamin B. Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Erin Kobetz
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136 USA
| | - Walter E. Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136 USA
| | - Jiangnan Lyu
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021 USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian D. Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136 USA
| | - Matthew A. Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Stephan C. Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136 USA
- Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146 USA
| | - Bhavarth S. Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Natasha Schaefer Solle
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Maritza M. Suarez
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Mario Stevenson
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - John J. Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146 USA
| | - Collette Thomas
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Dušica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136 USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Xue Yin
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Yalda Zarnegarnia
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Kristina Marie Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
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Oboh-Imafidon MA, Torbit SM, Jacob S, Schroeter MN, Tucker AR, Ojurongbe O, Thomas BN. Severity of Schistosoma haematobium co-infection with malaria in school-children is potentially modulated by host CD14 gene variants. BMC Res Notes 2023; 16:199. [PMID: 37684680 PMCID: PMC10486024 DOI: 10.1186/s13104-023-06479-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
OBJECTIVE Schistosomiasis remains a chronic disease of global importance, especially in many rural areas of the world where co-infection with Plasmodium falciparum is common. It is critical to decipher the role of single or co-infected disease scenarios on immune system regulation in such individuals and how such co-infections can either ameliorate or complicate immune response and the consequent disease outcome. First, 10 ml of urine samples, collected between 10:00 am and 2:00 pm, was filtered for diagnosis of schistosomiasis, while egg count, indicative of disease severity, was determined by microscopy. Furthermore, genomic DNA samples extracted from dried blood spots collected on filter paper from one hundred and forty-four Schistosoma haematobium-infected school-children was tested for P. falciparum parasite positivity by an allele-specific nested-PCR analysis of merozoite surface protein (msp)-1 and -2 genes and a real-time PCR assay. In addition, among P. falciparum parasite-positive individuals, we carried out a Taqman SNP genotyping assay to extrapolate the effect of host CD14 (-159 C/T; rs2569190) genetic variants on schistosome egg count. RESULTS Of the 144 individuals recruited, P. falciparum parasite positivity with msp-1 gene were 34%, 43% and 55% for MAD20, RO33 and K1 alleles respectively. Of the co-infected individuals, CD14 genetic variants ranged from 18.8% vs 21.5%, 33.3% vs 44.4%, 9.7% vs 11.8% for single versus schistosome co-infection for the wild type (CC), heterozygous (CT) and mutant (TT) variants respectively. Though the mean egg count for co-infected individuals with CD14 wild type (33.7 eggs per 10 ml of urine) and heterozygote variants (37.5 eggs per 10 ml of urine) were lower than that of schistosome infection alone (52.48 and 48.08 eggs/10 ml of urine respectively), it lacked statistical significance (p-value 0.12 and 0.29), possibly reflecting the benefit of the CD14 activation in schistosome plus malaria co-infection and not schistosome infection alone. In addition, the lower mean egg count in co-infected individuals reveal the benefit of downstream Th1 immune response mitigated by CD14 innate activation that is absent in schistosome infection alone.
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Affiliation(s)
- Mary A Oboh-Imafidon
- Department of Biomedical Sciences, Rochester Institute of Technology, 153 Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Sabrina M Torbit
- Department of Biomedical Sciences, Rochester Institute of Technology, 153 Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Swathi Jacob
- Department of Biomedical Sciences, Rochester Institute of Technology, 153 Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Marissa N Schroeter
- Department of Biomedical Sciences, Rochester Institute of Technology, 153 Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Ashley R Tucker
- Department of Biomedical Sciences, Rochester Institute of Technology, 153 Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Olusola Ojurongbe
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Humboldt-Bayer Foundation Research Hub, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, 153 Lomb Memorial Drive, Rochester, NY, 14623, USA.
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Khalid K, Poh CL. The development of DNA vaccines against SARS-CoV-2. Adv Med Sci 2023; 68:213-226. [PMID: 37364379 PMCID: PMC10290423 DOI: 10.1016/j.advms.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND The COVID-19 pandemic exerted significant impacts on public health and global economy. Research efforts to develop vaccines at warp speed against SARS-CoV-2 led to novel mRNA, viral vectored, and inactivated vaccines being administered. The current COVID-19 vaccines incorporate the full S protein of the SARS-CoV-2 Wuhan strain but rapidly emerging variants of concern (VOCs) have led to significant reductions in protective efficacies. There is an urgent need to develop next-generation vaccines which could effectively prevent COVID-19. METHODS PubMed and Google Scholar were systematically reviewed for peer-reviewed papers up to January 2023. RESULTS A promising solution to the problem of emerging variants is a DNA vaccine platform since it can be easily modified. Besides expressing whole protein antigens, DNA vaccines can also be constructed to include specific nucleotide genes encoding highly conserved and immunogenic epitopes from the S protein as well as from other structural/non-structural proteins to develop effective vaccines against VOCs. DNA vaccines are associated with low transfection efficiencies which could be enhanced by chemical, genetic, and molecular adjuvants as well as delivery systems. CONCLUSIONS The DNA vaccine platform offers a promising solution to the design of effective vaccines. The challenge of limited immunogenicity in humans might be solved through the use of genetic modifications such as the addition of nuclear localization signal (NLS) peptide gene, strong promoters, MARs, introns, TLR agonists, CD40L, and the development of appropriate delivery systems utilizing nanoparticles to increase uptake by APCs in enhancing the induction of potent immune responses.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia.
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Malekkou A, Theodosiou A, Alexandrou A, Papaevripidou I, Sismani C, Jacobs EH, Ruijter GJ, Anastasiadou V, Ourani S, Athanasiou E, Drousiotou A, Grafakou O, Petrou PP. GAA variants associated with reduced enzymatic activity but lack of Pompe-related symptoms, incidentally identified by exome sequencing. Mol Genet Metab Rep 2023; 36:100997. [PMID: 37600231 PMCID: PMC10433214 DOI: 10.1016/j.ymgmr.2023.100997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023] Open
Abstract
Pompe disease is a rare metabolic myopathy caused by pathogenic variants affecting the activity of the lysosomal glycogen-degrading enzyme acid alpha-glucosidase (GAA). Impaired GAA function results in the accumulation of undegraded glycogen within lysosomes in multiple tissues but predominantly affects the skeletal, smooth and cardiac muscle. The degree of residual enzymatic activity appears to roughly correlate with the age of onset and the severity of the clinical symptoms. Here, we report four siblings in which the GAA variants NM_000152.5:c.2237G > C p.(Trp746Ser) and NM_000152.5:c.266G > A p.(Arg89His) were identified as an incidental finding of clinical exome sequencing. These variants are listed in the ClinVar and the Pompe disease GAA variant databases but are reported here for the first time in compound heterozygosity. All four siblings displayed normal urine tetrasaccharide levels and no clinical manifestations related to Pompe disease. Nevertheless, GAA enzymatic activity was within the range for late onset Pompe patients. Our report shows an association between a novel genotype and attenuated GAA enzymatic activity. The clinical significance can only be established by the regular monitoring of these individuals. The study highlights the major challenges for clinical care arising from incidental findings of next generation sequencing.
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Affiliation(s)
- Anna Malekkou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683 Nicosia, Cyprus
| | - Athina Theodosiou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683 Nicosia, Cyprus
| | - Angelos Alexandrou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683 Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683 Nicosia, Cyprus
| | - Carolina Sismani
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683 Nicosia, Cyprus
| | - Edwin H. Jacobs
- Center for Lysosomal and Metabolic Diseases, Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - George J.G. Ruijter
- Center for Lysosomal and Metabolic Diseases, Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Violetta Anastasiadou
- Clinical Genetics Department, Archbishop Makarios III Hospital, Korytsas 6, 2012 Nicosia, Cyprus
- Karaiskakio Foundation, P.O. Box 22680, 1523 Nicosia, Cyprus
| | - Sofia Ourani
- Clinical Genetics Department, Archbishop Makarios III Hospital, Korytsas 6, 2012 Nicosia, Cyprus
| | - Emilia Athanasiou
- Clinical Genetics Department, Archbishop Makarios III Hospital, Korytsas 6, 2012 Nicosia, Cyprus
| | - Anthi Drousiotou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683 Nicosia, Cyprus
| | - Olga Grafakou
- Inborn Errors of Metabolism Clinic, Department of Pediatrics, Archbishop Makarios III Hospital, Korytsas 6, 2012 Nicosia, Cyprus
| | - Petros P. Petrou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, 1683 Nicosia, Cyprus
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Silva HDS, Teixeira HMP, Gomes LGDS, Cruz ÁA, Alcantara-Neves NM, Barreto M, Figueiredo CA, Costa RDS. PDE4D gene variants and haplotypes are associated with asthma and atopy in Brazilian children. Immunobiology 2023; 228:152724. [PMID: 37549468 DOI: 10.1016/j.imbio.2023.152724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/20/2023] [Accepted: 07/30/2023] [Indexed: 08/09/2023]
Abstract
PDE4D (Phosphodiesterase 4D) gene encodes a hydrolase of cyclic AMP. PDE4D genetic variants have been associated with asthma susceptibility. Therefore, this study aimed to investigate the association between PDE4D variants (and haplotypes) with asthma and atopy in a Brazilian population. The study comprised 1,246 unrelated participants from the SCAALA (Social Changes Asthma and Allergy in Latin America) program. Genotyping was performed using the Illumina 2.5 Human Omni bead chip. Multivariate logistic regression was used to investigate the association between PDE4D variants and asthma/atopy phenotypes in PLINK 1.09 software. Twenty-four SNVs in PDE4D were associated with atopy or asthma. The rs6898082 (A) variant increased asthma susceptibility (OR 2.76; CI 99% 1.26-6.03) and was also related to a greater PDE4D expression in the GTEx database. Also, the variant rs6870632 was further associated with asthma in meta-analysis with a replication cohort. In addition, the variants rs75699812 (C), rs8007656 (G), and rs958851 (T) were positively associated with atopy. Moreover, these variants formed an atopy risk haplotype (OR 1.82; CI 99% 1.15-2.88). Also, these variants were related to lower levels of IL-10. Functional in silico assessment showed that some PDE4D SNVs may have an impact on gene regulation and expression. Variants in the PDE4D are positively associated with asthma and allergy markers. It is possible that these variants lead to alteration in PDE4D expression and therefore impact immunity and pulmonary function.
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Affiliation(s)
| | | | | | | | | | - Maurício Barreto
- Centro de Integração de Dados e Conhecimento para Saúde (CIDACS), Fiocruz, Salvador, Bahia, Brazil; Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil
| | | | - Ryan Dos Santos Costa
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Brazil.
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Besin V, Yulianti T, Notopuro PB, Humardani FM. Genetic Polymorphisms of Ischemic Stroke in Asians. Clin Chim Acta 2023; 549:117527. [PMID: 37666385 DOI: 10.1016/j.cca.2023.117527] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023]
Abstract
The increasing incidence of ischemic stroke emphasizes the necessity for early detection and preventive strategies. Diagnostic biomarkers currently available for ischemic stroke only become detectable shortly before the manifestation of stroke symptoms. Genetic variants associated with ischemic stroke offer a potential solution to address this diagnostic limitation. However, it is crucial to acknowledge that genetic variants cannot be modified in the same way as epigenetic changes. Nevertheless, individuals carrying risk or protective variants can modify their lifestyle to potentially influence the associated epigenetic factors. This study aims to summarize specific variants relevant to Asian populations that may aid in the early detection of ischemic stroke and explore their impact on the disease's pathophysiology. These variants give us important information about the genes that play a role in ischemic stroke by affecting things like atherosclerosis pathway, blood coagulation pathway, homocysteine metabolism, transporter function, transcription, and the activity of neurons regulation. It is important to recognize the variations in genetic variants among different ethnicities and avoid generalizing the pathogenesis of ischemic stroke.
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Affiliation(s)
- Valentinus Besin
- Faculty of Medicine, University of Surabaya, Surabaya 60292, Indonesia
| | - Trilis Yulianti
- Faculty of Medicine, Universitas Sumatera Utara, Medan 20155, Indonesia
| | - Paulus Budiono Notopuro
- Department of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Farizky Martriano Humardani
- Faculty of Medicine, University of Surabaya, Surabaya 60292, Indonesia; Magister in Biomedical Science Program, Faculty of Medicine Universitas Brawijaya, Malang 65112, Indonesia.
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Chiswell K, Zaininger L, Semsarian C. Evolution of genetic testing and gene therapy in hypertrophic cardiomyopathy. Prog Cardiovasc Dis 2023; 80:38-45. [PMID: 37137376 DOI: 10.1016/j.pcad.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
Studies over the last 30 years have identified hypertrophic cardiomyopathy (HCM) as predominantly an autosomal dominant disorder caused by disease-causing variants in genes encoding the sarcomere proteins critical for contractile function. The two most common disease genes implicated are the MYBPC3 and MYH7 genes, with disease-causing variants in these two genes accounting for 70-80% of all genotype-positive HCM patients. This increased knowledge of the genetic basis of HCM has heralded the era of precision medicine, with genetic testing leading to more improved and precise diagnosis, effective cascade genetic testing in at-risk family members, assistance with reproductive decisions, targeted therapeutics guided by both phenotype and genotype, and providing important insights into risk stratification and prognosis. Most recently, novel insights into genetic mechanisms have been elucidated, spanning non-Mendelian aetiologies, non-familial forms of HCM, and development of polygenic risk scores. These advances have laid the platform for exciting future endeavours such as newer gene therapy approaches in HCM, including gene replacement studies and genome editing approaches to ultimately cure disease. This brief review summarises the current role of genetic testing in HCM patients and families, and introduces some new mechanistic insights leading to the consideration of gene therapy approaches for HCM.
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Affiliation(s)
- Katherine Chiswell
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Louisa Zaininger
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia; Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Christopher Semsarian
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia; Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.
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69
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Ko K, Takahashi K, Ito N, Sugiyama A, Nagashima S, Miwata K, Kitahara Y, Okimoto M, Ouoba S, Akuffo GA, E B, Akita T, Takafuta T, Tanaka J. Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification. BMC Med Genomics 2023; 16:199. [PMID: 37620887 PMCID: PMC10463848 DOI: 10.1186/s12920-023-01633-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND This study aimed to compare the performance of Sanger-based SARS-CoV-2 spike gene sequencing and Next Generation Sequencing (NGS)-based full-genome sequencing for variant identification in saliva samples with low viral titer. METHODS Using 241 stocked saliva samples collected from confirmed COVID-19 patients between November 2020 and March 2022 in Hiroshima, SARS-CoV-2 spike gene sequencing (nt22735-nt23532) was performed by nested RT-PCR and Sanger platform using in-house primers. The same samples underwent full-genome sequencing by NGS using Illumina NextSeq2000. RESULTS Among 241 samples, 147 were amplified by both the Sanger and the Illumina NextSeq2000 NGS, 86 by Sanger only, and 8 were not amplified at all. The overall amplification rates of Illumina NextSeq2000 NGS and Sanger were 61% and 96.7%, respectively. At low viral titer (< 103 copies/mL), Illumina NextSeq2000 NGS provided 19.2% amplification, while Sanger was 89.7% (p < 0.0001). Both platforms identified 38 wild type, 54 Alpha variants, 84 Delta variants, and 57 Omicron variants. CONCLUSIONS Our study provided evidence to expand the capacity of Sanger-based SARS-CoV-2 spike gene sequencing for variants identification over full-genome by Illumina NextSeq2000 NGS for mass screening. Therefore, the feasible and simple Sanger-based SARS-CoV-2 spike gene sequencing is practical for the initial variants screening, which might reduce the gap between the rapid evolution of SARS-CoV-2 and its molecular surveillance.
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Affiliation(s)
- Ko Ko
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kazuaki Takahashi
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Noriaki Ito
- Hiroshima City Funairi Citizens Hospital, Hiroshima, Japan
| | - Aya Sugiyama
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Shintaro Nagashima
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kei Miwata
- Hiroshima City Funairi Citizens Hospital, Hiroshima, Japan
| | | | - Mafumi Okimoto
- Hiroshima City Funairi Citizens Hospital, Hiroshima, Japan
| | - Serge Ouoba
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
- Unité de Recherche Clinique de Nanoro (URCN), Institut de Recherche en Science de La Santé (IRSS), Nanoro, Burkina Faso
| | - Golda Ataa Akuffo
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Bunthen E
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
- Payment Certification Agency (PCA), Ministry of Health, Phnom Penh, Cambodia
| | - Tomoyuki Akita
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | | | - Junko Tanaka
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
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Payot M, Monseur C, Stievenart M. Primary and Secondary Variants of Callous-Unemotional Traits in Early and Middle Childhood: Distinction, Evaluation and Empathic Differences. Child Psychiatry Hum Dev 2023:10.1007/s10578-023-01576-z. [PMID: 37552334 DOI: 10.1007/s10578-023-01576-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/09/2023]
Abstract
Current literature demonstrates the relevance of considering two variants of CU traits based on high or low levels of anxiety. However, there is limited information about these variants in young community samples. The current study used cluster analyses to investigate the primary and the secondary variants of CU traits in two samples of children: preschool (N = 107; Mage = 4.95, SD = 0.62) and school-age (N = 153; Mage = 7.49, SD = 1.11). The identified clusters were compared on empathic dimensions, aggressive behavior and criteria from the "with limited prosocial emotions" specifier from the DSM-V. The primary variant was identified as early as preschool age while the secondary variant was only identified in the school-age sample. In this latter sample, the two variants did not differ on assessed variables, except for aggressive behavior. Despite the similarities between the two variants, these results suggest distinct developmental trajectories.
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Affiliation(s)
- Morgane Payot
- Research Unit for a Life-Course Perspective on Health & Education, University of Liege, Place des Orateurs, 1, 4000, Liège, Belgium.
| | - Christian Monseur
- Research Unit for a Life-Course Perspective on Health & Education, University of Liege, Place des Orateurs, 1, 4000, Liège, Belgium
| | - Marie Stievenart
- Research Unit for a Life-Course Perspective on Health & Education, University of Liege, Place des Orateurs, 1, 4000, Liège, Belgium
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Zhang F, Fu C, Deng Y, Zhang M, Peng H, Li W, Zhong J, Zhou Q, Huang L, Xiao S, Zhao J. Association of CASZ1 genetic variants with stroke risk in the Chinese population. J Stroke Cerebrovasc Dis 2023; 32:107169. [PMID: 37182340 DOI: 10.1016/j.jstrokecerebrovasdis.2023.107169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Stroke is a heterogeneous disease with multiple etiologies, placing a heavy burden on the world. Our purpose was to clarify the association between CASZ1 genetic variants and stroke risk in the Chinese population. METHODS The Agena MassARRAY platform effectively genotyped three single nucleotide polymorphisms of CASZ1 in recruited 591 stroke patients and 553 healthy controls. Logistic regression genetic models were employed to evaluate the relationship between CASZ1 polymorphisms and stroke risk through odds ratios (ORs) and 95% confidence intervals (CIs). Then, the interaction between CASZ1 variants was detected by multifactor dimensionality reduction (MDR). Moreover, functional enrichment analyses of the CASZ1 gene were performed by Metascape. RESULTS In this study, CASZ1 rs4845941 and rs778228 were significantly associated with an increased risk of stroke. In particular, the gender-stratified analysis also showed that rs778228 of CASZ1 had an association with higher stroke risk in females. The relationship between stroke susceptibility and the interaction models of rs4845941, rs778228, and rs17035539 forecasted by MDR were analyzed to improve the ability to predict stroke risk. Furthermore, we found CASZ1 and related genes might facilitate the occurrence of stroke. CONCLUSIONS This study demonstrated that CASZ1 genetic variants (rs4845941 and rs778228) contribute to the occurrence of stroke in the Chinese population, and therefore has important implications for treating and preventing stroke.
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Affiliation(s)
- Fan Zhang
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Chuanyi Fu
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Yidong Deng
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Mao Zhang
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Hao Peng
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Wenan Li
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Jian Zhong
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Qing Zhou
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Li Huang
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Shuli Xiao
- Department of Cerebrovascular disease, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China
| | - Jiannong Zhao
- Neurosurgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570311, Hainan, China; Neurosurgery, Hainan Medical University, Haikou 571199, Hainan, China.
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Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. COVID-19 annual update: a narrative review. Hum Genomics 2023; 17:68. [PMID: 37488607 PMCID: PMC10367267 DOI: 10.1186/s40246-023-00515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world's response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- University of Florence, 50121, Florence, Italy
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | | | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Florence, Italy
- Institute of Clinical Physiology - National Council of Research (IFC-CNR), 56124, Pisa, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Instituto Gonçalo MonizFundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Gregg S Gonsalves
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
- IRCCS Neuromed, 86077, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, 89557, Reno, NV, USA.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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Haycroft ER, Davis SK, Ramanathan P, Lopez E, Purcell RA, Tan LL, Pymm P, Wines BD, Hogarth PM, Wheatley AK, Juno JA, Redmond SJ, Gherardin NA, Godfrey DI, Tham WH, Selva KJ, Kent SJ, Chung AW. Antibody Fc-binding profiles and ACE2 affinity to SARS-CoV-2 RBD variants. Med Microbiol Immunol 2023:10.1007/s00430-023-00773-w. [PMID: 37477828 PMCID: PMC10372118 DOI: 10.1007/s00430-023-00773-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
Emerging SARS-CoV-2 variants, notably Omicron, continue to remain a formidable challenge to worldwide public health. The SARS-CoV-2 receptor-binding domain (RBD) is a hotspot for mutations, reflecting its critical role at the ACE2 interface during viral entry. Here, we comprehensively investigated the impact of RBD mutations, including 5 variants of concern (VOC) or interest-including Omicron (BA.2)-and 33 common point mutations, both on IgG recognition and ACE2-binding inhibition, as well as FcγRIIa- and FcγRIIIa-binding antibodies, in plasma from two-dose BNT162b2-vaccine recipients and mild-COVID-19 convalescent subjects obtained during the first wave using a custom-designed bead-based 39-plex array. IgG-recognition and FcγR-binding antibodies were decreased against the RBD of Beta and Omicron, as well as point mutation G446S, found in several Omicron sub-variants as compared to wild type. Notably, while there was a profound decrease in ACE2 inhibition against Omicron, FcγR-binding antibodies were less affected, suggesting that Fc functional antibody responses may be better retained against the RBD of Omicron in comparison to neutralization. Furthermore, while measurement of RBD-ACE2-binding affinity via biolayer interferometry showed that all VOC RBDs have enhanced affinity to human ACE2, we demonstrate that human ACE2 polymorphisms, E35K (rs1348114695) has reduced affinity to VOCs, while K26R (rs4646116) and S19P (rs73635825) have increased binding kinetics to the RBD of VOCs, potentially affecting virus-host interaction and, thereby, host susceptibility. Collectively, our findings provide in-depth coverage of the impact of RBD mutations on key facets of host-virus interactions.
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Affiliation(s)
- Ebene R Haycroft
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Samantha K Davis
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Pradhipa Ramanathan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Ester Lopez
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Ruth A Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Li Lynn Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
| | - Phillip Pymm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bruce D Wines
- Immune Therapies Group, Burnet Institute, Melbourne, VIC, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - P Mark Hogarth
- Immune Therapies Group, Burnet Institute, Melbourne, VIC, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Samuel J Redmond
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kevin John Selva
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia.
| | - Stephen J Kent
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia.
- Melbourne Sexual Health Centre, Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
| | - Amy W Chung
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia.
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Gyöngyösi E, László B, Szalmás A, Kónya J, Veress G. Transcriptional activity of the long control region in human papillomavirus type 33 intratype variants. Virol J 2023; 20:152. [PMID: 37461035 DOI: 10.1186/s12985-023-02114-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND High-risk human papillomaviruses (HPVs) are responsible for the development of cervical and other anogenital cancers. Intratype sequence variants of certain high-risk HPV types (e.g. 16, 18 and 31) are thought to have different oncogenic potential, partly due to nucleotide sequence variation in the viral long control region (LCR). The LCR has an important role in the regulation of viral replication and transcription. The purpose of this study was to explore sequence variation in the LCR of HPV 33 intratype variants in Hungary and to see whether there are differences in the transcriptional activities of the variants. METHODS The complete HPV 33 LCR was amplified from HPV 33 positive cervical samples. After sequencing the LCR variants, multiple sequence alignment and phylogenetic analyses were carried out. Representative HPV 33 LCR sequence variants were selected for cloning and functional analysis. After transient transfection of HeLa cells, luciferase reporter assays were used to analyse the transcriptional activities of different LCR variants. RESULTS Altogether 10 different variants were identified by sequence analysis of the HPV 33 LCR. The results of phylogenetic analysis showed that 3 variants belonged to sublineage A1, while the other 7 variants clustered with sublineage A2. Variants belonging to sublineage A2 had significantly lower transcriptional activities than variants belonging to sublineage A1. Within sublineage A2, the two variants analysed had significantly different transcriptional activities, which was shown to be caused by the A7879G variation. CONCLUSIONS Nucleotide variation in the HPV 33 LCR can result in altered transcriptional activity of the intratype variants. Our results can help to understand the correlation between LCR polymorphism and the oncogenic potential of HPV 33 variants.
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Affiliation(s)
- Eszter Gyöngyösi
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Brigitta László
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Anita Szalmás
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - József Kónya
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - György Veress
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.
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75
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Hong J, Park AK, Radnaabaatar M, Kim EJ, Kim DW, Jung J. The Impact of Entry Restrictions on the Spread of Severe Acute Respiratory Syndrome Coronavirus Variants Between 2021 and 2022. J Korean Med Sci 2023; 38:e223. [PMID: 37463690 DOI: 10.3346/jkms.2023.38.e223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/25/2023] [Indexed: 07/20/2023] Open
Abstract
To contain the surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the South Korean government has implemented non-pharmacological interventions as well as border restrictions. The efficacy of entry restrictions should be evaluated to facilitate their preparation for new variants of SARS-CoV-2. This study explored the impact of border policy changes on overseas entrants and local cases of SARS-CoV-2 variants. Data from the Korea Disease Control and Prevention Agency randomly collected between April 11, 2021 and August 20, 2022 were evaluated using the Granger causality model. The results showed that the outbreak gap of delta variants between international and domestic cases was 10 weeks, while that of omicron variants was approximately 2 weeks, meaning that the quarantine policy helped contain delta variants rather than more transmissible variants. It is recommended that countries implement quarantine policies based on particular purposes accounting for the specific features of different variants to avoid potential negative impacts on the economy.
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Affiliation(s)
- Jinwook Hong
- Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
- Department of Preventive Medicine, Gachon University College of Medicine, Incheon, Korea
| | - Ae Kyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Munkhzul Radnaabaatar
- Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Dong Wook Kim
- Department of Information and Statistics, Research Institute of Natural Science, Gyeongsang National University, Jinju, Korea
- Department of Bio & Medical Bigdata (BK21 Plus), Gyeongsang National University, Jinju, Korea.
| | - Jaehun Jung
- Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
- Department of Preventive Medicine, Gachon University College of Medicine, Incheon, Korea.
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Haque R, Hossain ME, Miah M, Rahman M, Amin N, Rahman Z, Islam MS, Rahman MZ. Monitoring SARS-CoV-2 variants in wastewater of Dhaka City, Bangladesh: approach to complement public health surveillance systems. Hum Genomics 2023; 17:58. [PMID: 37420264 PMCID: PMC10326934 DOI: 10.1186/s40246-023-00505-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Wastewater-based epidemiological surveillance has been considered a powerful tool for early detection and monitoring of the dynamics of SARS-CoV-2 and its lineages circulating in a community. This study is aimed to investigate the complexity of SARS-CoV-2 infection dynamics in Dhaka city by examining its genetic variants in wastewater. Also, the study seeks to determine a connection between the SARS-CoV-2 variations detected in clinical testing and those found in wastewater samples. RESULTS Out of 504 samples tested in RT-qPCR, 185 (36.7%) tested positive for SARS-CoV-2 viral RNA. The median log10 concentration of SARS-CoV-2 N gene copies/Liter of wastewater (gc/L) was 5.2, and the median log10 concentration of ORF1ab was 4.9. To further reveal the genetic diversity of SARS-CoV-2, ten samples with ORF1ab real-time RT-PCR cycle threshold (Ct) values ranging from 28.78 to 32.13 were subjected to whole genome sequencing using nanopore technology. According to clade classification, sequences from wastewater samples were grouped into 4 clades: 20A, 20B, 21A, 21J, and the Pango lineage, B.1, B.1.1, B.1.1.25, and B.1.617.2, with coverage ranging from 94.2 to 99.8%. Of them, 70% belonged to clade 20B, followed by 10% to clade 20A, 21A, and 21J. Lineage B.1.1.25 was predominant in Bangladesh and phylogenetically related to the sequences from India, the USA, Canada, the UK, and Italy. The Delta variant (B.1.617.2) was first identified in clinical samples at the beginning of May 2021. In contrast, we found that it was circulating in the community and was detected in wastewater in September 2020. CONCLUSION Environmental surveillance is useful for monitoring temporal and spatial trends of existing and emerging infectious diseases and supports evidence-based public health measures. The findings of this study supported the use of wastewater-based epidemiology and provided the baseline data for the dynamics of SARS-CoV-2 variants in the wastewater environment in Dhaka, Bangladesh.
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Affiliation(s)
- Rehnuma Haque
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh.
- Department of Women's and Children's Health, Uppsala University, Akademiska Sjukhuset, 75185, Uppsala, Sweden.
| | - Mohammad Enayet Hossain
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mojnu Miah
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Nuhu Amin
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
- Institute for Sustainable Futures, The University of Technology Sydney, 235 Jones St, Ultimo, NSW, 2007, Australia
| | - Ziaur Rahman
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Shariful Islam
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
- The School of Public Health, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mohammed Ziaur Rahman
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
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Yuan LJ, Li XY, Ye F, Li XY, Li QQ, Zhong YS, Wang SY, Wang YH, Hu GX, Cai JP, Li JW. Enzymatic activity of 38 CYP2C9 genotypes on ibuprofen. Food Chem Toxicol 2023:113926. [PMID: 37406757 DOI: 10.1016/j.fct.2023.113926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND AND OBJECTIVE Ibuprofen, a common non-steroidal anti-inflammatory drug, is used clinically for pain relief and antipyretic treatment worldwide. However, regular or long-term use of ibuprofen may lead to a series of adverse reactions, including gastrointestinal bleeding, hypertension and kidney injury. Previous studies have shown that CYP2C9 gene polymorphism plays an important role in the elimination of various drugs, which leads to the variation in drug efficacy. This study aimed to evaluate the effect of 38 CYP2C9 genotypes on ibuprofen metabolism. METHODS Thirty-eight recombinant human CYP2C9 microsomal enzymes were obtained using a frugiperda 21 insect expression system according to a previously described method. Assessment of the catalytic function of these variants was completed via a mature incubation system: 5 pmol CYP2C9*1 and 38 CYP2C9 variants recombinant human microsomes, 5 μL cytochrome B5, ibuprofen (5-1000 μM), and Tris-HCl buffer (pH 7.4). The ibuprofen metabolite contents were determined using HPLC analysis. HPLC analysis included a UV detector, Plus-C18 column, and mobile phase [50% acetonitrile and 50% water (containing 0.05% trifluoroacetic acid)]. The kinetic parameters of the CYP2C9 genotypes were obtained by Michaelis-Menten curve fitting. RESULTS The intrinsic clearance (CLint) of eight variants was not significantly different from CYP2C9*1; four CYP2C9 variants (CYP2C9*38, *44, *53 and *59) showed significantly higher CLint (increase by 35%-230%) than that of the wild-type; the remaining twenty-six variants exhibited significantly reduced CLint (reduced by 30%-99%) compared to that of the wild-type. CONCLUSION This is the first systematic evaluation of the catalytic characteristics of 38 CYP2C9 genotypes involved ibuprofen metabolism. Our results provide a corresponding supplement to studies on CYP2C9 gene polymorphisms and kinetic characteristics of different variants. We need to focus on poor metabolizers (PMs) with severely abnormal metabolic functions, because they are more susceptible to drug exposure.
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Affiliation(s)
- Ling-Jing Yuan
- Department of Pharmacy, Shaoxing Second Hospital, Shaoxing, Zhejiang, China; School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiang-Yu Li
- Department of Pharmacy, Shaoxing Keqiao Women & Children΄s Hospital, Shaoxing, Zhejiang, China
| | - Feng Ye
- School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xin-Yue Li
- School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qing-Qing Li
- School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yun-Shan Zhong
- School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shi-Yu Wang
- School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ya-Hui Wang
- School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Guo-Xin Hu
- School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jian-Ping Cai
- The Ministry of Health (MOH) Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, PR China.
| | - Jun-Wei Li
- School of Pharmaceutical Sciences, School of Pharmacy of Wenzhou Medical University, Wenzhou, Zhejiang, China.
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Herregods N, Anisau A, Schiettecatte E, Vereecke E, Morbée L, Laloo F, Jaremko JL, Jans L. MRI in pediatric sacroiliitis, what radiologists should know. Pediatr Radiol 2023; 53:1576-1586. [PMID: 36856758 DOI: 10.1007/s00247-023-05602-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/21/2022] [Accepted: 01/11/2023] [Indexed: 03/02/2023]
Abstract
MRI is used for early detection of inflammation of sacroiliac joints as it shows active lesions of sacroiliitis long before radiographs show damage to the sacroiliac joints. Early diagnosis of arthritis allows early treatment of inflammation and can help delay disease progression and prevent irreversible damage. Also, early identification of axial involvement in juvenile spondyloarthropathy is crucial, as treatment options are different than for peripheral juvenile spondyloarthropathy. In general, standard sequences used in adults are also applied to children. However, interpreting MR images of pediatric sacroiliac joints is more challenging than in adults, because of normal physiological changes during skeletal maturation, which can simulate disease on MR images. Furthermore, classical definitions of sacroiliitis used in adults, for both active inflammatory and structural lesions, can be difficult to extrapolate to children. The development of reliable pediatric-specific definitions for sacroiliitis is still in active study. Understanding both normal and pathological signal changes in children is important to distinguish physiologic findings from disease and to make a correct diagnosis. In this review, the main imaging characteristics of sacroiliitis on MRI in children and its frequent pitfalls will be illustrated, while also citing some discussion points regarding the scan protocol.
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Affiliation(s)
- Nele Herregods
- Department of Radiology and Nuclear Medicine, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium.
| | - Aliaksandr Anisau
- Department of Radiology and Nuclear Medicine, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium
| | - Eva Schiettecatte
- Department of Radiology and Nuclear Medicine, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium
| | - Elke Vereecke
- Department of Radiology and Nuclear Medicine, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium
| | - Lieve Morbée
- Department of Radiology and Nuclear Medicine, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium
| | - Frederiek Laloo
- Department of Radiology and Nuclear Medicine, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium
| | - Jacob L Jaremko
- Department of Radiology & Diagnostic Imaging, University of Alberta, 8440-112 Street, EdmontonAlberta, T6G 2B7, Canada
- Medical Imaging Consultants, Edmonton, AB, Canada
| | - Lennart Jans
- Department of Radiology and Nuclear Medicine, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium
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Feris F, Ghusn W, Campos A, Cifuentes L, De la Rosa A, Sacoto D, Fansa S, Anazco D, Hurtado MD, Bublitz JT, Abu Dayyeh BK, Ghanem OM, Kellogg TA, Olson J, Camilleri M, Acosta A. The Effect of Heterozygous Gene Variants of the Leptin-Melanocortin Pathway on Weight Loss Following Sleeve Gastrectomy. Obes Surg 2023; 33:2246-2249. [PMID: 37166737 DOI: 10.1007/s11695-023-06604-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Affiliation(s)
- Fauzi Feris
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Wissam Ghusn
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Alejandro Campos
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Lizeth Cifuentes
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Alan De la Rosa
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Daniel Sacoto
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Sima Fansa
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Diego Anazco
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Maria Daniela Hurtado
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Department of Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Joshua T Bublitz
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Barham K Abu Dayyeh
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Omar M Ghanem
- Division of Endocrine & Metabolic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Todd A Kellogg
- Division of Endocrine & Metabolic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Janet Olson
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Michael Camilleri
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA
| | - Andres Acosta
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-142, 200 First St. S.W., Rochester, MN, 55902, USA.
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80
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Karam G, Molaro A. Casting histone variants during mammalian reproduction. Chromosoma 2023:10.1007/s00412-023-00803-9. [PMID: 37347315 PMCID: PMC10356639 DOI: 10.1007/s00412-023-00803-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
Abstract
During mammalian reproduction, germ cell chromatin packaging is key to prepare parental genomes for fertilization and to initiate embryonic development. While chromatin modifications such as DNA methylation and histone post-translational modifications are well known to carry regulatory information, histone variants have received less attention in this context. Histone variants alter the stability, structure and function of nucleosomes and, as such, contribute to chromatin organization in germ cells. Here, we review histone variants expression dynamics during the production of male and female germ cells, and what is currently known about their parent-of-origin effects during reproduction. Finally, we discuss the apparent conundrum behind these important functions and their recent evolutionary diversification.
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Affiliation(s)
- Germaine Karam
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Antoine Molaro
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
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81
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Senthilazhagan K, Sakthimani S, Kallanja D, Venkataraman S. SARS-CoV-2: analysis of the effects of mutations in non-structural proteins. Arch Virol 2023; 168:186. [PMID: 37344726 DOI: 10.1007/s00705-023-05818-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
A worldwide pandemic that started in China in late 2019 was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded RNA virus belonging to the family Coronaviridae. Due to its structural variability and mutability, this virus continues to evolve and pose a major health threat around the world. Its characteristics, such as transmissibility, antigenicity, and resistance to drugs and vaccines, are continually altered through mutations. Examining mutational hotspots and their structural repercussions can thus aid in the development of more-effective vaccinations and treatment plans. In this study, we used full genome sequences of SARS-CoV-2 variants to predict structural changes in viral proteins. These sequences were obtained from the Global Initiative on Sharing Avian Influenza Data (GISAID), and a set of significant mutations were identified in each of the non-structural proteins (NSP1-16) and structural proteins, including the envelope, nucleocapsid, membrane, and spike proteins. The mutations were characterized as stabilizing or destabilizing based on their effect on protein dynamics and stability, and their impact on structure and function was evaluated. Among all of the proteins, NSP6 stands out as especially variable. The results of this study augment our understanding of how mutational events influence virus pathogenicity and evolution.
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Affiliation(s)
- Kavya Senthilazhagan
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Seshagiri Sakthimani
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Deepthi Kallanja
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Sangita Venkataraman
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India.
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82
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Bunce M, Geoghegan JL, Winter D, de Ligt J, Wiles S. Exploring the depth and breadth of the genomics toolbox during the COVID-19 pandemic: insights from Aotearoa New Zealand. BMC Med 2023; 21:213. [PMID: 37316857 DOI: 10.1186/s12916-023-02909-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/13/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Genomic technologies have become routine in the surveillance and monitoring of the coronavirus disease 2019 (COVID-19) pandemic, as evidenced by the millions of SARS-CoV-2 sequences uploaded to international databases. Yet the ways in which these technologies have been applied to manage the pandemic are varied. MAIN TEXT Aotearoa New Zealand was one of a small number of countries to adopt an elimination strategy for COVID-19, establishing a managed isolation and quarantine system for all international arrivals. To aid our response, we rapidly set up and scaled our use of genomic technologies to help identify community cases of COVID-19, to understand how they had arisen, and to determine the appropriate action to maintain elimination. Once New Zealand pivoted from elimination to suppression in late 2021, our genomic response changed to focusing on identifying new variants arriving at the border, tracking their incidence around the country, and examining any links between specific variants and increased disease severity. Wastewater detection, quantitation and variant detection were also phased into the response. Here, we explore New Zealand's genomic journey through the pandemic and provide a high-level overview of the lessons learned and potential future capabilities to better prepare for future pandemics. CONCLUSIONS Our commentary is aimed at health professionals and decision-makers who might not be familiar with genetic technologies, how they can be used, and why this is an area with great potential to assist in disease detection and tracking now and in the future.
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Affiliation(s)
- Michael Bunce
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand
- Department of Conservation, Wellington, 6011, New Zealand
| | - Jemma L Geoghegan
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - David Winter
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand.
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.
- Te Pūnaha Matatini, Auckland, New Zealand.
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83
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Gabbert C, Schaake S, Lüth T, Much C, Klein C, Aasly JO, Farrer MJ, Trinh J. GBA1 in Parkinson's disease: variant detection and pathogenicity scoring matters. BMC Genomics 2023; 24:322. [PMID: 37312046 DOI: 10.1186/s12864-023-09417-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND GBA1 variants are the strongest genetic risk factor for Parkinson's disease (PD). However, the pathogenicity of GBA1 variants concerning PD is still not fully understood. Additionally, the frequency of GBA1 variants varies widely across populations. OBJECTIVES To evaluate Oxford Nanopore sequencing as a strategy, to determine the frequency of GBA1 variants in Norwegian PD patients and controls, and to review the current literature on newly identified variants that add to pathogenicity determination. METHODS We included 462 Norwegian PD patients and 367 healthy controls. We sequenced the full-length GBA1 gene on the Oxford Nanopore GridION as an 8.9 kb amplicon. Six analysis pipelines were compared using two aligners (NGMLR, Minimap2) and three variant callers (BCFtools, Clair3, Pepper-Margin-Deepvariant). Confirmation of GBA1 variants was performed by Sanger sequencing and the pathogenicity of variants was evaluated. RESULTS We found 95.8% (115/120) true-positive GBA1 variant calls, while 4.2% (5/120) variant calls were false-positive, with the NGMLR/Minimap2-BCFtools pipeline performing best. In total, 13 rare GBA1 variants were detected: two were predicted to be (likely) pathogenic and eleven were of uncertain significance. The odds of carrying one of the two common GBA1 variants, p.L483P or p.N409S, in PD patients were estimated to be 4.11 times the odds of carrying one of these variants in controls (OR = 4.11 [1.39, 12.12]). CONCLUSIONS In conclusion, we have demonstrated that Oxford long-read Nanopore sequencing, along with the NGMLR/Minimap2-BCFtools pipeline is an effective tool to investigate GBA1 variants. Further studies on the pathogenicity of GBA1 variants are needed to assess their effect on PD.
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Affiliation(s)
- Carolin Gabbert
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Theresa Lüth
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Christoph Much
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany
| | - Jan O Aasly
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthew J Farrer
- Department of Neurology, University of Florida, Gainesville, FL, USA
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany.
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84
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Sidhwani SK, Mirza T, Khatoon A, Shaikh F, Khan R, Shaikh OA, Nashwan AJ. Angiotensin-converting enzyme 2 (ACE2) polymorphisms and susceptibility of severe SARS-CoV-2 in a subset of Pakistani population. Virol J 2023; 20:120. [PMID: 37308887 DOI: 10.1186/s12985-023-02091-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/02/2023] [Indexed: 06/14/2023] Open
Abstract
Science is digging for the varied presentation of COVID-19 patients exposed to the same risk factors, and medical conditions may be influenced by the presence of polymorphic genetic variants. This study investigated the link between ACE2 gene polymorphisms and the severity of SARS-CoV-2. This cross-sectional study recruited COVID-19 PCR-positive patients by consecutive sampling from Ziauddin Hospital from April to September 2020. DNA was extracted from whole blood, followed by gene amplification and Sanger's sequencing. Most of the patients, 77: 53.8%, were serious. Males were higher (80; 55.9%) with age more than 50 years (106: 74.1%). We found 22 ACE2 SNPs. rs2285666 SNP was most prevalent with 49.2% CC, 45.2% TT, 4.8% CT heterozygosity, and 0.8% AA genotypes. Variants with multiple genotypes were also insignificantly associated with the severity of COVID-19 in the analysis of the dominant model. Only rs2285666 had a significant statistical link with gender (p-value 0.034, OR; 1.438, CI; 1.028-2.011) while rs768883316 with age groups (p-value 0.026, OR; 1.953, CI; 1.085-3.514). Haplotypes ATC of three polymorphisms (rs560997634, rs201159862, and rs751170930) commonly found in 120 (69.77%) and TTTGTAGTTAGTA haplotype consisting of 13 polymorphisms (rs756737634, rs146991645, rs1601703288, rs1927830489, rs1927831624, rs764947941, rs752242172, rs73195521, rs781378335, rs756597390, rs780478736, rs148006212, rs768583671) in 112 (90.32%) had statistically significant association with the severity having p = value 0.029 and 0.001 respectively. Males of old age and diabetics are found to have more severe COVID-19 infection in the current study. We also found that common ACE2 polymorphism rs2285666 influences the susceptibility of acquiring the severe SARS-CoV-2 infection.
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Affiliation(s)
| | - Talat Mirza
- Department of Research, Ziauddin University, Karachi, Pakistan
- Department of Molecular Medicine, Ziauddin University, Karachi, Pakistan
| | - Ambrina Khatoon
- Department of Molecular Medicine, Ziauddin University, Karachi, Pakistan.
| | - Fouzia Shaikh
- Department of Pathology, Ziauddin University, Karachi, Pakistan
| | - Rizma Khan
- Department of Molecular Genetics, Ziauddin University, Karachi, Pakistan
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85
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Ko Y, Mendoza VM, Mendoza R, Seo Y, Lee J, Jung E. Risk estimation of lifted mask mandates and emerging variants using mathematical model. Heliyon 2023; 9:e16841. [PMID: 37303548 PMCID: PMC10246937 DOI: 10.1016/j.heliyon.2023.e16841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023] Open
Abstract
Background More than half of the population in Korea had a prior COVID-19 infection. In 2022, most nonpharmaceutical interventions, except mask-wearing indoors, had been lifted. And in 2023, the indoor mask mandates were eased. Methods We developed an age-structured compartmental model that distinguishes vaccination history, prior infection, and medical staff from the rest of the population. Contact patterns among hosts were separated based on age and location. We simulated scenarios with the lifting of the mask mandate all at once or sequentially according to the locations. Furthermore, we investigated the impact of a new variant assuming that it has higher transmissibility and risk of breakthrough infection. Results We found that the peak size of administered severe patients may not exceed 1100 when the mask mandate is lifted everywhere, and 800 if the mask mandate only remains in the hospital. If the mask mandate is lifted in a sequence (except hospital), then the peak size of administered severe patients may not exceed 650. Moreover, if the new variant has both higher transmissibility and immune reduction, the effective reproductive number of the new variant is approximately 3 times higher than that of the current variant, and additional interventions may be needed to keep the administered severe patients from exceeding 2,000, which is the critical level we set. Conclusion Our findings showed that the lifting of the mask mandate, except in hospitals, would be more manageable if implemented sequentially. Considering a new variant, we found that depending on the population immunity and transmissibility of the variant, wearing masks and other interventions may be necessary for controlling the disease.
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Affiliation(s)
- Youngsuk Ko
- Department of Mathematics, Konkuk University, Seoul, South Korea
| | - Victoria May Mendoza
- Department of Mathematics, Konkuk University, Seoul, South Korea
- Institute of Mathematics, University of the Philippines Diliman, Quezon City, Philippines
| | - Renier Mendoza
- Department of Mathematics, Konkuk University, Seoul, South Korea
- Institute of Mathematics, University of the Philippines Diliman, Quezon City, Philippines
| | - Yubin Seo
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Jacob Lee
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Eunok Jung
- Department of Mathematics, Konkuk University, Seoul, South Korea
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Yu M, Lee SE, Lee HY, Kim HJ, Song YJ, Jeong J, Park AK, Kim IH, Kim EJ, Park YJ. Results of contact tracing for SARS-CoV-2 Omicron sub-lineages (BA.4, BA.5, BA.2.75) and the household secondary attack risk. Osong Public Health Res Perspect 2023; 14:173-179. [PMID: 37415434 PMCID: PMC10522828 DOI: 10.24171/j.phrp.2022.0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 03/28/2023] [Accepted: 05/01/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND This study aimed to assess the contact tracing outcomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sub-lineages BA.4, BA.5, and BA.2.75 within Republic of Korea, and to generate foundational data for responding to future novel variants. METHODS We conducted investigations and contact tracing for 79 confirmed BA.4 cases, 396 confirmed BA.5 cases, and 152 confirmed BA.2.75 cases. These cases were identified through random sampling of both domestically confirmed and imported cases, with the goal of evaluating the pattern of occurrence and transmissibility. RESULTS We detected 79 instances of Omicron sub-lineage BA.4 across a span of 46 days, 396 instances of Omicron sub-lineage BA.5 in 46 days, and 152 instances of Omicron sub-lineage BA.2.75 over 62 days. One patient with severe illness was confirmed among the BA.5 cases; however, there were no reports of severe illness in the confirmed BA.4 and BA.2.75 cases. The secondary attack risk among household contacts were 19.6% for BA.4, 27.8% for BA.5, and 24.3% for BA.2.75. No statistically significant difference was found between the Omicron sub-lineages. CONCLUSION BA.2.75 did not demonstrate a higher tendency for transmissibility, disease severity, or secondary attack risk within households when compared to BA.4 and BA.5. We will continue to monitor major SARS-CoV-2 variants, and we plan to enhance the disease control and response systems.
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Affiliation(s)
- Mi Yu
- Division of Epidemiological Investigation, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Sang-Eun Lee
- Division of Epidemiological Investigation, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Hye Young Lee
- Division of Epidemiological Investigation, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Hye-jin Kim
- Division of Epidemiological Investigation, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Yeong-Jun Song
- Division of Epidemiological Investigation, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jian Jeong
- Division of Epidemiological Investigation, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Ae Kyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Eun-jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Young-Joon Park
- Division of Epidemiological Investigation, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
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Khan M, Li L, Haak L, Payen SH, Carine M, Adhikari K, Uppal T, Hartley PD, Vasquez-Gross H, Petereit J, Verma SC, Pagilla K. Significance of wastewater surveillance in detecting the prevalence of SARS-CoV-2 variants and other respiratory viruses in the community - A multi-site evaluation. One Health 2023; 16:100536. [PMID: 37041760 PMCID: PMC10074727 DOI: 10.1016/j.onehlt.2023.100536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/13/2023] Open
Abstract
Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome in wastewater has proven to be useful for tracking the trends of virus prevalence within the community. The surveillance also provides precise and early detection of any new and circulating variants, which aids in response to viral outbreaks. Site-specific monitoring of SARS-CoV-2 variants provides valuable information on the prevalence of new or emerging variants in the community. We sequenced the genomic RNA of viruses present in the wastewater samples and analyzed for the prevalence of SARS-CoV-2 variants as well as other respiratory viruses for a period of one year to account for seasonal variations. The samples were collected from the Reno-Sparks metropolitan area on a weekly basis between November 2021 to November 2022. Samples were analyzed to detect the levels of SARS-CoV-2 genomic copies and variants identification. This study confirmed that wastewater monitoring of SARS-CoV-2 variants can be used for community surveillance and early detection of circulating variants and supports wastewater-based epidemiology (WBE) as a complement to clinical respiratory virus testing as a healthcare response effort. Our study showed the persistence of the SARS-CoV-2 virus throughout the year compared to a seasonal presence of other respiratory viruses, implicating SARS-CoV-2's broad genetic diversity and strength to persist and infect susceptible hosts. Through secondary analysis, we further identified antimicrobial resistance (AMR) genes in the same wastewater samples and found WBE to be a feasible tool for community AMR detection and monitoring.
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Affiliation(s)
- Majid Khan
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Lin Li
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Laura Haak
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Shannon Harger Payen
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Madeline Carine
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Kabita Adhikari
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Paul D. Hartley
- Nevada Genomics Center, University of Nevada, Reno, NV 89557, USA
| | - Hans Vasquez-Gross
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, USA
| | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Krishna Pagilla
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
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Fauzia KA, Aftab H, Miftahussurur M, Waskito LA, Tuan VP, Alfaray RI, Matsumoto T, Yurugi M, Subsomwong P, Kabamba ET, Akada J, Yamaoka Y. Genetic determinants of Biofilm formation of Helicobacter pylori using whole-genome sequencing. BMC Microbiol 2023; 23:159. [PMID: 37264297 DOI: 10.1186/s12866-023-02889-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Infection with Helicobacter pylori as the cause of gastric cancer is a global public health concern. In addition to protecting germs from antibiotics, biofilms reduce the efficacy of H. pylori eradication therapy. The nucleotide polymorphisms (SNPs) related with the biofilm forming phenotype of Helicobacter pylori were studied. RESULTS Fifty-six H. pylori isolate from Bangladeshi patients were included in this cross-sectional study. Crystal violet assay was used to quantify biofilm amount, and the strains were classified into high- and low-biofilm formers As a result, strains were classified as 19.6% high- and 81.4% low-biofilm formers. These phenotypes were not related to specific clades in the phylogenetic analysis. The accessories genes associated with biofilm from whole-genome sequences were extracted and analysed, and SNPs among the previously reported biofilm-related genes were analysed. Biofilm formation was significantly associated with SNPs of alpA, alpB, cagE, cgt, csd4, csd5, futB, gluP, homD, and murF (P < 0.05). Among the SNPs reported in alpB, strains encoding the N156K, G160S, and A223V mutations were high-biofilm formers. CONCLUSIONS This study revealed the potential role of SNPs in biofilm formation and proposed a method to detect mutation in biofilm from whole-genome sequences.
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Affiliation(s)
- Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Hafeza Aftab
- Department of Gastroenterology, Dhaka Medical College and Hospital, Dhaka, 1000, Bangladesh
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Langgeng Agung Waskito
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
- Department of Physiology and Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, 749000, Vietnam
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Michiyuki Yurugi
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Phawinee Subsomwong
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, 036-8562, Aomori, Japan
| | - Evariste Tshibangu Kabamba
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Research Center for Infectious Sciences, Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan.
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, 60115, Indonesia.
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, 77030, USA.
- Borneo Medical and Health Research Centre, University Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia.
- The Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu, 879-5593, Oita, Japan.
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Lu Y, Shen F, He W, Li A, Li M, Feng X, Zheng Y, Pang W. HR121 targeting HR2 domain in S2 subunit of spike protein can serve as a broad-spectrum SARS-CoV-2 inhibitor via intranasal administration. Acta Pharm Sin B 2023:S2211-3835(23)00192-2. [PMID: 37360013 PMCID: PMC10219671 DOI: 10.1016/j.apsb.2023.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
The continuously emerging SARS-CoV-2 variants pose a great challenge to the efficacy of current drugs, this necessitates the development of broad-spectrum antiviral drugs. In the previous study, we designed a recombinant protein, heptad repeat (HR) 121, as a variant-proof vaccine. Here, we found it can act as a fusion inhibitor and demonstrated broadly neutralizing activities against SARS-CoV-2 and its main variants. Structure analysis suggested that HR121 targets the HR2 domain in SARS-CoV-2 spike (S) 2 subunit to block virus-cell fusion. Functional experiments demonstrated that HR121 can bind HR2 at serological-pH and endosomal-pH, highlighting its inhibition capacity when SARS-CoV-2 enters via either cellular membrane fusion or endosomal route. Importantly, HR121 can effectively inhibit SARS-CoV-2 and Omicron variant pseudoviruses entering the cells, as well as block authentic SARS-CoV-2 and Omicron BA.2 replications in human pulmonary alveolar epithelial cells. After intranasal administration to Syrian golden hamsters, it can protect hamsters from SARS-CoV-2 and Omicron BA.2 infection. Together, our results suggest that HR121 is a potent drug candidate with broadly neutralizing activities against SARS-CoV-2 and its variants.
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Affiliation(s)
- Ying Lu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Shen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang He
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anqi Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghua Li
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Xiaoli Feng
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Yongtang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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90
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Torra-Massana M, Rodríguez A, Vassena R. Exonic genetic variants associated with unexpected fertilization failure and zygotic arrest after ICSI: a systematic review. ZYGOTE 2023:1-26. [PMID: 37212058 DOI: 10.1017/s096719942300014x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Fertilization failure (FF) and zygotic arrest after ICSI have a huge effect on both patients and clinicians, but both problems are usually unexpected and cannot be properly diagnosed. Fortunately, in recent years, gene sequencing has allowed the identification of multiple genetic variants underlying failed ICSI outcomes, but the use of this approach is still far from routine in the fertility clinic. In this systematic review, the genetic variants associated with FF, abnormal fertilization and/or zygotic arrest after ICSI are compiled and analyzed. Forty-seven studies were included. Data from 141 patients carrying 121 genetic variants affecting 16 genes were recorded and analyzed. In total, 27 variants in PLCZ1 (in 50 men) and 26 variants in WEE2 (in 24 women) are two of the factors related to oocyte activation failure that could explain a high percentage of male-related and female-related FF. Additional variants identified were reported in WBP2NL, ACTL9, ACTLA7, and DNAH17 (in men), and TUBB8, PATL2, TLE6, PADI6, TRIP13, BGT4, NLRP5, NLRP7, CDC20 and ZAR1 (in women). Most of these variants are pathogenic or potentially pathogenic (89/121, 72.9%), as demonstrated by experimental and/or in silico approaches. Most individuals carried bi-allelic variants (89/141, 63.1%), but pathogenic variants in heterozygosity have been identified for PLCZ1 and TUBB8. Clinical treatment options for affected individuals, such as chemical-assisted oocyte activation (AOA) or PLCZ1 cRNA injection in the oocyte, are still experimental. In conclusion, a genetic study of known pathogenic variants may help in diagnosing recurrent FF and zygotic arrest and guide patient counselling and future research perspectives.
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Yang Z, Zhang C, Luo P, Sun F, Mei B. Genetic diversity and functional implication of the long control region in human papillomavirus types 52, 58, and 16 from Central China. Infect Genet Evol 2023:105447. [PMID: 37217029 DOI: 10.1016/j.meegid.2023.105447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/14/2023] [Accepted: 03/22/2023] [Indexed: 05/24/2023]
Abstract
OBJECT High-risk human papillomavirus (HR-HPV) is a main reason for cervical cancer. The long control region (LCR) of the genome plays a variety of roles in the transcription of the virus. METHODS LCR sequences were amplified by polymerase chain reaction (PCR) and confirmed by DNA sequencing. MEGA 11.0 software and NCBI blast were used to analyze the sequences and construct the Neighbor-Joining tree. In addition, the JASPAR database was used to predict the potential transcription factor binding sites (TFBS). RESULTS For HPV-52 LCR, 68 single nucleotide polymorphisms (SNPs), 8 deletions, and 1 insertion were found, 17 of which were novel variations. Most of the variants were clustered in B2 sub-lineage (96.22%). For HPV-58 LCR, 25.43% of samples were prototype. 49 SNPs, 2 deletions, and 1 insertion were observed in the remaining samples. A1 sub-lineage was the most frequent (64.16%). For HPV-16 LCR, 75 SNPs and 2 deletions were identified, 13 of which were newly identified. A total of 55.68% of the variants were distributed in A4 sub-lineage. The JASPAR results suggested that multiple variations occurred in TFBSs, which might affect the function of transcription factors. CONCLUSIONS This study provides experimental data for further studies on the epidemiology and biological function of LCR. Various LCR mutational data may prove useful for exploring the carcinogenic mechanism of HPV.
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Affiliation(s)
- ZhiPing Yang
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Chunlin Zhang
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Ping Luo
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Fenglan Sun
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Bing Mei
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China.
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Sabbatucci M, Vitiello A, Clemente S, Zovi A, Boccellino M, Ferrara F, Cimmino C, Langella R, Ponzo A, Stefanelli P, Rezza G. Omicron variant evolution on vaccines and monoclonal antibodies. Inflammopharmacology 2023:10.1007/s10787-023-01253-6. [PMID: 37204696 DOI: 10.1007/s10787-023-01253-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV)-2 responsible for the global COVID-19 pandemic has caused almost 760 million confirmed cases and 7 million deaths worldwide, as of end-February 2023. Since the beginning of the first COVID-19 case, several virus variants have emerged: Alpha (B1.1.7), Beta (B135.1), Gamma (P.1), Delta (B.1.617.2) and then Omicron (B.1.1.529) and its sublineages. All variants have diversified in transmissibility, virulence, and pathogenicity. All the newly emerging SARS-CoV-2 variants appear to contain some similar mutations associated with greater "evasiveness" of the virus to immune defences. From early 2022 onward, several Omicron subvariants named BA.1, BA.2, BA.3, BA.4, and BA.5, with comparable mutation forms, have followed. After the wave of contagions caused by Omicron BA.5, a new Indian variant named Centaurus BA.2.75 and its new subvariant BA.2.75.2, a second-generation evolution of the Omicron variant BA.2, have recently been identified. From early evidence, it appears that this new variant has higher affinity for the cell entry receptor ACE-2, making it potentially able to spread very fast. According to the latest studies, the BA.2.75.2 variant may be able to evade more antibodies in the bloodstream generated by vaccination or previous infection, and it may be more resistant to antiviral and monoclonal antibody drug treatments. In this manuscript, the authors highlight and describe the latest evidences and critical issues have emerged on the new SARS-CoV-2 variants.
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Affiliation(s)
- Michela Sabbatucci
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
- Department Infectious Diseases, Italian National Institute of Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Antonio Vitiello
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Salvatore Clemente
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Andrea Zovi
- Ministry of Health, Directorate General of Hygiene, Food Safety and Nutrition, Viale Giorgio Ribotta 5, 00144, Rome, Italy.
| | | | - Francesco Ferrara
- Pharmaceutical Department, Local Health Unit Napoli 3 Sud, Dell'amicizia Street 22, 80035, Nola, Italy
| | - Carla Cimmino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Roberto Langella
- Department of Pharmaceutics, Agency for Health Protection of the Metropolitan Area of Milan, Milan, Italy
| | | | - Paola Stefanelli
- Department Infectious Diseases, Italian National Institute of Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Giovanni Rezza
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
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93
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Bedoya-Joaqui V, Gutiérrez-López MI, Caicedo PA, Villegas-Torres MF, Albornoz-Tovar LL, Vélez JD, Hidalgo-Cardona A, Tobón GJ, Cañas CA. Persistent and fatal severe acute respiratory syndrome coronavirus 2 infection in a patient with severe hypogammaglobulinemia: a case report. J Med Case Rep 2023; 17:194. [PMID: 37173711 PMCID: PMC10181880 DOI: 10.1186/s13256-023-03917-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/29/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Viruses are constantly changing as a result of mutations, and new viral variants are expected to appear over time. The virus that causes coronavirus disease 2019, severe acute respiratory syndrome coronavirus 2, is not excluded from this condition. Patients with some types of immunodeficiency have been reported to experience symptoms that vary from mild to severe, or even death, after being infected with severe acute respiratory syndrome coronavirus 2. We report a case of a woman with severe hypogammaglobulinemia who developed a prolonged and fatal severe acute respiratory syndrome coronavirus 2 infection. CASE PRESENTATION A 60-year-old mestizo female with a previous history of severe hypogammaglobulinemia manifested by recurrent pulmonary infections and follicular bronchiolitis. She received a monthly treatment of intravenous immunoglobulins and was admitted after report of a neurological manifestation related to a left thalamic inflammatory lesion, for a duration of 2 weeks of hospitalization, indicated for the study of her neurological condition, including brain biopsy. Both on admission and 1 week later, nasopharyngeal polymerase chain reaction tests for severe acute respiratory syndrome coronavirus 2 were performed and reported negative. In the third week of hospitalization, she developed pulmonary symptoms, and a positive test result for severe acute respiratory syndrome coronavirus 2 was evidenced. On Day 3, the patients' condition worsened as the infection progressed to respiratory failure and required mechanical ventilation. On Day 8 after the coronavirus disease 2019 diagnosis, the polymerase chain reaction test for severe acute respiratory syndrome coronavirus 2 showed persistent detection of the virus. Various bacterial coinfections, including Klebsiella pneumoniae and Enterobacter cloacae, were diagnosed and treated. On Day 35, her pulmonary symptoms worsened, and the results of the severe acute respiratory syndrome coronavirus 2 polymerase chain reaction test remained positive. On Day 36, despite all the respiratory support, the patient died. The severe acute respiratory syndrome coronavirus 2 virus was sequenced at the beginning and 8 days after the onset of the disease, and the strain, without obvious mutations in the gene that encodes spike protein, was identified. CONCLUSIONS This clinical case showed persistent severe acute respiratory syndrome coronavirus 2 detection after 35 days of infection in a patient with severe hypogammaglobulinemia. The sequencing of the virus showed no mutations on the spike protein at 8 days, indicating that, in this case, the persistence of the viral detection was associated with immunodeficiency instead of changes in the viral components.
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Affiliation(s)
- Vanessa Bedoya-Joaqui
- Departamento de Medicina Interna, Unidad de Reumatología, Universidad Icesi, Facultad de Ciencias de la Salud, 760031, Cali, Colombia
| | - María I Gutiérrez-López
- Departamento de Biología, Universidad Icesi, Facultad de Ciencias de la Salud, 760031, Cali, Colombia
| | - Paola A Caicedo
- Departamento de Biología, Universidad Icesi, Facultad de Ciencias de la Salud, 760031, Cali, Colombia
| | - María F Villegas-Torres
- Departamento de Biología, Universidad Icesi, Facultad de Ciencias de la Salud, 760031, Cali, Colombia
- Centro de Investigaciones Microbiológicas, Departamento de Ciencias Biológicas, Universidad de los Andes, 111711, Bogotá, Colombia
| | | | - Juan D Vélez
- Unidad de Infectología, Fundación Valle del Lili, 760032, Cali, Colombia
| | | | - Gabriel J Tobón
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, 62794-9620, USA
| | - Carlos A Cañas
- Departamento de Medicina Interna, Unidad de Reumatología, Universidad Icesi, Facultad de Ciencias de la Salud, 760031, Cali, Colombia.
- Unidad de Reumatología, Fundación Valle del Lili, Cra.98 No. 18-49, 760032, Cali, Colombia.
- CIRAT: Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Universidad Icesi, 760031, Cali, Colombia.
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Iwamoto R, Yamaguchi K, Katayama K, Ando H, Setsukinai KI, Kobayashi H, Okabe S, Imoto S, Kitajima M. Identification of SARS-CoV-2 variants in wastewater using targeted amplicon sequencing during a low COVID-19 prevalence period in Japan. Sci Total Environ 2023; 887:163706. [PMID: 37105480 PMCID: PMC10129341 DOI: 10.1016/j.scitotenv.2023.163706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/20/2023]
Abstract
Wastewater-based epidemiology is expected to be able to identify SARS-CoV-2 variants at an early stage via next-generation sequencing. In the present study, we developed a highly sensitive amplicon sequencing method targeting the spike gene of SARS-CoV-2, which allows for sequencing viral genomes from wastewater containing a low amount of virus. Primers were designed to amplify a relatively long region (599 bp) around the receptor-binding domain in the SARS-CoV-2 spike gene, which could distinguish initial major variants of concern. To validate the methodology, we retrospectively analyzed wastewater samples collected from a septic tank installed in a COVID-19 quarantine facility between October and December 2020. The relative abundance of D614G mutant in SARS-CoV-2 genomes in the facility wastewater increased from 47.5 % to 83.1 % during the study period. The N501Y mutant, which is the characteristic mutation of the Alpha-like strain, was detected from wastewater collected on December 24, 2020, which agreed with the fact that a patient infected with the Alpha-like strain was quarantined in the facility on this date. We then analyzed archived municipal wastewater samples collected between November 2020 and January 2021 that contained low SARS-CoV-2 concentrations ranging from 0.23 to 0.43 copies/qPCR reaction (corresponding to 3.30 to 4.15 log10 copies/L). The targeted amplicon sequencing revealed that the Alpha-like variant with D614G and N501Y mutations was present in municipal wastewater collected on December 4, 2020 and later, suggesting that the variant had already spread in the community before its first clinical confirmation in Japan on December 25, 2020. These results demonstrate that targeted amplicon sequencing of wastewater samples is a powerful surveillance tool applicable to low COVID-19 prevalence periods and may contribute to the early detection of emerging variants.
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Affiliation(s)
- Ryo Iwamoto
- Shionogi & Co., Ltd., 1-8, Doshomachi 3-Chome, Chuo-ku, Osaka 541-0045, Japan; AdvanSentinel Inc., 1-8, Doshomachi 3-Chome, Chuo-ku, Osaka 541-0045, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kotoe Katayama
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Hiroki Ando
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Ken-Ichi Setsukinai
- Shionogi & Co., Ltd., 1-8, Doshomachi 3-Chome, Chuo-ku, Osaka 541-0045, Japan
| | - Hiroyuki Kobayashi
- Shionogi & Co., Ltd., 1-8, Doshomachi 3-Chome, Chuo-ku, Osaka 541-0045, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Seiya Imoto
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
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Lamba S, Ganesan S, Daroch N, Paul K, Joshi SG, Sreenivas D, Nataraj A, Srikantaiah V, Mishra R, Ramakrishnan U, Ishtiaq F. SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater - a longitudinal study in Bengaluru, India. Lancet Reg Health Southeast Asia 2023; 11:100151. [PMID: 36688230 PMCID: PMC9847225 DOI: 10.1016/j.lansea.2023.100151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023]
Abstract
Background Environmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS-CoV-2 has complemented routine diagnostic surveillance by capturing near real-time virus circulation at a population level. Methods In this longitudinal study conducted between January 2022 and June 2022 in 28 sewershed sites in Bengaluru city (∼11 million inhabitants), we quantified weekly SARS-CoV-2 RNA concentrations to track infection dynamics and provide evidence of change in the relative abundance of emerging variants. Findings We describe an early warning system using the exponentially weighted moving average control chart and demonstrate how SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 8-14 days earlier in wastewater than in clinical data. This was further corroborated by showing that the estimated number of infections is strongly correlated with SARS-CoV-2 RNA copies detected in the wastewater. Using a deconvolution matrix, we detected emerging variants of concern up to two months earlier in wastewater samples. In addition, we found a huge diversity in variants detected in wastewater compared to clinical samples. The findings from this study have been discussed regularly with local authorities to inform policy-making decisions. Interpretation Our study highlights that quantifying viral titre, correlating it with a known number of cases in the area, and combined with genomic surveillance helps in tracking variants of concern (VOC) over time and space, enabling timely and making informed policy decisions. Funding This work has been supported by funding from the Rockefeller Foundation grant to National Centre for Biological Sciences, TIFR) and the Indian Council of Medical Research grant to (FI) Tata Institute for Genetics and Society and Tata Trusts.
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Affiliation(s)
- Sanjay Lamba
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Sutharsan Ganesan
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Namrta Daroch
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Kiran Paul
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Soumya Gopal Joshi
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Darshan Sreenivas
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru, 560065, India
| | - Annamalai Nataraj
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | | | - Rakesh Mishra
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru, 560065, India
| | - Farah Ishtiaq
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India,Corresponding author. Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
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96
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Padasas BT, Españo E, Kim SH, Song Y, Lee CK, Kim JK. COVID-19 Therapeutics: An Update on Effective Treatments Against Infection With SARS-CoV-2 Variants. Immune Netw 2023; 23:e13. [PMID: 37179752 PMCID: PMC10166656 DOI: 10.4110/in.2023.23.e13] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 05/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is one of the most consequential global health crises in over a century. Since its discovery in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to mutate into different variants and sublineages, rendering previously potent treatments and vaccines ineffective. With significant strides in clinical and pharmaceutical research, different therapeutic strategies continue to be developed. The currently available treatments can be broadly classified based on their potential targets and molecular mechanisms. Antiviral agents function by disrupting different stages of SARS-CoV-2 infection, while immune-based treatments mainly act on the human inflammatory response responsible for disease severity. In this review, we discuss some of the current treatments for COVID-19, their mode of actions, and their efficacy against variants of concern. This review highlights the need to constantly evaluate COVID-19 treatment strategies to protect high risk populations and fill in the gaps left by vaccination.
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Affiliation(s)
| | - Erica Españo
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | - Sang-Hyun Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | - Youngcheon Song
- Department of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Chong-Kil Lee
- Department of Pharmaceutics, College of Pharmacy, Chungbuk National University, Cheongju 28644, Korea
| | - Jeong-Ki Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
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Varghese R, Kumar D, Sharma R. Global threat from novel SARS-CoV-2 variants, BF.7, XBB.1.5, BQ.1, and BQ.1.1: variants of concern? Hum Cell 2023; 36:1218-1221. [PMID: 37000399 PMCID: PMC10063927 DOI: 10.1007/s13577-023-00903-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/26/2023] [Indexed: 04/01/2023]
Affiliation(s)
- Ryan Varghese
- Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to Be) University, Pune, Maharashtra, 411038, India
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Dileep Kumar
- Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to Be) University, Pune, Maharashtra, 411038, India.
- Department of Entomology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
- UC Davis Comprehensive Cancer Center, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India.
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98
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Akerman A, Milogiannakis V, Jean T, Esneau C, Silva MR, Ison T, Fichter C, Lopez JA, Chandra D, Naing Z, Caguicla J, Li D, Walker G, Amatayakul-Chantler S, Roth N, Manni S, Hauser T, Barnes T, Condylios A, Yeang M, Wong M, Foster CSP, Sato K, Lee S, Song Y, Mao L, Sigmund A, Phu A, Vande More AM, Hunt S, Douglas M, Caterson I, Britton W, Sandgren K, Bull R, Lloyd A, Triccas J, Tangye S, Bartlett NW, Darley D, Matthews G, Stark DJ, Petoumenos K, Rawlinson WD, Murrell B, Brilot F, Cunningham AL, Kelleher AD, Aggarwal A, Turville SG. Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level. EBioMedicine 2023; 90:104545. [PMID: 37002990 PMCID: PMC10060887 DOI: 10.1016/j.ebiom.2023.104545] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND The Omicron era of the COVID-19 pandemic commenced at the beginning of 2022 and whilst it started with primarily BA.1, it was latter dominated by BA.2 and the related sub-lineage BA.5. Following resolution of the global BA.5 wave, a diverse grouping of Omicron sub-lineages emerged derived from BA.2, BA.5 and recombinants thereof. Whilst emerging from distinct lineages, all shared similar changes in the Spike glycoprotein affording them an outgrowth advantage through evasion of neutralising antibodies. METHODS Over the course of 2022, we monitored the potency and breadth of antibody neutralization responses to many emerging variants in the Australian community at three levels: (i) we tracked over 420,000 U.S. plasma donors over time through various vaccine booster roll outs and Omicron waves using sequentially collected IgG pools; (ii) we mapped the antibody response in individuals using blood from stringently curated vaccine and convalescent cohorts. (iii) finally we determine the in vitro efficacy of clinically approved therapies Evusheld and Sotrovimab. FINDINGS In pooled IgG samples, we observed the maturation of neutralization breadth to Omicron variants over time through continuing vaccine and infection waves. Importantly, in many cases, we observed increased antibody breadth to variants that were yet to be in circulation. Determination of viral neutralization at the cohort level supported equivalent coverage across prior and emerging variants with isolates BQ.1.1, XBB.1, BR.2.1 and XBF the most evasive. Further, these emerging variants were resistant to Evusheld, whilst increasing neutralization resistance to Sotrovimab was restricted to BQ.1.1 and XBF. We conclude at this current point in time that dominant variants can evade antibodies at levels equivalent to their most evasive lineage counterparts but sustain an entry phenotype that continues to promote an additional outgrowth advantage. In Australia, BR.2.1 and XBF share this phenotype and, in contrast to global variants, are uniquely dominant in this region in the later months of 2022. INTERPRETATION Whilst the appearance of a diverse range of omicron lineages has led to primary or partial resistance to clinically approved monoclonal antibodies, the maturation of the antibody response across both cohorts and a large donor pools importantly observes increasing breadth in the antibody neutralisation responses over time with a trajectory that covers both current and known emerging variants. FUNDING This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (SGT, GM & WDR), Medical Research Future Fund Antiviral Development Call grant (WDR), the New South Wales Health COVID-19 Research Grants Round 2 (SGT & FB) and the NSW Vaccine Infection and Immunology Collaborative (VIIM) (ALC). Variant modeling was supported by funding from SciLifeLab's Pandemic Laboratory Preparedness program to B.M. (VC-2022-0028) and by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 101003653 (CoroNAb) to B.M.
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Affiliation(s)
- Anouschka Akerman
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | | | - Tyra Jean
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Camille Esneau
- Hunter Medical Research Institute, University of Newcastle, Callaghan, Australia
| | - Mariana Ruiz Silva
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Timothy Ison
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Christina Fichter
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Joseph A Lopez
- Brain Autoimmunity Group, Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, School of Medical Sciences, New South Wales, Australia
| | - Deborah Chandra
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Zin Naing
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Joanna Caguicla
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Daiyang Li
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Gregory Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | | | - Nathan Roth
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Sandro Manni
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Hauser
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Barnes
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Anna Condylios
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Malinna Yeang
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Maureen Wong
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Charles S P Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Kenta Sato
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Sharon Lee
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | - Yang Song
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | - Lijun Mao
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | - Allison Sigmund
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | - Amy Phu
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | | | - Stephanie Hunt
- Royal Prince Alfred Hospital, SLHD, New South Wales, Australia
| | - Mark Douglas
- The Westmead Institute for Medical Research, Westmead, New South Wales, Australia; Centre for Infectious Diseases and Microbiology, Sydney Institute for Infectious Diseases, The University of Sydney at Westmead Hospital, Westmead, NSW, Australia
| | - Ian Caterson
- Royal Prince Alfred Hospital, SLHD, New South Wales, Australia
| | - Warwick Britton
- The Centenary Institute, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Kerrie Sandgren
- The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Rowena Bull
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Andrew Lloyd
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Jamie Triccas
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Stuart Tangye
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Nathan W Bartlett
- Hunter Medical Research Institute, University of Newcastle, Callaghan, Australia
| | - David Darley
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Gail Matthews
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Damien J Stark
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Kathy Petoumenos
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - William D Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Fabienne Brilot
- Brain Autoimmunity Group, Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, School of Medical Sciences, New South Wales, Australia
| | - Anthony L Cunningham
- The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia.
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99
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Adhisantoso YG, Voges J, Rohlfing C, Tunev V, Ohm JR, Ostermann J. GVC: efficient random access compression for gene sequence variations. BMC Bioinformatics 2023; 24:121. [PMID: 36978010 PMCID: PMC10044409 DOI: 10.1186/s12859-023-05240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND In recent years, advances in high-throughput sequencing technologies have enabled the use of genomic information in many fields, such as precision medicine, oncology, and food quality control. The amount of genomic data being generated is growing rapidly and is expected to soon surpass the amount of video data. The majority of sequencing experiments, such as genome-wide association studies, have the goal of identifying variations in the gene sequence to better understand phenotypic variations. We present a novel approach for compressing gene sequence variations with random access capability: the Genomic Variant Codec (GVC). We use techniques such as binarization, joint row- and column-wise sorting of blocks of variations, as well as the image compression standard JBIG for efficient entropy coding. RESULTS Our results show that GVC provides the best trade-off between compression and random access compared to the state of the art: it reduces the genotype information size from 758 GiB down to 890 MiB on the publicly available 1000 Genomes Project (phase 3) data, which is 21% less than the state of the art in random-access capable methods. CONCLUSIONS By providing the best results in terms of combined random access and compression, GVC facilitates the efficient storage of large collections of gene sequence variations. In particular, the random access capability of GVC enables seamless remote data access and application integration. The software is open source and available at https://github.com/sXperfect/gvc/ .
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Affiliation(s)
- Yeremia Gunawan Adhisantoso
- Institut für Informationsverarbeitung and L3S Research Center, Leibniz University Hannover, Hannover, Germany.
| | - Jan Voges
- Institut für Informationsverarbeitung and L3S Research Center, Leibniz University Hannover, Hannover, Germany
| | - Christian Rohlfing
- Institut für Nachrichtentechnik, RWTH Aachen University, Aachen, Germany
| | - Viktor Tunev
- Institut für Nachrichtentechnik, RWTH Aachen University, Aachen, Germany
| | - Jens-Rainer Ohm
- Institut für Nachrichtentechnik, RWTH Aachen University, Aachen, Germany
| | - Jörn Ostermann
- Institut für Informationsverarbeitung and L3S Research Center, Leibniz University Hannover, Hannover, Germany
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100
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Alkhamis FA, Alabdali MM, Alsulaiman AA, Alamri AS, Alali R, Akhtar MS, Alsalman SA, Cyrus C, Albakr AI, Alduhalan AS, Gandla D, Al-Romaih K, Abouelhoda M, Loza BL, Keating B, Al-Ali AK. Whole-exome sequencing analyses in a Saudi Ischemic Stroke Cohort reveal association signals, and shows polygenic risk scores are related to Modified Rankin Scale Risk. Funct Integr Genomics 2023; 23:102. [PMID: 36973604 PMCID: PMC10042957 DOI: 10.1007/s10142-023-01039-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Ischemic stroke represents a significant societal burden across the globe. Rare high penetrant monogenic variants and less pathogenic common single nucleotide polymorphisms (SNPs) have been described as being associated with risk of diseases. Genetic studies in Saudi Arabian patients offer a greater opportunity to detect rare high penetrant mutations enriched in these consanguineous populations. We performed whole exome sequencing on 387 ischemic stroke subjects from Saudi Arabian hospital networks with up to 20,230 controls from the Saudi Human Genome Project and performed gene burden analyses of variants in 177 a priori loci derived from knowledge-driven curation of monogenic and genome-wide association studies of stroke. Using gene-burden analyses, we observed significant associations in numerous loci under autosomal dominant and/or recessive modelling. Stroke subjects with modified Rankin Scale (mRSs) above 3 were found to carry greater cumulative polygenic risk score (PRS) from rare variants in stroke genes (standardized PRS mean > 0) compared to the population average (standardized PRS mean = 0). However, patients with mRS of 3 or lower had lower cumulative genetic risk from rare variants in stroke genes (OR (95%CI) = 1.79 (1.29-2.49), p = 0.0005), with the means of standardized PRS at or lower than 0. In conclusion, gene burden testing in Saudi stroke populations reveals a number of statistically significant signals under different disease inheritance models. However, interestingly, stroke subjects with mRS of 3 or lower had lower cumulative genetic risk from rare variants in stroke genes and therefore, determining the potential mRS cutoffs to use for clinical significance may allow risk stratification of this population.
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Affiliation(s)
- Fahad A Alkhamis
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Majed M Alabdali
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Abdulla A Alsulaiman
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Abdullah S Alamri
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Rudaynah Alali
- Department of Internal Medicine, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Mohammed S Akhtar
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Sadiq A Alsalman
- Department of Neurology, King Fahd Hospital, Alhafof, Saudi Arabia
| | - Cyril Cyrus
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Aishah I Albakr
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Anas S Alduhalan
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Divya Gandla
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | | | | | - Bao-Li Loza
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Brendan Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Amein K Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia.
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