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Chaudhary S, Kishen S, Singh M, Jassal S, Pathania R, Bisht K, Sareen D. Phylogeny-guided genome mining of roseocin family lantibiotics to generate improved variants of roseocin. AMB Express 2023; 13:34. [PMID: 36940043 PMCID: PMC10027976 DOI: 10.1186/s13568-023-01536-9] [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: 02/26/2023] [Accepted: 03/04/2023] [Indexed: 03/21/2023] Open
Abstract
Roseocin, the two-peptide lantibiotic from Streptomyces roseosporus, carries extensive intramolecular (methyl)lanthionine bridging in the peptides and exhibits synergistic antibacterial activity against clinically relevant Gram-positive pathogens. Both peptides have a conserved leader but a diverse core region. The biosynthesis of roseocin involves post-translational modification of the two precursor peptides by a single promiscuous lanthipeptide synthetase, RosM, to install an indispensable disulfide bond in the Rosα core along with four and six thioether rings in Rosα and Rosβ cores, respectively. RosM homologs in the phylum actinobacteria were identified here to reveal twelve other members of the roseocin family which diverged into three types of biosynthetic gene clusters (BGCs). Further, the evolutionary rate among the BGC variants and analysis of variability within the core peptide versus leader peptide revealed a phylum-dependent lanthipeptide evolution. Analysis of horizontal gene transfer revealed its role in the generation of core peptide diversity. The naturally occurring diverse congeners of roseocin peptides identified from the mined novel BGCs were carefully aligned to identify the conserved sites and the substitutions in the core peptide region. These selected sites in the Rosα peptide were mutated for permitted substitutions, expressed heterologously in E. coli, and post-translationally modified by RosM in vivo. Despite a limited number of generated variants, two variants, RosαL8F and RosαL8W exhibited significantly improved inhibitory activity in a species-dependent manner compared to the wild-type roseocin. Our study proves that a natural repository of evolved variants of roseocin is present in nature and the key variations can be used to generate improved variants.
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Affiliation(s)
- Sandeep Chaudhary
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Shweta Kishen
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Sunanda Jassal
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Reeva Pathania
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Kalpana Bisht
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Dipti Sareen
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India.
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He C, Chen L, Yang J, Chen Z, Lei H, Hong W, Song X, Yang L, Li J, Wang W, Shen G, Lu G, Wei X. Trimeric protein vaccine based on Beta variant elicits robust immune response against BA.4/5-included SARS-CoV-2 Omicron variants. Mol Biomed 2023; 4:9. [PMID: 36894743 PMCID: PMC9998262 DOI: 10.1186/s43556-023-00121-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/07/2023] [Indexed: 03/11/2023] Open
Abstract
The current Coronavirus Disease 2019 (COVID-19) pandemic, induced by newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants, posed great threats to global public health security. There is an urgent need to design effective next‑generation vaccines against Omicron lineages. Here, we investigated the immunogenic capacity of the vaccine candidate based on the receptor binding domain (RBD). An RBDβ-HR self-assembled trimer vaccine including RBD of Beta variant (containing K417, E484 and N501) and heptad repeat (HR) subunits was developed using an insect cell expression platform. Sera obtained from immunized mice effectively blocked RBD-human angiotensin-converting enzyme 2 (hACE2) binding for different viral variants, showing robust inhibitory activity. In addition, RBDβ-HR/trimer vaccine durably exhibited high titers of specific binding antibodies and high levels of cross-protective neutralizing antibodies against newly emerging Omicron lineages, as well as other major variants including Alpha, Beta, and Delta. Consistently, the vaccine also promoted a broad and potent cellular immune response involving the participation of T follicular helper (Tfh) cells, germinal center (GC) B cells, activated T cells, effector memory T cells, and central memory T cells, which are critical facets of protective immunity. These results demonstrated that RBDβ-HR/trimer vaccine candidates provided an attractive next-generation vaccine strategy against Omicron variants in the global effort to halt the spread of SARS-CoV-2.
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Affiliation(s)
- Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Li Chen
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jingyun Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zimin Chen
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hong Lei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiangrong Song
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Li Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiong Li
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wei Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Guobo Shen
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Guangwen Lu
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Jassat W, Mudara C, Vika C, Welch R, Arendse T, Dryden M, Blumberg L, Mayet N, Tempia S, Parker A, Nel J, Perumal R, Groome MJ, Conradie F, Ndjeka N, Sigfrid L, Merson L, Cohen C. A cohort study of post-COVID-19 condition across the Beta, Delta, and Omicron waves in South Africa: 6-month follow-up of hospitalized and nonhospitalized participants. Int J Infect Dis 2023; 128:102-111. [PMID: 36587841 PMCID: PMC9800016 DOI: 10.1016/j.ijid.2022.12.036] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The study aimed to describe the prevalence of and risk factors for post-COVID-19 condition (PCC). METHODS This was a prospective, longitudinal observational cohort study. Hospitalized and nonhospitalized adults were randomly selected to undergo telephone assessment at 1, 3, and 6 months. Participants were assessed using a standardized questionnaire for the evaluation of symptoms and health-related quality of life. We used negative binomial regression models to determine factors associated with the presence of ≥1 symptoms at 6 months. RESULTS A total of 46.7% of hospitalized and 18.5% of nonhospitalized participants experienced ≥1 symptoms at 6 months (P ≤0.001). Among hospitalized people living with HIV, 40.4% had persistent symptoms compared with 47.1% among participants without HIV (P = 0.108). The risk factors for PCC included older age, female sex, non-Black race, presence of a comorbidity, greater number of acute COVID-19 symptoms, hospitalization/COVID-19 severity, and wave period (lower risk of persistent symptoms for the Omicron compared with the Beta wave). There were no associations between self-reported vaccination status with persistent symptoms. CONCLUSION The study revealed a high prevalence of persistent symptoms among South African participants at 6 months but decreased risk for PCC among participants infected during the Omicron BA.1 wave. These findings have serious implications for countries with resource-constrained health care systems.
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Affiliation(s)
- Waasila Jassat
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa.
| | - Caroline Mudara
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Caroline Vika
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Richard Welch
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa
| | - Tracy Arendse
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa
| | - Murray Dryden
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Lucille Blumberg
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa
| | - Natalie Mayet
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arifa Parker
- Divisions of General Medicine and Infectious Diseases, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Jeremy Nel
- Division of Infectious Diseases, Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - Rubeshan Perumal
- Division of Pulmonology and Critical Care, Department of Medicine, University of KwaZulu-Natal, Berea, Durban, South Africa; South African Medical Research Council-CAPRISA HIV/TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle J Groome
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Francesca Conradie
- Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Norbert Ndjeka
- Drug-Resistant TB, TB & HIV Directorate, National Department of Health, Pretoria, South Africa and University of KwaZulu-Natal, Durban, South Africa
| | - Louise Sigfrid
- International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | - Laura Merson
- International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | - Cheryl Cohen
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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104
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Kienast P, Prayer D, Binder J, Prayer F, Dekan S, Langthaler E, Sigl B, Eichinger S, Perkmann-Nagele N, Stuempflen I, Stuempflen M, Schirwani N, Pateisky P, Mitter C, Kasprian G. SARS-CoV-2 variant-related abnormalities detected by prenatal MRI: a prospective case-control study. Lancet Reg Health Eur 2023; 26:100587. [PMID: 36713638 PMCID: PMC9860502 DOI: 10.1016/j.lanepe.2023.100587] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/22/2023]
Abstract
Background There are known complications for fetuses after infection with SARS-CoV-2 during pregnancy. However, previous studies of SARS-CoV-2 in pregnancy have largely been limited to histopathologic studies of placentas and prenatal studies on the effects of different SARS-CoV-2 variants are scarce to date. To examine the effects of SARS-CoV-2 variants on the placenta and fetus, we investigated fetal and extra-fetal structures using prenatal MRI. Methods For this prospective case-control study, two obstetric centers consecutively referred pregnant women for prenatal MRI after confirmed SARS-CoV-2 infection. Thirty-eight prenatal MRI examinations were included after confirmed infection with SARS-CoV-2 and matched 1:1 with 38 control cases with respect to sex, MRI field strength, and gestational age (average deviation 1.76 ± 1.65, median 1.5 days). Where available, the pathohistological examination and vaccination status of the placenta was included in the analysis. In prenatal MRI, the shape and thickness of the placenta, possible lobulation, and vascular lesions were quantified. Fetuses were scanned for organ or brain abnormalities. Findings Of the 38 included cases after SARS-CoV-2 infection, 20/38 (52.6%) were infected with pre-Omicron variants and 18/38 (47.4%) with Omicron. Prenatal MRIs were performed on an average of 83 days (±42.9, median 80) days after the first positive PCR test. Both pre-Omicron (P = .008) and Omicron (P = .016) groups showed abnormalities in form of a globular placenta compared to control cases. In addition, placentas in the pre-Omicron group were significantly thickened (6.35, 95% CI .02-12.65, P = .048), and showed significantly more frequent lobules (P = .046), and hemorrhages (P = .002). Fetal growth restriction (FGR) was observed in 25% (n = 5/20, P = .017) in the pre-Omicron group. Interpretation SARS-CoV-2 infections in pregnancy can lead to placental lesions based on vascular events, which can be well visualized on prenatal MRI. Pre-Omicron variants cause greater damage than Omicron sub-lineages in this regard. Funding Vienna Science and Technology Fund.
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Affiliation(s)
- Patric Kienast
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Neuroradiology and Musculoskeletal Radiology, Medical University of Vienna, Vienna, Austria
| | - Daniela Prayer
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Neuroradiology and Musculoskeletal Radiology, Medical University of Vienna, Vienna, Austria
| | - Julia Binder
- Department of Obstetrics and Feto-Maternal Medicine, Medical University of Vienna, Vienna, Austria
| | - Florian Prayer
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Neuroradiology and Musculoskeletal Radiology, Medical University of Vienna, Vienna, Austria
| | - Sabine Dekan
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Eva Langthaler
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Benjamin Sigl
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Neuroradiology and Musculoskeletal Radiology, Medical University of Vienna, Vienna, Austria
| | - Sabine Eichinger
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | | | - Ingrid Stuempflen
- Department of Obstetrics & Gynecology, Klinik Floridsdorf, Vienna, Austria
| | - Marlene Stuempflen
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Neuroradiology and Musculoskeletal Radiology, Medical University of Vienna, Vienna, Austria
| | - Nawa Schirwani
- Department of Obstetrics and Feto-Maternal Medicine, Medical University of Vienna, Vienna, Austria
| | - Petra Pateisky
- Department of Obstetrics and Feto-Maternal Medicine, Medical University of Vienna, Vienna, Austria
| | - Christian Mitter
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Neuroradiology and Musculoskeletal Radiology, Medical University of Vienna, Vienna, Austria
| | - Gregor Kasprian
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Neuroradiology and Musculoskeletal Radiology, Medical University of Vienna, Vienna, Austria,Corresponding author. Universitätsklinik für Radiologie und Nuklearmedizin, Währinger Gürtel 18-20, 1090, Wien, Austria
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105
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Xiong T, Di W, Zuo H, Shao C. The "Hand as Foot" teaching method in variants of the brain Willis circle anatomy. Asian J Surg 2023; 46:1254-5. [PMID: 36041905 DOI: 10.1016/j.asjsur.2022.08.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
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Lv X, Wu C, Hu H, Fu Y, Yan L, Wang Z, Lv G, Wang G, Bai Z. Transcriptome analysis of growth and shell color between two genetic variants of Corbicula fluminea with different shell colors. Comp Biochem Physiol Part D Genomics Proteomics 2023; 45:101056. [PMID: 36736150 DOI: 10.1016/j.cbd.2023.101056] [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] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 01/22/2023]
Abstract
To clarify the molecular mechanism of the black and yellow shell coloration, we performed a transcriptome analysis of whole tissue of Corbicula fluminea in Hongze Lake (Jiangsu Province, China). After assembly, 335,247 unigenes were obtained, and 136,804 unigenes were functionally identified using public databases (NR, GO, KEGG, eggnog, and Swissprot). 1567 differentially expressed genes (DEGs) were detected through pairwise comparisons, of which 941 DEGs were up-regulated and 626 were down-regulated in the black-shelled clam. We compared the DEGs between two clams and identified some coloration-related genes. Notably, the black-shelled clam was larger than the yellow-shelled. We speculated that higher digestion and anabolic ability of black-shelled clam might lead to this phenomenon. In contrast, the yellow-shelled clam appeared to be more sensitive to environmental stress. The metabolic energy of the yellow-shelled clam was depleted to maintain or recover from stress, and provide less energy for growth. In summary, our finding provides a theoretical basis for the molecular mechanism of pigmentation and the difference of somatotype in bivalve, as well as promotes the future breeding of more elite varieties.
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Affiliation(s)
- Xuefeng Lv
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China. https://twitter.com/
| | - Congdi Wu
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Honghui Hu
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Yuanshuai Fu
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Ling Yan
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Zhiyan Wang
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Gaolun Lv
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Guiling Wang
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Zhiyi Bai
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China.
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107
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Patarca R, Haseltine WA. Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 DOI: 10.1186/s12985-023-01998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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Saini S, Khurana S, Saini D, Rajput S, Thakur CJ, Singh J, Jaswal A, Kapoor Y, Kumar V, Saini A. In silico analysis of genomic landscape of SARS-CoV-2 and its variant of concerns (Delta and Omicron) reveals changes in the coding potential of miRNAs and their target genes. Gene X 2023; 853:147097. [PMID: 36470485 PMCID: PMC9721428 DOI: 10.1016/j.gene.2022.147097] [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: 09/11/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
COVID-19 related morbidities and mortalities are still continued due to the emergence of new variants of SARS-CoV-2. In the last few years, viral miRNAs have been the centre of study to understand the disease pathophysiology. In this work, we aimed to predict the change in coding potential of the viral miRNAs in SARS-CoV-2's VOCs, Delta and Omicron compared to the Reference (Wuhan origin) strain using bioinformatics tools. After ab-intio based screening by the Vmir tool and validation, we retrieved 22, 6, and 6 pre-miRNAs for Reference, Delta, and Omicron. Most of the predicted unique pre-miRNAs of Delta and Omicron were found to be encoded from the terminal and origin of the genomic sequence, respectively. Mature miRNAs identified by MatureBayes from the unique pre-miRNAs were used for target identification using miRDB. A total of 1786, 216, and 143 high-confidence target genes were captured for GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. The GO and KEGG pathways terms analysis revealed the involvement of Delta miRNAs targeted genes in the pathways such as Human cytomegalovirus infection, Breast cancer, Apoptosis, Neurotrophin signaling, and Axon guidance whereas the Sphingolipid signaling pathway was found for the Omicron. Furthermore, we focussed our analysis on target genes that were validated through GEO's (Gene Expression Omnibus) DEGs (Differentially Expressed Genes) dataset, in which FGL2, TNSF12, OGN, GDF11, and BMP11 target genes were found to be down-regulated by Reference miRNAs and YAE1 and RSU1 by Delta. Few genes were also observed to be validated among in up-regulated gene set of the GEO dataset, in which MMP14, TNFRSF21, SGMS1, and TMEM192 were related to Reference whereas ZEB2 was detected in all three strains. This study thus provides an in-silico based analysis that deciphered the unique pre-miRNAs in Delta and Omicron compared to Reference. However, the findings need future wet lab studies for validation.
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Affiliation(s)
- Sandeep Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India,Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India,Corresponding authors at: Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India (S. Saini)
| | - Savi Khurana
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Dikshant Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Saru Rajput
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Chander Jyoti Thakur
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Jeevisha Singh
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Akanksha Jaswal
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Yogesh Kapoor
- Department of Engineering and Technology, Shoolini University, Solan, Himachal Pradesh, India
| | - Varinder Kumar
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India,Corresponding authors at: Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India (S. Saini)
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109
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Jin B, Li J, Yang Q, Tang X, Wang C, Zhao Y, Zheng F, Zhang Y, Ma J, Yan M. Genetic characteristics of suspected retinitis pigmentosa in a cohort of Chinese patients. Gene 2023; 853:147087. [PMID: 36464167 DOI: 10.1016/j.gene.2022.147087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The study aimed to screen for the causative variants in Chinese patients with suspected retinitis pigmentosa (RP). A cohort of 75 unrelated Chinese patients with a clinical diagnosis of RP and their available family members were enrolled in this study. Genomic DNA of all subjects was extracted and whole-exome sequencing (WES) was applied. Candidate variants were identified, and minigene assays were conducted to evaluate the pathogenicity of novel splicing variants. Totally, the diagnostic yield was 44 % (33/75) and 16 novel variants that had not been reported previously were found. Among the genetically solved 33 cases, 31 patients were identified as carrying causative variants of RP and 2 patients carried pathogenic variants implicated in other retinal diseases. USH2A, CYP4V2, and RPGR were the most common causative genes, accounting for about half of the genetically solved cases. Moreover, minigene assays validated that the novel splicing variants were detrimental. Additionally, 9 patients carried a single deleterious heterozygous variant in 6 genes with autosomal recessive hereditary patterns, and no corresponding copy number variants (CNVs) was detected. The findings of this study revealed the genetic landscape of RP in China and provided guidance for clinicians.
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110
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Alam MS. Insight into SARS-CoV-2 Omicron variant immune escape possibility and variant independent potential therapeutic opportunities. Heliyon 2023; 9:e13285. [PMID: 36744070 PMCID: PMC9886571 DOI: 10.1016/j.heliyon.2023.e13285] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
The Omicron, the latest variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected in November 2021 in Botswana, South Africa. Compared to other variants of SARS-CoV-2, the Omicron is the most highly mutated, with 50 mutations throughout the genome, most of which are in the spike (S) protein. These mutations may help the Omicron to evade host immunity against the vaccine. Epidemiological studies suggest that Omicron is highly infectious and spreads rapidly, but causes significantly less severe disease than the wild-type strain and the other variants of SARS-CoV-2. With the increased transmissibility and a higher rate of re-infection, Omicron has now become a dominant variant worldwide and is predicted to be able to evade vaccine-induced immunity. Several clinical studies using plasma samples from individuals receiving two doses of US Food and Drugs Administration (FDA)-approved COVID-19 vaccines have shown reduced humoral immune response against Omicron infection, but T cell-mediated immunity was well preserved. In fact, T cell-mediated immunity protects against severe disease, and thus the disease caused by Omicron remains mild. In this review, I surveyed the current status of Omicron variant mutations and mechanisms of immune response in the context of immune escape from COVID-19 vaccines. I also discuss the potential implications of therapeutic opportunities that are independent of SARS-CoV-2 variants, including Omicron. A better understanding of vaccine-induced immune responses and variant-independent therapeutic interventions that include potent antiviral, antioxidant, and anti-cytokine activities may pave the way to reducing Omicron-related COVID-19 complications, severity, and mortality. Collectively, these insights point to potential research gaps and will aid in the development of new-generation COVID-19 vaccines and antiviral drugs to combat Omicron, its sublineages, or upcoming new variants of SARS-CoV-2.
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Affiliation(s)
- Mohammad Shah Alam
- Department of Anatomy and Histology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
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111
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Wang W, Hu Y, Li B, Wang H, Shen J. Applications of nanobodies in the prevention, detection, and treatment of the evolving SARS-CoV-2. Biochem Pharmacol 2023; 208:115401. [PMID: 36592707 PMCID: PMC9801699 DOI: 10.1016/j.bcp.2022.115401] [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: 10/25/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Global health and economy are deeply influenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its newly emerging variants. Nanobodies with nanometer-scale size are promising for the detection and treatment of SARS-CoV-2 and its variants because they are superior to conventional antibodies in terms of cryptic epitope accessibility, tissue penetration, cost, formatting adaptability, and especially protein stability, which enables their aerosolized specific delivery to lung tissues. This review summarizes the progress in the prevention, detection, and treatment of SARS-CoV-2 using nanobodies, as well as strategies to combat the evolving SARS-CoV-2 variants. Generally, highly efficient generation of potent broad-spectrum nanobodies targeting conserved epitopes or further construction of multivalent formats targeting non-overlapping epitopes can promote neutralizing activity against SARS-CoV-2 variants and suppress immune escape.
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Affiliation(s)
- Wenyi Wang
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China,Corresponding author
| | - Yue Hu
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
| | - Bohan Li
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
| | - Huanan Wang
- Department of Respiratory Medicine, The 990th Hospital of Joint Logistics Support Force, Zhumadian, Henan 463000, PR China
| | - Jinhua Shen
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
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Omame A, Abbas M, Din A. Global asymptotic stability, extinction and ergodic stationary distribution in a stochastic model for dual variants of SARS-CoV-2. Math Comput Simul 2023; 204:302-336. [PMID: 36060108 PMCID: PMC9422832 DOI: 10.1016/j.matcom.2022.08.012] [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: 03/16/2022] [Revised: 07/14/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Several mathematical models have been developed to investigate the dynamics SARS-CoV-2 and its different variants. Most of the multi-strain SARS-CoV-2 models do not capture an important and more realistic feature of such models known as randomness. As the dynamical behavior of most epidemics, especially SARS-CoV-2, is unarguably influenced by several random factors, it is appropriate to consider a stochastic vaccination co-infection model for two strains of SARS-CoV-2. In this work, a new stochastic model for two variants of SARS-CoV-2 is presented. The conditions of existence and the uniqueness of a unique global solution of the stochastic model are derived. Constructing an appropriate Lyapunov function, the conditions for the stochastic system to fluctuate around endemic equilibrium of the deterministic system are derived. Stationary distribution and ergodicity for the new co-infection model are also studied. Numerical simulations are carried out to validate theoretical results. It is observed that when the white noise intensities are larger than certain thresholds and the associated stochastic reproduction numbers are less than unity, both strains die out and go into extinction with unit probability. More-over, it is observed that, for weak white noise intensities, the solution of the stochastic system fluctuates around the endemic equilibrium (EE) of the deterministic model. Frequency distributions are also studied to show random fluctuations due to stochastic white noise intensities. The results presented herein also reveal the impact of vaccination in reducing the co-circulation of SARS-CoV-2 variants within a given population.
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Affiliation(s)
- Andrew Omame
- Department of Mathematics, Federal University of Technology, Owerri, Nigeria
- Abdus Salam School of Mathematical Sciences, Government College University Katchery Road, Lahore 54000, Pakistan
| | - Mujahid Abbas
- Department of Mathematics, Government College University Katchery Road, Lahore 54000, Pakistan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Anwarud Din
- Department of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
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Zhang C, Wei B, Liu Z, Yao W, Li Y, Lu J, Ge C, Yu X, Li D, Zhu Y, Shang C, Jin N, Li X. Bafilomycin A1 inhibits SARS-CoV-2 infection in a human lung xenograft mouse model. Virol J 2023; 20:18. [PMID: 36721152 PMCID: PMC9887234 DOI: 10.1186/s12985-023-01971-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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/10/2023] [Indexed: 02/01/2023] Open
Abstract
Coronavirus disease 2019 is a global pandemic caused by SARS-CoV-2. The emergence of its variant strains has posed a considerable challenge to clinical treatment. Therefore, drugs capable of inhibiting SARS-CoV-2 infection, regardless of virus variations, are in urgently need. Our results showed that the endosomal acidification inhibitor, Bafilomycin A1 (Baf-A1), had an inhibitory effect on the viral RNA synthesis of SARS-CoV-2, and its Beta and Delta variants at the concentration of 500 nM. Moreover, the human lung xenograft mouse model was used to investigate the anti-SARS-CoV-2 effect of Baf-A1. It was found that Baf-A1 significantly inhibited SARS-CoV-2 replication in the human lung xenografts by in situ hybridization and RT-PCR assays. Histopathological examination showed that Baf-A1 alleviated SARS-CoV-2-induced diffuse inflammatory infiltration of granulocytes and macrophages and alveolar endothelial cell death in human lung xenografts. In addition, immunohistochemistry analysis indicated that Baf-A1 decreased inflammatory exudation and infiltration in SARS-CoV-2-infected human lung xenografts. Therefore, Baf-A1 may be a candidate drug for SARS-CoV-2 treatment.
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Affiliation(s)
- Cuiling Zhang
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122 Jilin People’s Republic of China
| | - Bingjie Wei
- grid.144022.10000 0004 1760 4150Veterinary Medicine College, Northwest A&F University, Shaanxi, 712100 People’s Republic of China
| | - Zirui Liu
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122 Jilin People’s Republic of China
| | - Wei Yao
- Healthcare Department, Agency for Offices Administration, 23 Xinwai Street, Haidian District, Beijing, 100082 People’s Republic of China
| | - Yiquan Li
- grid.440665.50000 0004 1757 641XChangchun University of Chinese Medicine, Changchun, People’s Republic of China
| | - Jing Lu
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122 Jilin People’s Republic of China
| | - Chenchen Ge
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122 Jilin People’s Republic of China
| | - Xiaoyang Yu
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122 Jilin People’s Republic of China
| | - Dapeng Li
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122 Jilin People’s Republic of China
| | - Yilong Zhu
- Changchun University of Chinese Medicine, Changchun, People's Republic of China.
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122, Jilin, People's Republic of China.
| | - Ningyi Jin
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122, Jilin, People's Republic of China. .,Changchun University of Chinese Medicine, Changchun, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, People's Republic of China.
| | - Xiao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Yujinxiang road, 573, Jingyue Economic and Technological Development Zone, Changchun, 130122, Jilin, People's Republic of China. .,Changchun University of Chinese Medicine, Changchun, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, People's Republic of China.
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114
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Kohil A, Abdallah AM, Hussain K, Al-Shafai M. Genetic epidemiology of Woodhouse-Sakati Syndrome in the Greater Middle East region and beyond: a systematic review. Orphanet J Rare Dis 2023; 18:22. [PMID: 36721231 PMCID: PMC9887781 DOI: 10.1186/s13023-023-02614-8] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Woodhouse-Sakati syndrome (WSS) is a rare, autosomal recessive genetic disorder with variable clinical manifestations mainly affecting the endocrine and nervous systems. The aim of this study was to systematically review the genetic basis of WSS and report the genetic variants and clinical phenotypes associated with the disease. METHODS PubMed, Science Direct, Scopus, and Web of Science databases were searched from the time of inception until June 2022. Broad search terms were used to capture the literature describing all genetic variants associated with WSS. The search keywords used are "Woodhouse Sakati" along with the term "mutation" OR "gene" OR "variant" OR "polymorphism". RESULTS Twenty-five eligible studies were included in this study. One hundred and eighty-five patients in 97 families from 12 different countries were diagnosed with WSS. In patients from the Greater Middle East (GME) region, consanguineous marriages were common (67%). Thirteen different DCAF17 variants were associated with WSS development (including 8 identified in the GME region). The most frequent variant was a frameshift deletion variant (c.436delC, p.Ala147Hisfs*9) unique to Arabs that was reported in 11 cases from Tunisia, Kuwait, Qatar, Bahrain, and Saudi Arabia. There were no clear genotype-phenotype correlations for the different variants. CONCLUSIONS This systematic review highlights the molecular basis and clinical manifestations of WSS globally, including the GME region, where the disease is prevalent due to consanguinity. Additional studies are now needed to understand the genotype-phenotype correlation for different DCAF17 variants and their impact on the phenotypic heterogeneity observed in WSS patients.
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Affiliation(s)
- Amira Kohil
- grid.412603.20000 0004 0634 1084Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713 Doha, Qatar
| | - Atiyeh M. Abdallah
- grid.412603.20000 0004 0634 1084Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713 Doha, Qatar
| | - Khalid Hussain
- grid.467063.00000 0004 0397 4222Department of Pediatrics, Division of Endocrinology, Sidra Medicine, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713, Doha, Qatar.
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115
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Jia C, Zhao D, Li Y, Gao Y, Zhang X, Li X, Lv S, Li R, Zhu X, Liu S. Newborn screening and genomic analysis of duchenne muscular dystrophy in Henan, China. Clin Chim Acta 2023; 539:90-6. [PMID: 36516925 DOI: 10.1016/j.cca.2022.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Duchenne Muscular Dystrophy (DMD) is a rare disorder caused by mutations in the dystrophin gene. Recent availability in treatment for DMD raised the need of early screening in our center, but newborn screening (NBS) for DMD has not been carried out in Henan Province. OBJECTIVES To determine an optimal cutoff value through the quantitative determination of the creatine kinase isoform MM (CK-MM) concentration dried blood spot (DBS) to identify male DMD, and to evaluate assess the detection rate and mutation spectrum of DMD in Henan, China. METHODS The CK-MM level in DBS was measured using with a GSP® neonatal creatine kinase -MM kit from 13,110 male newborns to establish the cut-off value for CK-MM. Multiplex ligation-dependent probe amplification (MLPA) were carried out for infants with elevated CK levels to detect DMD gene deletions/ duplications, NGS and sanger sequencing were then applied to exclude MLPA-negative samples to single-nucleotide variants. Phenotype-genotype correlations were analyzed using REVEL For novel missense mutations. RESULTS Statistical analysis of CK-MM value of the 13,110 neonates suggested that the cut-off value may be set as 472 ng/mL. 3 cases of DMD were screened among 13,110 newborns, all of whom had CK-MM levels >600 ng/mL. We detected 4 rare variants in DMD gene, including 2 exon deletions (deletion of exon 52 and deletion from exon 3 to exon 7) and 2 point variants (c.9568C>T and c.4030C>T). Two cases were all exon deletions, one case was compound heterozygous variants. CONCLUSIONS The estimated incidence of male neonatal DMD was 1:4,370 in Henan province. NBS is of great value to the early intervention and treatment of the disease, and is fundamental to support public health decision-making. The experience from this study provided a model that will allow further expansion and facilitate establishment a universal public health screening in Henan hospital systems.
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Sharma S, Shrivastava S, Kausley SB, Rai B, Pandit AB. Coronavirus: a comparative analysis of detection technologies in the wake of emerging variants. Infection 2023; 51:1-19. [PMID: 35471631 DOI: 10.1007/s15010-022-01819-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/30/2022] [Indexed: 01/31/2023]
Abstract
An outbreak of the coronavirus disease caused by a novel pathogen created havoc and continues to affect the entire world. As the pandemic progressed, the scientific community was faced by the limitations of existing diagnostic methods. In this review, we have compared the existing diagnostic techniques such as reverse transcription polymerase chain reaction (RT-PCR), antigen and antibody detection, computed tomography scan, etc. and techniques in the research phase like microarray, artificial intelligence, and detection using novel materials; on the prospect of sample preparation, detection procedure (qualitative/quantitative), detection time, screening efficiency, cost-effectiveness, and ability to detect different variants. A detailed comparison of different techniques showed that RT-PCR is still the most widely used and accepted coronavirus detection method despite certain limitations (single gene targeting- in context to mutations). New methods with similar efficiency that could overcome the limitations of RT-PCR may increase the speed, simplicity, and affordability of diagnosis. In addition to existing devices, we have also discussed diagnostic devices in the research phase showing high potential for clinical use. Our approach would be of enormous benefit in selecting a diagnostic device under a given scenario, which would ultimately help in controlling the current pandemic caused by the coronavirus, which is still far from over with new variants emerging.
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117
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Hirschhorn JW, Dunne J. SARS-CoV-2 Sequencing for Variant Surveillance. Methods Mol Biol 2023; 2621:279-292. [PMID: 37041451 DOI: 10.1007/978-1-0716-2950-5_16] [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] [Indexed: 04/13/2023]
Abstract
In this chapter, next-generation sequencing of the entire viral genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is described. Successful sequencing of the SARS-CoV-2 virus is dependent upon quality of the specimen, adequate coverage of the entire genome, and up-to-date annotation. Some of the advantages of performing SARS-CoV-2 surveillance using next-generation sequencing are scalability, high-throughput, cost, and full genome analysis. Some of the disadvantages can be expensive instrumentation, large upfront reagent and supply costs, increased time-to-result, computational needs, and complicated bioinformatics. This chapter will provide an overview of a modified FDA Emergency Use Authorization procedure for the genomic sequencing of SARS-CoV-2. The procedure is also referred to as the research use only (RUO) version.
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Affiliation(s)
- Julie Woolworth Hirschhorn
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA.
| | - Jaclyn Dunne
- College of Graduate Studies, Medical University of South Carolina, Charleston, SC, USA
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Deepanshi, Budhiraja I, Garg D, Kumar N, Sharma R. A comprehensive review on variants of SARS-CoVs-2: Challenges, solutions and open issues. Comput Commun 2023; 197:34-51. [PMID: 36313592 PMCID: PMC9598046 DOI: 10.1016/j.comcom.2022.10.013] [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: 07/19/2022] [Revised: 09/14/2022] [Accepted: 10/19/2022] [Indexed: 10/29/2023]
Abstract
SARS-CoV-2 is an infected disease caused by one of the variants of Coronavirus which emerged in December 2019. It is declared a pandemic by WHO in March 2020. COVID-19 outbreak has put the world on a halt and is a major threat to the public health system. It has shattered the world with its effects on different areas as the pandemic hit the world in a number of waves with different variants and mutations. Each variant and mutation have different transmission and infection rates in the human population. More than 609 million people have tested positive and more than 6.5 million people have died due to this disease as per 14th September 2022. Despite of numerous efforts, precautions and vaccination the infection has grown rapidly in the world. In this paper, we aim to give a holistic overview of COVID-19 its variants, game theory perspective, effects on the different social and economic areas, diagnostic advancements, treatment methods. A taxonomy is made for the proper insight of the work demonstrated in the paper. Finally, we discuss the open issues associated with COVID-19 in different fields and futuristic research trends in the area. The main aim of the paper is to provide comprehensive literature that covers all the areas and provide an expert understanding of the COVID-19 techniques and potentially be further utilized to combat the outbreak of COVID-19.
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Affiliation(s)
- Deepanshi
- School of Computer Science Engineering and Technology, Bennett University, Uttar Pradesh, India
| | - Ishan Budhiraja
- School of Computer Science Engineering and Technology, Bennett University, Uttar Pradesh, India
| | - Deepak Garg
- School of Computer Science Engineering and Technology, Bennett University, Uttar Pradesh, India
| | - Neeraj Kumar
- Department of Computer Science and Engineering, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
- Department of Electrical and Computer Engineering, Lebanese American University, Beirut, Lebanon
- School of Computer Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand
- Faculty of Computing and IT, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Rohit Sharma
- Department of Electronics & Communication Engineering, SRM Institute of Science and Technology, NCR Campus, Modinagar, Ghaziabad, UP, India
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Bansal V. HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data. Methods Mol Biol 2023; 2590:139-147. [PMID: 36335497 DOI: 10.1007/978-1-0716-2819-5_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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Rapid advances in high-throughput DNA sequencing technologies have enabled variant discovery from whole-genome sequencing (WGS) datasets; however linking variants on a chromosome together into haplotypes, also known as haplotype phasing, remains difficult. Human genomes are diploid and haplotype phasing is crucial for the complete interpretation and analysis of genetic variation.Hapcut2 ( https://github.com/vibansal/HapCUT2 ) is an open-source software for phasing diploid genomes using sequence data generated using different sequencing technologies and experimental methods. In this article, we give an overview of the algorithm used by Hapcut2 and describe how to use Hapcut2 for haplotype phasing of individual genomes using different types of sequence data.
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Affiliation(s)
- Vikas Bansal
- School of Medicine, University of California San Diego, La Jolla, CA, USA.
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120
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Grunin M, Palmer E, de Jong S, Jin B, Rinker D, Moth C, Capra JA, Haines JL, Bush WS, den Hollander AI. Integrating Computational Approaches to Predict the Effect of Genetic Variants on Protein Stability in Retinal Degenerative Disease. Adv Exp Med Biol 2023; 1415:157-163. [PMID: 37440029 DOI: 10.1007/978-3-031-27681-1_24] [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] [Indexed: 07/14/2023]
Abstract
Protein function can be impacted by changes in protein structure stability, but determining which change has impact is complex. Stability can be affected by a large change in the tertiary (3D) structure of the protein or due to free-energy changes caused by single amino acid substitutions. Changes in the DNA sequence can have minor or major impact on protein stability, which can lead to disease. Inherited retinal degenerations are generally caused by single mutations which are mostly located in protein-coding regions, while age-related macular degeneration (AMD) is a complex disorder that can be influenced by some genetic variants impacting proteins involved in the disease, although not all AMD risk variants lead to amino acid changes. Here, we review ways that proteins may be affected, the identification and understanding of these changes, and how to identify causal changes that can be targeted to develop treatments to alleviate retinal degenerative disease.
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Affiliation(s)
- Michelle Grunin
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
| | - Ellen Palmer
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Bowen Jin
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Christopher Moth
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
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Chugh A, Sehgal I, Khurana N, Verma K, Rolta R, Vats P, Salaria D, Fadare OA, Awofisayo O, Verma A, Phartyal R, Verma M. Comparative docking studies of drugs and phytocompounds for emerging variants of SARS-CoV-2. 3 Biotech 2023; 13:36. [PMID: 36619821 PMCID: PMC9815891 DOI: 10.1007/s13205-022-03450-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 08/27/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
In the last three years, COVID-19 has impacted the world with back-to-back waves leading to devastating consequences. SARS-CoV-2, the causative agent of COVID-19, was first detected in 2019 and since then has spread to 228 countries. Even though the primary focus of research groups was diverted to fight against COVID-19, yet no dedicated drug has been developed to combat the emergent life-threatening medical conditions. In this study, 35 phytocompounds and 43 drugs were investigated for comparative docking analysis. Molecular docking and virtual screening were performed against SARS-CoV-2 spike glycoprotein of 13 variants using AutoDock Vina tool 1.5.6 and Discovery Studio, respectively, to identify the most efficient drugs. Selection of the most suitable compounds with the best binding affinity was done after screening for toxicity, ADME (absorption, distribution, metabolism and excretion) properties and drug-likeliness. The potential candidates were discovered to be Liquiritin (binding affinities ranging between -7.0 and -8.1 kcal/mol for the 13 variants) and Apigenin (binding affinities ranging between -6.8 and -7.3 kcal/mol for the 13 variants) based on their toxicity and consistent binding affinity with the Spike protein of all variants. The stability of the protein-ligand complex was determined using Molecular dynamics (MD) simulation of Apigenin with the Delta plus variant of SARS-CoV-2. Furthermore, Liquiritin and Apigenin were also found to be less toxic than the presently used drugs and showed promising results based on in silico studies, though, confirmation using in vitro studies is required. This in-depth comparative investigation suggests potential drug candidates to fight against SARS-CoV-2 variants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03450-6.
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Affiliation(s)
- Ananya Chugh
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Ishita Sehgal
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Nimisha Khurana
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Kangna Verma
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Rajan Rolta
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Pranjal Vats
- School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Deeksha Salaria
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Olatomide A. Fadare
- Organic Chemistry Research Lab, Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Osun 220282 Nigeria
| | - Oladoja Awofisayo
- Department of Pharmaceutical and Medical Chemistry, University of Uyo, Uyo, 520003 Nigeria
| | - Anita Verma
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Rajendra Phartyal
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Delhi, 110007 India
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Barmania F, Mellet J, Holborn MA, Pepper MS. Genetic Associations with Coronavirus Susceptibility and Disease Severity. Adv Exp Med Biol 2023; 1412:119-140. [PMID: 37378764 DOI: 10.1007/978-3-031-28012-2_6] [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] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) global public health emergency, and the disease it causes is highly variable in its clinical presentation. Host genetic factors are increasingly recognised as a determinant of infection susceptibility and disease severity. Several initiatives and groups have been established to analyse and review host genetic epidemiology associated with COVID-19 outcomes. Here, we review the genetic loci associated with COVID-19 susceptibility and severity focusing on the common variants identified in genome-wide association studies.
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Affiliation(s)
- Fatima Barmania
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Megan A Holborn
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
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Alquraan L, Alzoubi KH, Rababa'h SY. Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity. Inform Med Unlocked 2023; 39:101256. [PMID: 37131549 PMCID: PMC10127666 DOI: 10.1016/j.imu.2023.101256] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 02/24/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/04/2023] Open
Abstract
Numerous variations of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), including D614G, B.1.1.7 (United Kingdom), B.1.1.28 (Brazil P1, P2), CAL.20C (Southern California), B.1.351 (South Africa), B.1.617 (B.1.617.1 Kappa & Delta B.1.617.2) and B.1.1.529, have been reported worldwide. The receptor-binding domain (RBD) of the spike (S) protein is involved in virus-cell binding, where virus-neutralizing antibodies (NAbs) react. Novel variants in the S-protein could maximize viral affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor and increase virus transmission. Molecular detection with false-negative results may refer to mutations in the part of the virus's genome used for virus diagnosis. Furthermore, these changes in S-protein structure alter the neutralizing ability of NAbs, resulting in a reduction in vaccine efficiency. Further information is needed to evaluate how new mutations may affect vaccine efficacy.
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Affiliation(s)
- Laiali Alquraan
- Department of Biology, Faculty of Science, Yarmouk University, Irbid, Jordan
| | - Karem H Alzoubi
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Suzie Y Rababa'h
- Department of Medical Science, Irbid Faculty, Al-Balqa Applied University (BAU), Irbid, Jordan
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Abulsoud AI, El-Husseiny HM, El-Husseiny AA, El-Mahdy HA, Ismail A, Elkhawaga SY, Khidr EG, Fathi D, Mady EA, Najda A, Algahtani M, Theyab A, Alsharif KF, Albrakati A, Bayram R, Abdel-Daim MM, Doghish AS. Mutations in SARS-CoV-2: Insights on structure, variants, vaccines, and biomedical interventions. Biomed Pharmacother 2023; 157:113977. [PMID: 36370519 PMCID: PMC9637516 DOI: 10.1016/j.biopha.2022.113977] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
COVID-19 is a worldwide pandemic caused by SARS-coronavirus-2 (SARS-CoV-2). Less than a year after the emergence of the Covid-19 pandemic, many vaccines have arrived on the market with innovative technologies in the field of vaccinology. Based on the use of messenger RNA (mRNA) encoding the Spike SARS-Cov-2 protein or on the use of recombinant adenovirus vectors enabling the gene encoding the Spike protein to be introduced into our cells, these strategies make it possible to envisage the vaccination in a new light with tools that are more scalable than the vaccine strategies used so far. Faced with the appearance of new variants, which will gradually take precedence over the strain at the origin of the pandemic, these new strategies will allow a much faster update of vaccines to fight against these new variants, some of which may escape neutralization by vaccine antibodies. However, only a vaccination policy based on rapid and massive vaccination of the population but requiring a supply of sufficient doses could make it possible to combat the emergence of these variants. Indeed, the greater the number of infected individuals, the faster the virus multiplies, with an increased risk of the emergence of variants in these RNA viruses. This review will discuss SARS-CoV-2 pathophysiology and evolution approaches in altered transmission platforms and emphasize the different mutations and how they influence the virus characteristics. Also, this article summarizes the common vaccines and the implication of the mutations and genetic variety of SARS-CoV-2 on the COVID-19 biomedical arbitrations.
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Affiliation(s)
- Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Hussein M El-Husseiny
- Laboratory of Veterinary Surgery, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt.
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Emad Gamil Khidr
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Doaa Fathi
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Eman A Mady
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Animal Hygiene, Behavior and Management, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt
| | - Agnieszka Najda
- Department of Vegetable Crops and Medicinal Plants University of Life Sciences, Lublin 50A Doświadczalna Street, 20-280, Lublin, Poland.
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia
| | - Abdulrahman Theyab
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia; College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Khalaf F Alsharif
- Department of Clinical Laboratory sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Roula Bayram
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia; Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt.
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Santos GRBD, Cunha APA, Batista ZDS, Silva MACND, Figueiredo FVD, Santos FRBD, Fraga EDC, Barros MC, Vidal FCB, Nascimento MDDSB. HPV 18 variants in women with cervical cancer in Northeast Brazil. Braz J Infect Dis 2022; 27:102734. [PMID: 36587927 PMCID: PMC9871062 DOI: 10.1016/j.bjid.2022.102734] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Human Papillomavirus (HPV) is the main etiological factor for the development of cervical cancer. HPV 18 is the second most frequent type, accounting for up to 65% of all cases. HPV intratypic variation may influence the potential for progression to invasive cancer. The aim of this study was to evaluate the prevalence of human papillomavirus 18 intratypic variants in cervical cancer samples from women in the state of Maranhão, Brazil. METHODS The study included 118 women over 18 years of age with a diagnosis of cervical cancer. Tumor fragments were collected and subjected to DNA extraction and Polymerase Chain Reaction (PCR) for HPV detection using the PGMY09/11 and GP+5/6 primers. Positive samples were submitted to automated sequencing for viral genotyping. To determine the HPV 18 lineages, positive samples were submitted to PCR, using specific primers to amplify the LCR and E6 regions of HPV 18 virus. RESULTS HPV was present in 88 women (73.3%). Of those, 48 (54%) were HPV 16, the most prevalent, followed by 12 (13.6%) HPV 18. Histologically, squamous cell carcinoma was predominant (79.1%). Among the HPV 18 variants identified, 10 (80%) belonged to lineage A, and sublineages A1, A2, A3, and A4. Two (29%) HPV 18 B variant was also detected, with the sublineages B1 and B2. In this study, the C variant was not found. There was no statistically significant association between the HPV 18 lineages found and sociodemographic and lifestyle variables (p > 0.05). CONCLUSIONS A higher frequency of HPV 16 and 18 were found in women with cervical cancer in the state of Maranhão, Brazil, with a high prevalence of the lineage A among women with HPV 18.
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Affiliation(s)
| | - Ana Paula Almeida Cunha
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Saúde do Adulto, São Luís, MA, Brazil
| | - Zulmira da Silva Batista
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Saúde do Adulto, São Luís, MA, Brazil
| | | | - Fábio Vidal de Figueiredo
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Saúde do Adulto, São Luís, MA, Brazil
| | | | - Elmary da Costa Fraga
- Centro de Estudos Superiores de Caxias (CESC), da Universidade Estadual do Maranhão (UEMA), Caxias, MA, Brazil
| | - Maria Claudene Barros
- Centro de Estudos Superiores de Caxias (CESC), da Universidade Estadual do Maranhão (UEMA), Caxias, MA, Brazil
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Choi G, Lim AY, Choi S, Park K, Lee SY, Kim JH. Viral shedding patterns of symptomatic SARS-CoV-2 infections by periods of variant predominance and vaccination status in Gyeonggi Province, Korea. Epidemiol Health 2022; 45:e2023008. [PMID: 36596734 PMCID: PMC10581894 DOI: 10.4178/epih.e2023008] [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: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES We compared the viral cycle threshold (Ct) values of infected patients to better understand viral kinetics by vaccination status during different periods of variant predominance in Gyeonggi Province, Korea. METHODS We obtained case-specific data from the coronavirus disease 2019 (COVID-19) surveillance system, Gyeonggi in-depth epidemiological report system, and Health Insurance Review & Assessment Service from January 2020 to January 2022. We defined periods of variant predominance and explored Ct values by analyzing viral sequencing test results. Using a generalized additive model, we performed a nonlinear regression analysis to determine viral kinetics over time. RESULTS Cases in the Delta variant's period of predominance had higher viral shedding patterns than cases in other periods. The temporal change of viral shedding did not vary by vaccination status in the Omicron-predominant period, but viral shedding decreased in patients who had completed their third vaccination in the Delta-predominant period. During the Delta-predominant and Omicron-predominant periods, the time from symptom onset to peak viral shedding based on the E gene was approximately 2.4 days (95% confidence interval [CI], 2.2 to 2.5) and 2.1 days (95% CI, 2.0 to 2.1), respectively. CONCLUSIONS In one-time tests conducted to diagnose COVID-19 in a large population, although no adjustment for individual characteristics was conducted, it was confirmed that viral shedding differed by the predominant strain and vaccination history. These results show the value of utilizing hundreds of thousands of test data produced at COVID-19 screening test centers.
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Affiliation(s)
- Gawon Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Ah-Young Lim
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Sojin Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Kunhee Park
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Soon Young Lee
- Department of Preventive Medicine and Public Health, Ajou University School of Medicine, Suwon, Korea
| | - Jong-Hun Kim
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
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Al Anazi AH, Ammar AS, Al-Hajj M, Cyrus C, Aljaafari D, Khoda I, Abdelfatah AK, Alsulaiman AA, Alanazi F, Alanazi R, Gandla D, Lad H, Barayan S, Keating BJ, Al-Ali AK. Whole-exome sequencing of a Saudi epilepsy cohort reveals association signals in known and potentially novel loci. Hum Genomics 2022; 16:71. [PMID: 36539902 PMCID: PMC9764464 DOI: 10.1186/s40246-022-00444-6] [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: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Epilepsy, a serious chronic neurological condition effecting up to 100 million people globally, has clear genetic underpinnings including common and rare variants. In Saudi Arabia, the prevalence of epilepsy is high and caused mainly by perinatal and genetic factors. No whole-exome sequencing (WES) studies have been performed to date in Saudi Arabian epilepsy cohorts. This offers a unique opportunity for the discovery of rare genetic variants impacting this disease as there is a high rate of consanguinity among large tribal pedigrees. RESULTS We performed WES on 144 individuals diagnosed with epilepsy, to interrogate known epilepsy-related genes for known and functional novel variants. We also used an American College of Medical Genetics (ACMG) guideline-based variant prioritization approach in an attempt to discover putative causative variants. We identified 32 potentially causative pathogenic variants across 30 different genes in 44/144 (30%) of these Saudi epilepsy individuals. We also identified 232 variants of unknown significance (VUS) across 101 different genes in 133/144 (92%) subjects. Strong enrichment of variants of likely pathogenicity was observed in previously described epilepsy-associated loci, and a number of putative pathogenic variants in novel loci are also observed. CONCLUSION Several putative pathogenic variants in known epilepsy-related loci were identified for the first time in our population, in addition to several potential new loci which may be prioritized for further investigation.
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Affiliation(s)
- Abdulrahman H. Al Anazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ahmed S. Ammar
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mahmoud Al-Hajj
- grid.415296.d0000 0004 0607 1539Department of Neurosurgery, King Fahd Hospital, Alhafof, Saudi Arabia
| | - Cyril Cyrus
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, 31441 Dammam, Saudi Arabia
| | - Danah Aljaafari
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Iname Khoda
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ahmed K. Abdelfatah
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdullah A. Alsulaiman
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Firas Alanazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Rawan Alanazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Divya Gandla
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Hetal Lad
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Samar Barayan
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Brendan J. Keating
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Amein K. Al-Ali
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, 31441 Dammam, Saudi Arabia
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Kuanyshbek A, Wang M, Andersson Å, Tuifua M, Palmer EE, Sachdev RK, Mu TW, Vetter I, Keramidas A. Anti-seizure mechanisms of midazolam and valproate at the β2(L51M) variant of the GABA A receptor. Neuropharmacology 2022; 221:109295. [PMID: 36257447 PMCID: PMC9981329 DOI: 10.1016/j.neuropharm.2022.109295] [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: 02/13/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
Genetic sequencing is identifying an expanding number of variants of GABAA receptors associated with human epilepsies. We identified a new de novo variant of the β2 subunit (β2L51M) of the inhibitory GABAA receptor associated with seizures. Our analysis determined the pathogenicity of the variant and the effects of anti-seizure medications. Our data demonstrates that the variant reduced cell surface trafficking and peak GABA-gated currents. Synaptic currents mediated by variant-containing receptors decayed faster than wild-type and single receptor currents showed that the variant shortened the duration of receptor activity by decreasing receptor open times. We tested the effects of the anti-seizure medications, midazolam, carbamazepine and valproate and found that all three enhance variant receptor surface expression. Additionally, midazolam restored receptor function by increasing single receptor active periods and synaptic current decay times towards wild-type levels. By contrast, valproate increased synaptic peak currents, event frequency and promoted synaptic bursting. Our study identifies a new disease-causing variant to the GABAA receptor, profiles its pathogenic effects and demonstrates how anti-seizure drugs correct its functional deficits.
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Affiliation(s)
- Alibek Kuanyshbek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Meng Wang
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Åsa Andersson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Marie Tuifua
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Elizabeth E Palmer
- Sydney Children's Hospital Network, Randwick Sydney Australia and School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Rani K Sachdev
- Sydney Children's Hospital Network, Randwick Sydney Australia and School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Ting-Wei Mu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; School of Pharmacy, The University of Queensland, Woolloongabba, Queensland, 4102, Australia
| | - Angelo Keramidas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
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Li M, Wu Z, Bian X, Jiang Q, Fan S, Zhang K, Guo Z, Hui L, Guo M, Zhen F, Zhang J. Clinical and psychological status analysis of children and parents infected with familial aggregation omicron variant in Shanghai in parent-child ward. Heliyon 2022; 8:e12151. [PMID: 36578400 DOI: 10.1016/j.heliyon.2022.e12151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/21/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Aims To analyze the clinical characteristics, treatment outcomes and sleep psychological problems of children and parents infected with familial aggregation Omicron variants under a parent-child ward treatment mode to provide a theoretical reference for the diagnosis and comprehensive treatment of Omicron variant strains. Methods The clinical data of 225 children and 230 adult family members admitted were retrospectively collected and analyzed to investigate their clinical characteristics and response to treatments. Results The proportion of infected adults and children was the same, and the proportion of children with mild disease was higher than that of adults, but the clinical symptoms were milder. The clinical symptoms of fever, nausea, vomiting and wheezing in children were significantly higher than in adults (P < 0.05). In addition, dry pharynx, pharynx itching and pharyngeal pain were lower than in adults (P < 0.05). The time of turning negative in the moderate group was longer than in the mild group, and the time of turning negative in the unvaccinated group was higher than in the vaccinated group (P < 0.05). The Cycle Threshold Value (Ct value) of Open Reading Frame 1ab (ORF1ab) and Nucleocapsid protein (N) gene of children were higher adults. The increase in the rate of Ct value of ORF1ab and N gene in adults treated with Traditional Chinese Medicine (TCM) was significantly higher than in those who underwent symptomatic treatment (P < 0.01). Based on the Children's Sleep Habits Questionnaire (CSHQ)score, we found varying levels of sleep problems in sleeping habits, latency and anxiety, night awakenings and abnormal sleep at all ages (P < 0.05). In the adult group, those with Self-Rating Scale of Sleep (SRSS) scores ≥3 accounted for more than 50% of adults with insomnia, sleep deprivation, sleep instability and early awakening. The proportion of adults with anxiety and depression was 21.3% and 16.4%. Conclusion Infections in children and adults during this pandemic were mainly associated with familial aggregation infections, and their clinical symptoms were mainly located in the upper respiratory tract. With comprehensive treatment, children became negative faster, vaccination led to faster recovery, and although some patients experienced sleeping and psychological issues, all patients had good prognoses following comprehensive diagnosis under a parent-child ward treatment mode.
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Campos DMDO, Silva MKD, Barbosa ED, Leow CY, Fulco UL, Oliveira JIN. Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants. Comput Biol Chem 2022; 101:107754. [PMID: 36037724 PMCID: PMC9385604 DOI: 10.1016/j.compbiolchem.2022.107754] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
The current COVID-19 pandemic, an infectious disease caused by the novel coronavirus (SARS-CoV-2), poses a threat to global health because of its high rate of spread and death. Currently, vaccination is the most effective method to prevent the spread of this disease. In the present study, we developed a novel multiepitope vaccine against SARS-CoV-2 containing Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (BA.1) variants. To this end, we performed a robust immunoinformatics approach based on multiple epitopes of the four structural proteins of SARS-CoV-2 (S, M, N, and E) from 475 SARS-CoV-2 genomes sequenced from the regions with the highest number of registered cases, namely the United States, India, Brazil, France, Germany, and the United Kingdom. To investigate the best immunogenic epitopes for linear B cells, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL), we evaluated antigenicity, allergenicity, conservation, immunogenicity, toxicity, human population coverage, IFN-inducing, post-translational modifications, and physicochemical properties. The tertiary structure of a vaccine prototype was predicted, refined, and validated. Through docking experiments, we evaluated its molecular coupling to the key immune receptor Toll-Like Receptor 3 (TLR3). To improve the quality of docking calculations, quantum mechanics/molecular mechanics calculations (QM/MM) were used, with the QM part of the simulations performed using the density functional theory formalism (DFT). Cloning and codon optimization were performed for the successful expression of the vaccine in E. coli. Finally, we investigated the immunogenic properties and immune response of our SARS-CoV-2 multiepitope vaccine. The results of the simulations show that administering our prototype three times significantly increases the antibody response and decreases the amount of antigens. The proposed vaccine candidate should therefore be tested in clinical trials for its efficacy in neutralizing SARS-CoV-2.
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Affiliation(s)
- Daniel Melo de Oliveira Campos
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Maria Karolaynne da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Emmanuel Duarte Barbosa
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | | | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
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Abstract
As an important part of adaptive immunity, T cells are indispensable in the defense against pathogens including viruses. SARS-CoV-2 is a new human coronavirus that occurred at the end of 2019 and has caused the COVID-19 pandemic. Nevertheless, most of the infected patients recovered without any antiviral therapies, suggesting an effective immunity developed in the bodies. T cell immunity responds upon SARS-CoV-2 infection or vaccination and plays crucial roles in eliminating the viruses and generating T cell memory. Specifically, a subpopulation of CD4+ T cells could support the production of anti-SARS-CoV-2 antibodies, and cytotoxic CD8+ T cells are also protective against the infection. SARS-CoV-2-recognizing T cells could be detected in SARS-CoV-2-unexposed donors, but the role of these cross-reactive T cells is still in debate. T cell responses could be diverse across individuals, mainly due to the polymorphism of HLAs. Thus, compared to antibodies, T cell responses are generally less affected by the mutations of SARS-CoV-2 variants. Up to now, a huge number of studies on SARS-CoV-2-responsive T cells have been published. In this review, we introduced some major findings addressing the questions in the main aspects about T cell responses elicited by SARS-CoV-2, to summarize the current understanding of COVID-19.
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Affiliation(s)
- Xiuyuan Lu
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Epitope Analysis Team, Center for Advanced Modalities and DDS, Osaka University, Suita, 565-0871 Japan
| | - Sho Yamasaki
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Epitope Analysis Team, Center for Advanced Modalities and DDS, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, 565-0871 Japan ,grid.177174.30000 0001 2242 4849Division of Molecular Design, Research Center for Systems Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
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Sheikh A, Huang H, Parvin S, Badruzzaman M, Ahamed T, Hossain E, Baran IS, Saud ZA. A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2. J Genet Eng Biotechnol 2022; 20:149. [PMID: 36318347 PMCID: PMC9626712 DOI: 10.1186/s43141-022-00431-3] [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: 10/25/2021] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
Background COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs. Objective In this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies. Methods SARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes. Results We have identified six unique variants, G---AAC, T---AAC---T, AAC---T, AAC--------T, C----------T, and C--------C, at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3′-5′ exonuclease, and 2′-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis. Conclusion Studying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00431-3.
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Affiliation(s)
- Afzal Sheikh
- grid.443108.a0000 0000 8550 5526Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - He Huang
- Research and Development Department, Bioengineering Lab. Co., Ltd, 657 Nagatake Midori-ku, Sagamihara-shi, Kanagawa-ken 252-0154 Japan
| | - Sultana Parvin
- grid.263023.60000 0001 0703 3735Department of Biology, Faculty of Science and Engineering, Saitama University, Saitama, Japan
| | - Mohammad Badruzzaman
- grid.443108.a0000 0000 8550 5526Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - Tofayel Ahamed
- grid.443108.a0000 0000 8550 5526Department of Agroforestry and Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - Ekhtear Hossain
- grid.263880.70000 0004 0386 0655Department of Biological Sciences and Chemistry, Southern University and A&M College, 244 William James Hall, Baton Rouge, LA 70813 USA
| | - Iri Sato Baran
- Genesis Institute of Genetic Research, Genesis Healthcare Corporation, Yebisu Garden Place Tower 15F/26F 4-20-3 Ebisu, Shibuya-ku, Tokyo, Japan
| | - Zahangir Alam Saud
- grid.412656.20000 0004 0451 7306Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205 Bangladesh
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Zuo JY, Chen HX, Liu ZG, Yang Q, He GW. Identification and functional analysis of variants of MYH6 gene promoter in isolated ventricular septal defects. BMC Med Genomics 2022; 15:213. [PMID: 36209093 PMCID: PMC9548206 DOI: 10.1186/s12920-022-01365-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 06/14/2022] [Accepted: 09/21/2022] [Indexed: 11/11/2022] Open
Abstract
Background Ventricular septal defect is the most common form of congenital heart diseases. MYH6 gene has a critical effect on the growth and development of the heart but the variants in the promoter of MYH6 is unknown. Patients and methods In 604 of the subjects (311 isolated and sporadic ventricular septal defect patients and 293 healthy controls), DNA was extracted from blood samples and MYH6 gene promoter region variants were analyzed by sequencing. Further functional verification was performed by cellular experiments using dual luciferase reporter gene analysis, electrophoretic mobility shift assays, and bioinformatics analysis. Results Nine variants were identified in the MYH6 gene promoter and two of those variants [g.4085G>C(rs1222539675) and g.4716G>A(rs377648095)] were only found in the ventricular septal defect patients. Cellular function experiments showed that these two variants reduced the transcriptional activity of the MYH6 gene promoter (p < 0.001). Further analysis with online JASPAR database suggests that these variants may alter a set of putative transcription factor binding sites that possibly lead to changes in myosin subunit expression and ventricular septal defect formation. Conclusions Our study for the first time identifies variants in the promoter region of the MYH6 gene in Chinese patients with isolated and sporadic ventricular septal defect. These variants significantly reduced MYH6 gene expression and affected transcription factor binding sites and therefore are pathogenic. The present study provides new insights in the role of the MYH6 gene promoter region to better understand the genetic basis of VSD formation. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01365-y.
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Affiliation(s)
- Ji-Yang Zuo
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China.,Clinical School of Cardiovascular Disease, Tianjin Medical University, Tianjin, China
| | - Huan-Xin Chen
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Zhi-Gang Liu
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Qin Yang
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Guo-Wei He
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China.
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Helmy SA, El-Morsi RM, Helmy SAM, El-Masry SM. Towards novel nano-based vaccine platforms for SARS-CoV-2 and its variants of concern: Advances, challenges and limitations. J Drug Deliv Sci Technol 2022; 76:103762. [PMID: 36097606 PMCID: PMC9452404 DOI: 10.1016/j.jddst.2022.103762] [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: 02/28/2022] [Revised: 08/07/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022]
Abstract
Vaccination is the most effective tool available for fighting the spread of COVID-19. Recently, emerging variants of SARS-CoV-2 have led to growing concerns about increased transmissibility and decreased vaccine effectiveness. Currently, many vaccines are approved for emergency use and more are under development. This review highlights the ongoing advances in the design and development of different nano-based vaccine platforms. The challenges, limitations, and ethical consideration imposed by these nanocarriers are also discussed. Further, the effectiveness of the leading vaccine candidates against all SARS-CoV-2 variants of concern are highlighted. The review also focuses on the possibility of using an alternative non-invasive routes of vaccine administration using micro and nanotechnologies to enhance vaccination compliance and coverage.
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Affiliation(s)
- Sally A Helmy
- Department of Clinical and Hospital Pharmacy, Faculty of Pharmacy, Taibah University, AL-Madinah AL-Munawarah, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Rasha M El-Morsi
- Department of Microbiology and Immunology, Faculty of Pharmacy, Delta University for Science and Technology, Egypt
| | - Soha A M Helmy
- Department of Languages and Translation, College of Arts and Humanities, Taibah University, AL-Madinah AL-Munawarah, Saudi Arabia
- Department of Foreign Languages, Faculty of Education, Tanta University, Tanta, Egypt
| | - Soha M El-Masry
- Department of Pharmaceutics, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
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Asghar A, Imran HM, Bano N, Maalik S, Mushtaq S, Hussain A, Varjani S, Aleya L, Iqbal HMN, Bilal M. SARS-COV-2/COVID-19: scenario, epidemiology, adaptive mutations, and environmental factors. Environ Sci Pollut Res Int 2022; 29:69117-69136. [PMID: 35947257 PMCID: PMC9363873 DOI: 10.1007/s11356-022-22333-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The coronavirus pandemic of 2019 has already exerted an enormous impact. For over a year, the worldwide pandemic has ravaged the whole globe, with approximately 250 million verified human infection cases and a mortality rate surpassing 4 million. While the genetic makeup of the related pathogen (SARS-CoV-2) was identified, many unknown facets remain a mystery, comprising the virus's origin and evolutionary trend. There were many rumors that SARS-CoV-2 was human-borne and its evolution was predicted many years ago, but scientific investigation proved them wrong and concluded that bats might be the origin of SARS-CoV-2 and pangolins act as intermediary species to transmit the virus from bats to humans. Airborne droplets were found to be the leading cause of human-to-human transmission of this virus, but later studies showed that contaminated surfaces and other environmental factors are also involved in its transmission. The evolution of different SARS-CoV-2 variants worsens the condition and has become a challenge to overcome this pandemic. The emergence of COVID-19 is still a mystery, and scientists are unable to explain the exact origin of SARS-CoV-2. This review sheds light on the possible origin of SARS-CoV-2, its transmission, and the key factors that worsen the situation.
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Affiliation(s)
- Asma Asghar
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Hafiz Muhammad Imran
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Naheed Bano
- Department of Fisheries & Aquaculture, MNS-University of Agriculture, Multan, Pakistan
| | - Sadia Maalik
- Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Asim Hussain
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, 382 010, Gujarat, India
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, 64849, Monterrey, Mexico
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China.
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Dhawan M, Saied AA, Mitra S, Alhumaydhi FA, Emran TB, Wilairatana P. Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2? Biomed Pharmacother 2022; 154:113522. [PMID: 36030585 PMCID: PMC9376347 DOI: 10.1016/j.biopha.2022.113522] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/19/2022] Open
Abstract
Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid the serious containment efforts against COVID-19 that include physical measures, pharmacological repurposing, immunization, and genomic/community surveillance. Omicron variant (B.1.1.529) has been identified as a highly modified, contagious, and crucial variant among the five VOCs of SARS-CoV-2. The increased affinity of the spike protein (S-protein), and host receptor, angiotensin converting enzyme-2 (ACE-2), due to a higher number of mutations in the receptor-binding domain (RBD) of the S-protein has been proposed as the primary reason for the decreased efficacy of majorly available vaccines against the Omicron variant and the increased transmissible nature of the Omicron variant. Because of its significant competitive advantage, the Omicron variant and its sublineages swiftly surpassed other variants to become the dominant circulating lineages in a number of nations. The Omicron variant has been identified as a prevalent strain in the United Kingdom and South Africa. Furthermore, the emergence of recombinant variants through the conjunction of the Omicron variant with other variants or by the mixing of the Omicron variant's sublineages/subvariants poses a major threat to humanity. This raises various issues and hazards regarding the Omicron variant and its sublineages, such as an Omicron variant breakout in susceptible populations among fully vaccinated persons. As a result, understanding the features and genetic implications of this variant is crucial. Hence, we explained in depth the evolution and features of the Omicron variant and analyzed the repercussions of spike mutations on infectiousness, dissemination ability, viral entry mechanism, and immune evasion. We also presented a viewpoint on feasible strategies for precluding and counteracting any future catastrophic emergence and spread of the omicron variant and its sublineages that could result in a detrimental wave of COVID-19 cases.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, Punjab, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
| | - AbdulRahman A Saied
- National Food Safety Authority (NFSA), Aswan Branch, Aswan 81511, Egypt; Ministry of Tourism and Antiquities, Aswan Office, Aswan 81511, Egypt
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh.
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
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Oehler RL, Vega VR. Worldwide vaccine inequality threatens to unleash the next COVID-19 variant. Int J Infect Dis 2022; 123:133-135. [PMID: 35988865 PMCID: PMC9385581 DOI: 10.1016/j.ijid.2022.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/19/2022] [Accepted: 08/13/2022] [Indexed: 12/14/2022] Open
Abstract
The emergence of the Omicron variant (B.1.1.529 BA.1) near Johannesburg heralded the development of an unprecedented number of new COVID-19 infections across South Africa in November 2021. Omicron and its subvariants would soon become the dominant strains across Africa, Europe, and the United States. As with the Delta variant (B.1.617.2), Omicron emerged from an industrialized nation with one of the lowest vaccination rates of any well-developed country. The emergence of variants from undervaccinated regions is a direct consequence of the virus replicating unchecked through an unprotected population. Despite this, the United States and other higher-income nations have adopted a strategy of preferentially inoculating their citizens with multiple and booster doses, whereas lower-income nations struggle with vaccine availability, infrastructure, and their own vaccine manufacturing capability. Much more needs to be done to address worldwide vaccine inequities and prevent the emergence of the next devastating variant. The persistence of the pandemic anywhere remains an ongoing threat to citizens everywhere.
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Affiliation(s)
- Richard L Oehler
- James A Haley Veterans Hospital, Division of Infectious Diseases and International Medicine, University of South Florida Morsani College of Medicine, Tampa, USA.
| | - Vivian R Vega
- James A Haley Veterans Hospital, Division of Infectious Diseases and International Medicine, University of South Florida Morsani College of Medicine, Tampa, USA.
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Vitiello A, La Porta R, Trama U, Ferrara F, Zovi A, Auti AM, Di Domenico M, Boccellino M. Pandemic COVID-19, an update of current status and new therapeutic strategies. Naunyn Schmiedebergs Arch Pharmacol 2022; 395:1159-1165. [PMID: 35779085 DOI: 10.1007/s00210-022-02265-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 02/28/2022] [Accepted: 06/14/2022] [Indexed: 12/15/2022]
Abstract
The global COVID-19 pandemic is underway. In recent weeks, several countries throughout the globe, and particularly in Europe, have experienced an exponential increase in the number of individuals infected with COVID-19, probably induced by a new variant of SARS-CoV-2, called the "Omicron variant." Mass vaccination against COVID-19 continues worldwide. Are authorized mRNA vaccines effective against the new Omicron variant? Recently, several pharmaceutical companies have developed oral antiviral pills against SARS-CoV-2, i.e., molnupiravir and paxlovid, that inhibit SARS-CoV-2 viral replication by acting on the RNA polymerase of SARS-CoV. In pre-registration clinical trials, molnupiravir and paxlovid have shown excellent clinical efficacy results, but what impact will these new oral antiviral agents have against pandemic COVID-19? In what specific clinical situations are they preferred over other antivirals such as remdesivir? In this brief review, we explore these important aspects.
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Affiliation(s)
- Antonio Vitiello
- Pharmaceutical Department, Usl Umbria 1, Via XIV Settembre, 06132, Perugia, Italy
| | - Raffaele La Porta
- Clinical Pathologist, Pathology Department, ASUR Marche, Area Vasta 1, Urbino, Italy
| | - Ugo Trama
- Directorate General for Healthcare and Coordination of the Regional Healthcare System, Naples, Italy
| | - Francesco Ferrara
- Pharmaceutical Department, Asl Napoli 3 Sud, Via Dell'amicizia 22, 80035, Naples, Nola, Italy.
| | - Andrea Zovi
- Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Amogh Milind Auti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Marina Di Domenico
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Mariarosaria Boccellino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
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Motorykin I, Li A, Wu Z. Monitoring and Identifying Insulin-Like Growth Factor 1 Variants by Liquid Chromatography-High-Resolution Mass Spectrometry in a Clinical Laboratory. Methods Mol Biol 2022; 2546:239-251. [PMID: 36127594 DOI: 10.1007/978-1-0716-2565-1_22] [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] [Indexed: 11/26/2022]
Abstract
Protein and peptide hormones often exist as sequence variants with different molecular mass. Monitoring these variants of different molecular mass by mass spectrometry using mass-to-charge (m/z) ratio that is indicative of the wild type may lead to inaccurate quantitative results. However, liquid chromatography-high-resolution mass spectrometry (LC-HRMS)-based techniques can capture these differences and provide an opportunity to resolve, or partially resolve, variant complexity. In this chapter, we describe a general approach for monitoring a set of peptide variants with similar m/z ratios and isotopic envelopes, but different in amino acid sequences. As an example, we use insulin-like growth factor-1 (IGF-1) to demonstrate a DNA database-guided approach to monitor protein variants by LC-HRMS in a clinical laboratory. The workflow is automated and therefore avoids manual calculations that are prone to human error. The method can also monitor multiple IGF-1 variants and discover new ones. It can also provide a profile of a patient's IGF-1 status and be used to explore genotype-phenotype relationships in IGF-1 variants.
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Affiliation(s)
| | - Allison Li
- Quest Diagnostics, San Juan Capistrano, CA, USA
| | - Zengru Wu
- Quest Diagnostics, San Juan Capistrano, CA, USA.
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Reynolds LJ, Gonzalez G, Sala-Comorera L, Martin NA, Byrne A, Fennema S, Holohan N, Kuntamukkula SR, Sarwar N, Nolan TM, Stephens JH, Whitty M, Bennett C, Luu Q, Morley U, Yandle Z, Dean J, Joyce E, O'Sullivan JJ, Cuddihy JM, McIntyre AM, Robinson EP, Dahly D, Fletcher NF, Carr M, De Gascun C, Meijer WG. SARS-CoV-2 variant trends in Ireland: Wastewater-based epidemiology and clinical surveillance. Sci Total Environ 2022; 838:155828. [PMID: 35588817 PMCID: PMC9110007 DOI: 10.1016/j.scitotenv.2022.155828] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 02/14/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 05/21/2023]
Abstract
SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants of concern (VOCs) emerge there is also a need to identify the primary circulating variants in a community, accomplished to date by sequencing clinical samples. Quantifying variants in wastewater offers a cost-effective means to augment these sequencing efforts. In this study, SARS-CoV-2 N1 RNA concentrations and daily loadings were determined and compared to case-based data collected as part of a national surveillance programme to determine the validity of wastewater surveillance to monitor infection spread in the greater Dublin area. Further, sequencing of clinical samples was conducted to determine the primary SARS-CoV-2 lineages circulating in Dublin. Finally, digital PCR was employed to determine whether SARS-CoV-2 VOCs, Alpha and Delta, were quantifiable from wastewater. No lead or lag time was observed between SARS-CoV-2 wastewater and case-based data and SARS-CoV-2 trends in Dublin wastewater significantly correlated with the notification of confirmed cases through case-based surveillance preceding collection with a 5-day average. This demonstrates that viral RNA in Dublin's wastewater mirrors the spread of infection in the community. Clinical sequence data demonstrated that increased COVID-19 cases during Ireland's third wave coincided with the introduction of the Alpha variant, while the fourth wave coincided with increased prevalence of the Delta variant. Interestingly, the Alpha variant was detected in Dublin wastewater prior to the first genome being sequenced from clinical samples, while the Delta variant was identified at the same time in clinical and wastewater samples. This work demonstrates the validity of wastewater surveillance for monitoring SARS-CoV-2 infections and also highlights its effectiveness in identifying circulating variants which may prove useful when sequencing capacity is limited.
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Affiliation(s)
- Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Gabriel Gonzalez
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10 Kita-ku, Sapporo 001-0020, Japan
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Alannah Byrne
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Sanne Fennema
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Niamh Holohan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Sailusha Ratnam Kuntamukkula
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Natasha Sarwar
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Tristan M Nolan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Jayne H Stephens
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Megan Whitty
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Charlene Bennett
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Quynh Luu
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Ursula Morley
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Zoe Yandle
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Jonathan Dean
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Eadaoin Joyce
- Irish Water, Colvill House, 24-26 Talbot Street, Dublin 1, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - John M Cuddihy
- HSE - Health Protection Surveillance Centre, Dublin, Ireland
| | | | - Eve P Robinson
- HSE - Health Protection Surveillance Centre, Dublin, Ireland
| | - Darren Dahly
- Health Research Board Clinical Research Facility, University College Cork, Cork, Ireland
| | - Nicola F Fletcher
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Michael Carr
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10 Kita-ku, Sapporo 001-0020, Japan
| | - Cillian De Gascun
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
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Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
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Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
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Hosseinpour M, Ardalani F, Mohseni M, Beheshtian M, Arzhangi S, Ossareh S, Najmabadi H, Nobakht A, Kahrizi K, Broumand B. Targeted Next Generation Sequencing Revealed Novel Variants in the PKD1 and PKD2 Genes of Iranian Patients with Autosomal Dominant Polycystic Kidney Disease. Arch Iran Med 2022; 25:600-608. [PMID: 37543885 PMCID: PMC10685772 DOI: 10.34172/aim.2022.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/17/2022] [Accepted: 04/10/2022] [Indexed: 08/07/2023]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD), one of the common inherited disorders in humans, is characterized by the development and enlargement of renal cysts, often leading to end-stage renal disease (ESRD). In this study, Iranian ADPKD families were subjected to high-throughput DNA sequencing to find potential causative variants facilitating the way toward risk assessment and targeted therapy. METHODS Our protocol was based on the targeted next generation sequencing (NGS) panel previously developed in our center comprising 12 genes involved in PKD. This panel has been applied to investigate the genetic causes of 32 patients with a clinical suspicion of ADPKD. RESULTS We identified a total of 31 variants for 32 individuals, two of which were each detected in two individuals. Twenty-seven out of 31 detected variants were interpreted as pathogenic/likely pathogenic and the remaining 4 of uncertain significance with a molecular diagnostic success rate of 87.5%. Among these variants, 25 PKD1/2 pathogenic/likely pathogenic variants were detected in 32 index patients (78.1%), and variants of uncertain significance in four individuals (12.5% in PKD1/2). The majority of variants was identified in PKD1 (74.2%). Autosomal recessive PKD was identified in one patient, indicating the similarities between recessive and dominant PKD. In concordance with earlier studies, this biallelic PKD1 variant, p.Arg3277Cys, leads to rapidly progressive and severe disease with very early-onset ADPKD. CONCLUSION Our findings suggest that targeted gene panel sequencing is expected to be the method of choice to improve diagnostic and prognostic accuracy in PKD patients with heterogeneity in genetic background.
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Affiliation(s)
- Maryam Hosseinpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fariba Ardalani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahrzad Ossareh
- Division of Nephrology, Department of Medicine, Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ali Nobakht
- Department of Nephrology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Behrooz Broumand
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Tehran, Iran
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143
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Sorg AL, Schönfeld V, Siedler A, Hufnagel M, Doenhardt M, Diffloth N, Berner R, V Kries R, Armann J. SARS-CoV-2 variants and the risk of pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 among children in Germany. Infection 2022. [PMID: 36048361 DOI: 10.1007/s15010-022-01908-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Purpose To investigate the relationship between the risk of pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) in children and the predominance of different SARS-CoV-2 variants of concern (VOC) over time. Methods In relation to the Alpha, Delta, and Omicron VOC phases of the pandemic, the risk of developing PIMS-TS was calculated by analyzing data for rtPCR-confirmed SARS-CoV-2 infections reported to the German statutory notification system, along with data captured by a separate, national PIMS-TS registry. Both overall infection rates and age group-specific ratios of PIMS-TS during the different pandemic phases were calculated using the Alpha period as the baseline. Results The PIMS-TS rate changed significantly over time. When the Alpha VOC was dominant [calendar week (CW) 11 in March–CW 31 in August 2021], the PIMS-TS rate was 6.19 [95% confidence intervals (95% CI) 5.17, 7.20]. When Delta prevailed (CW 32 in August 2021–CW 4 in January 2022), the rate decreased to 1.68 (95% CI 1.49, 1.87). During the Omicron phase (CW 5 in January–CW 16 in April 2022), the rate fell further to 0.89 (95% CI 0.79, 1.00). These changes correspond to a decreased PIMS-TS rate of 73% (rate ratio 0.271, 95% CI 0.222; 0.332) and 86% (rate ratio 0.048, 95% CI 0.037; 0.062), respectively, in comparison to the Alpha period. Rate ratios were nearly identical for all age groups. Conclusion The data strongly suggest an association between the risk for PIMS-TS and the prevailing VOC, with highest risk related to Alpha and the lowest to Omicron. Given the uniformity of the decreased risk across age groups, vaccination against SARS-CoV-2 does not appear to have a significant impact on the risk of children developing PIMS-TS.
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Ntagereka PB, Oyola SO, Baenyi SP, Rono GK, Birindwa AB, Shukuru DW, Baharanyi TC, Kashosi TM, Buhendwa JC, Bisimwa PB, Kusinza AB, Basengere RA, Mukwege D. Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second, and third waves of COVID-19 in South Kivu, east of the Democratic Republic of the Congo. Int J Infect Dis 2022; 122:136-43. [PMID: 35598737 DOI: 10.1016/j.ijid.2022.05.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES We used whole-genome sequencing of SARS-CoV-2 to identify variants circulating in the Democratic Republic of the Congo and obtain molecular information useful for diagnosis, improving treatment, and general pandemic control strategies. METHODS A total of 74 SARS-CoV-2 isolates were sequenced using Oxford Nanopore platforms. Generated reads were processed to obtain consensus genome sequences. Sequences with more than 80% genome coverage were used for variant calling, phylogenetic analysis, and classification using Pangolin lineage annotation nomenclature. RESULTS Phylogenetic analysis based on Pangolin classification clustered South Kivu sequences into seven lineages (A.23.1, B.1.1.6, B.1.214, B.1.617.2, B.1.351, C.16, and P.1). The Delta (B.1.617.2) variant was the most dominant and responsible for outbreaks during the third wave. Based on the Wuhan reference genome, 289 distinct mutations were detected, including 141 missenses, 123 synonymous, and 25 insertions/deletions when our isolates were mapped to the Wuhan reference strain. Most of these point mutations were located within the coding sequences of the SARS-CoV-2 genome that includes spike, ORF1ab, ORF3, and nucleocapsid protein genes. The most common mutation was D614G (1841A>G) observed in 61 sequences, followed by L4715L (14143 C>T) found in 60 sequences. CONCLUSION Our findings highlight multiple introductions of SARS-CoV-2 into South Kivu through different sources and subsequent circulation of variants in the province. These results emphasize the importance of timely monitoring of genetic variation and its effect on disease severity. This work set a foundation for the use of genomic surveillance as a tool for future global pandemic management and control.
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Khatri R, Parray HA, Siddiqui G, Chiranjivi AK, Raj S, Kaul R, Maithil V, Samal S, Ahmed S. Biophysical and Biochemical Characterization of the Receptor Binding Domain of SARS-CoV-2 Variants. Protein J 2022; 41:457-467. [PMID: 36048314 PMCID: PMC9434506 DOI: 10.1007/s10930-022-10073-6] [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] [Accepted: 08/16/2022] [Indexed: 11/17/2022]
Abstract
The newly emerging SARS-CoV-2 variants are potential threat and posing new challenges for medical intervention due to high transmissibility and escaping neutralizing antibody (NAb) responses. Many of these variants have mutations in the receptor binding domain (RBD) of SARS-CoV-2 spike protein that interacts with the host cell receptor. Rapid mutation in the RBD through natural selection to improve affinity for host receptor and antibody pressure from vaccinated or infected individual will greatly impact the presently adopted strategies for developing interventions. Understanding the nature of mutations and how they impact the biophysical, biochemical and immunological properties of the RBD will help immensely to improve the intervention strategies. To understand the impact of mutation on the protease sensitivity, thermal stability, affinity for the receptor and immune response, we prepared several mutants of soluble RBD that belong to the variants of concern (VoCs) and interest (VoIs) and characterize them. Our results show that the mutations do not impact the overall structure of the RBD. However, the mutants showed increase in the thermal melting point, few mutants were more sensitive to protease degradation, most of them have enhanced affinity for ACE2 and some of them induced better immune response compared to the parental RBD.
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Affiliation(s)
- Ritika Khatri
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India
| | - Hilal Ahmad Parray
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India
| | - Gazala Siddiqui
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India
| | - Adarsh Kumar Chiranjivi
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India
| | - Sneha Raj
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India
| | - Rachel Kaul
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India
| | - Vikas Maithil
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India
| | - Sweety Samal
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India
| | - Shubbir Ahmed
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, Haryana, India. .,Centralized Core Research Facility (CCRF), All India Institute of Medical Science (AIIMS), New Delhi, 110029, India.
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Bonsignore M, Hohenstein S, Kodde C, Leiner J, Schwegmann K, Bollmann A, Möller R, Kuhlen R, Nachtigall I. Burden of Hospital-acquired SARS-CoV-2 Infections in Germany. J Hosp Infect 2022; 129:82-88. [PMID: 35995339 PMCID: PMC9391075 DOI: 10.1016/j.jhin.2022.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 07/21/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 12/15/2022]
Abstract
Background Avoiding in-hospital transmissions has been crucial in the COVID-19 pandemic. Little is known on the extent to which hospital-acquired SARS-CoV-2 variants have caused infections in Germany. Aim To analyse the occurrence and the outcomes of HAI with regard to different SARS-CoV-2 variants. Methods Patients with SARS-CoV-2 infections hospitalized between March 1st, 2020 and May 17th, 2022 in 79 hospitals of the Helios Group were included. Information on patients' characteristics and outcomes were retrieved from claims data. In accordance with the Robert Koch Institute, infections were classified as hospital-acquired when tested positive >6 days after admission and if no information hinted at a different source. Findings In all, 62,875 SARS-CoV-2 patients were analysed, of whom 10.6% had HAI. HAIs represented 14.7% of SARS-CoV-2 inpatients during the Wildtype period, 3.5% during Alpha (odds ratio: 0.21; 95% confidence interval: 0.19–0.24), 8.8% during Delta (2.70; 2.35–3.09) and 10.1% during Omicron (1.10; 1.03–1.19). When age and comorbidities were accounted for, HAI had lower odds for death than community-acquired infections (0.802; 0.740–0.866). Compared to the Wildtype period, HAIs during Omicron were associated with lower odds for ICU (0.78; 0.69–0.88), ventilation (0.47; 0.39–0.56), and death (0.33; 0.28–0.40). Conclusion Hospital-acquired SARS-CoV-2 infections occurred throughout the pandemic, affecting highly vulnerable patients. Although transmissibility increased with newer variants, the proportion of HAIs decreased, indicating improved infection prevention and/or the effect of immunization. Furthermore, the Omicron period was associated with improved outcomes. However, the burden of hospital-acquired SARS-CoV-2 infections remains high.
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Affiliation(s)
- Marzia Bonsignore
- Department of Infectiology and Infection Prevention, Helios Klinikum Duisburg, Duisburg, Germany; Center for Clinical and Translational Research, Helios Universitätsklinikum Wuppertal, University of Witten/Herdecke, Wuppertal, Germany.
| | - Sven Hohenstein
- Heart Centre Leipzig at University of Leipzig and Helios Health Institute, Berlin, Germany
| | - Cathrin Kodde
- Department of Pneumology, Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, Berlin, Germany.
| | - Johannes Leiner
- Heart Centre Leipzig at University of Leipzig and Helios Health Institute, Berlin, Germany
| | - Karin Schwegmann
- Central Department for Hygiene, Helios Kliniken, Hildesheim, Germany
| | - Andreas Bollmann
- Heart Centre Leipzig at University of Leipzig and Helios Health Institute, Berlin, Germany
| | | | | | - Irit Nachtigall
- Department of Infectious Diseases and Infection Prevention, HELIOS Hospital Emil-von-Behring, Berlin, Germany; Charité - Universitaetsmedizin Berlin, Institute of Hygiene and Environmental Medicine, Berlin, Germany
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Hirabidian M, Bocket L, Demaret J, Vuotto F, Rabat A, Faure K, Labalette M, Hober D, Lefevre G, Alidjinou EK. Evaluation of a rapid semiquantitative lateral flow assay for the prediction of serum neutralizing activity against SARS-CoV-2 variants. J Clin Virol 2022; 155:105268. [PMID: 35998394 PMCID: PMC9383946 DOI: 10.1016/j.jcv.2022.105268] [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: 03/06/2022] [Revised: 07/08/2022] [Accepted: 08/14/2022] [Indexed: 12/01/2022]
Abstract
Background Neutralizing antibodies (NAbs) against SARS-CoV-2 have been shown to correlate with protection against infection. Simple tools such as lateral flow assays (LFA) that can accurately measure NAbs may be useful for monitoring anti-SARS-CoV-2 immunity in the future. Objectives We assessed the performance of the ichroma™ COVID-19 nAb test, a rapid semiquantitative LFA, for the prediction of serum neutralizing activity against SARS-CoV-2 variants. Study design Serum samples were collected from COVID-19 recovered patients and vaccinated individuals. The result of the ichroma assay was provided as inhibition rate, and was compared to anti-SARS-CoV-2 IgG levels, and NAbs against Alpha, Delta and Omicron variants. Results A total of 90 sera from recovered unvaccinated patients and 209 sera from the vaccine cohort were included in this study. In post-infection samples, the ichroma inhbition rate was found to be correlated with IgG levels (ρ = 0.83), and with anti-Alpha NAbs levels (ρ = 0.78). In the vaccine cohort, a good correlation was also observed between the ichroma inhibition rate and IgG levels (ρ = 0.84), as well as NAbs against Alpha (ρ = 0.62), Delta (ρ = 0.88) and Omicron (ρ = 0.74). An ichroma inhbition rate of 77.2%, 90.8% and 99.6% accurately predicted neutralization against Alpha, Delta and Omicron variants respectively. Conclusions The ichroma™ COVID-19 nAb assay, with appropriate variant cut-offs, can be useful for the monitoring of anti-SARS-CoV-2 immunization and may provide a rapid prediction of protection, especially in individuals with significant levels of NAbs.
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Affiliation(s)
- Mickael Hirabidian
- Univ Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Laurence Bocket
- Univ Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Julie Demaret
- CHU Lille, Institut d'Immunologie, U1286 - INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, F-59000, Lille, France
| | - Fanny Vuotto
- CHU Lille, Département de Maladies Infectieuses, F-59000 Lille France
| | - Anthony Rabat
- Univ Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Karine Faure
- CHU Lille, Département de Maladies Infectieuses, F-59000 Lille France
| | - Myriam Labalette
- CHU Lille, Institut d'Immunologie, U1286 - INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, F-59000, Lille, France
| | - Didier Hober
- Univ Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Guillaume Lefevre
- CHU Lille, Institut d'Immunologie, U1286 - INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, F-59000, Lille, France
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148
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Abdel Megeid AK, Refeat MM, Ashaat EA, El-Kamah G, El-Saiedi SA, Elfalaki MM, El Ruby MO, Amr KS. Correlating SFTPC gene variants to interstitial lung disease in Egyptian children. J Genet Eng Biotechnol 2022; 20:117. [PMID: 35939165 PMCID: PMC9360361 DOI: 10.1186/s43141-022-00399-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/31/2021] [Accepted: 07/10/2022] [Indexed: 01/04/2023]
Abstract
Background Interstitial lung disease (ILD) is a broad heterogeneous group of lung disorders that is characterized by inflammation of the lungs. Surfactant dysfunction disorders are a rare form of ILD diseases that result from mutations in surfactant protein C gene (SFTPC) with prevalence of approximately 1/1.7 million births. SFTPC patients are presented with clinical manifestations of ILD ranging from fatal respiratory failure of newborn to chronic respiratory problems in children. In the current study, we aimed to investigate the spectrum of SFTPC genetic variants as well as the correlation of the SFTPC gene mutations with ILD disease in twenty unrelated Egyptian children with diffuse lung disease and suspected surfactant dysfunction using Sanger sequencing. Results Sequencing of SFTPC gene revealed five variants: c.42+35G>A (IVS1+35G>A) (rs8192340) and c.43-21T>C (IVS1-21T>C) (rs13248346) in intron 1, c.436-8C>G (IVS4-8C>G) (rs2070687) in intron 4, c.413C>A p.T138N (rs4715) in exon 4, and c.557G>Ap.S186N (rs1124) in exon 5. Conclusion The present study confirms the association of detecting variants of SFTPC with surfactant dysfunction disorders.
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Affiliation(s)
| | - Miral M Refeat
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Engy A Ashaat
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Ghada El-Kamah
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | | | | | - Mona O El Ruby
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Khalda S Amr
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.
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149
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Zhang Y, Wu H, Yu Z, Li L, Zhang J, Liang X, Huang Q. Germline variants profiling of BRCA1 and BRCA2 in Chinese Hakka breast and ovarian cancer patients. BMC Cancer 2022; 22:842. [PMID: 35918668 PMCID: PMC9347172 DOI: 10.1186/s12885-022-09943-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/05/2022] [Accepted: 07/25/2022] [Indexed: 12/26/2022] Open
Abstract
Objective To investigate the prevalence and spectrum of BRCA1 and BRCA2 mutations in Chinese Hakka patients with breast and ovarian cancer. Methods A total of 1,664 breast or ovarian cancer patients were enrolled for genetic testing at our hospital. Germline mutations of the BRCA gene were analysed by next-generation sequencing, including the coding regions and exon intron boundary regions. Results The 1,664 patients included 1,415 (85.04%) breast cancer patients and 245 (14.72%) ovarian cancer patients, while four (0.24%) patients had both the breast and ovarian cancers. A total of 151 variants, including 71 BRCA1 variants and 80 BRCA2 variants, were detected in the 234 (14.06%) patients. The 151 variants included 58 pathogenic variants, 8 likely pathogenic variants, and 85 variants of unknown significance (VUS). A total of 56.25% (18/32) and 65.38% (17/26) of pathogenic variants (likely pathogenic variants are not included) were distributed in exon 14 of BRCA1 and exon 11 of BRCA2, respectively. The most common pathogenic variants among this Hakka population are c.2635G > T (p.Glu879*) (n = 7) in the BRCA1 gene and c.5164_5165del (p.Ser1722Tyrfs*4) (n = 7) in the BRCA2 gene among the Hakka population. A hotspot mutation in the Chinese population, the BRCA1 c.5470_5477del variant was not found in this Hakka population. The prevalence and spectrum of variants in the BRCA genes in the Hakka patients are different from that in other ethnic groups. Conclusions The most common pathogenic variant in this population is c.2635G > T in the BRCA1 gene, and c.5164_5165delAG in the BRCA2 gene in this population. The prevalence and spectrum of variants in the BRCA1 and BRCA2 genes in the Hakka patients from southern China are different from those in other ethnic groups. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09943-0.
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Affiliation(s)
- Yunuo Zhang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Heming Wu
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhikang Yu
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Liang Li
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Jinhong Zhang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Xinhong Liang
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Radiology department, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Qingyan Huang
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China. .,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China. .,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.
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150
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García-Pérez J, González-Pérez M, Castillo de la Osa M, Borobia AM, Castaño L, Bertrán MJ, Campins M, Portolés A, Lora D, Bermejo M, Conde P, Hernández-Gutierrez L, Carcas A, Arana-Arri E, Tortajada M, Fuentes I, Ascaso A, García-Morales MT, Erick de la Torre-Tarazona H, Arribas JR, Imaz-Ayo N, Mellado-Pau E, Agustí A, Pérez-Ingidua C, Gómez de la Cámara A, Ochando J, Belda-Iniesta C, Frías J, Alcamí J, Pérez-Olmeda M. Immunogenic dynamics and SARS-CoV-2 variant neutralisation of the heterologous ChAdOx1-S/BNT162b2 vaccination: Secondary analysis of the randomised CombiVacS study. EClinicalMedicine 2022; 50:101529. [PMID: 35795713 PMCID: PMC9249304 DOI: 10.1016/j.eclinm.2022.101529] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The CombiVacS study was designed to assess immunogenicity and reactogenicity of the heterologous ChAdOx1-S/BNT162b2 combination, and 14-day results showed a strong immune response. The present secondary analysis addresses the evolution of humoral and cellular response up to day 180. METHODS Between April 24 and 30, 2021, 676 adults primed with ChAdOx1-S were enrolled in five hospitals in Spain, and randomised to receive BNT162b2 as second dose (interventional group [IG]) or no vaccine (control group [CG]). Individuals from CG received BNT162b2 as second dose and also on day 28, as planned based on favourable results on day 14. Humoral immunogenicity, measured by immunoassay for SARS-CoV-2 receptor binding domain (RBD), antibody functionality using pseudovirus neutralisation assays for the reference (G614), Alpha, Beta, Delta, and Omicron variants, as well as cellular immune response using interferon-γ and IL-2 immunoassays were assessed at day 28 after BNT162b2 in both groups, at day 90 (planned only in the interventional group) and at day 180 (laboratory data cut-off on Nov 19, 2021). This study was registered with EudraCT (2021-001978-37) and ClinicalTrials.gov (NCT04860739). FINDINGS In this secondary analysis, 664 individuals (441 from IG and 223 from CG) were included. At day 28 post vaccine, geometric mean titres (GMT) of RBD antibodies were 5616·91 BAU/mL (95% CI 5296·49-5956·71) in the IG and 7298·22 BAU/mL (6739·41-7903·37) in the CG (p < 0·0001). RBD antibodies titres decreased at day 180 (1142·0 BAU/mL [1048·69-1243·62] and 1836·4 BAU/mL [1621·62-2079·62] in the IG and CG, respectively; p < 0·0001). Neutralising antibodies also waned from day 28 to day 180 in both the IG (1429·01 [1220·37-1673·33] and 198·72 [161·54-244·47], respectively) and the CG (1503·28 [1210·71-1866·54] and 295·57 [209·84-416·33], respectively). The lowest variant-specific response was observed against Omicron-and Beta variants, with low proportion of individuals exhibiting specific neutralising antibody titres (NT50) >1:100 at day 180 (19% and 22%, respectively). INTERPRETATION Titres of RBD antibodies decay over time, similar to homologous regimes. Our findings suggested that delaying administration of the second dose did not have a detrimental effect after vaccination and may have improved the response obtained. Lower neutralisation was observed against Omicron and Beta variants at day 180. FUNDING Funded by Instituto de Salud Carlos III (ISCIII).
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Affiliation(s)
- Javier García-Pérez
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María González-Pérez
- Laboratorio de Referencia en Inmunología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Castillo de la Osa
- Laboratorio de Serología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Alberto M. Borobia
- Servicio de Farmacología Clínica, Departamento de Farmacología y Terapéutica, Facultad de Medicina, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Castaño
- Biocruces Bizkaia, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, UPV-EHU, Barakaldo, Spain
| | - María Jesús Bertrán
- Servicio de Medicina Preventiva y Epidemiologia, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Magdalena Campins
- Servicio de Medicina Preventiva y Epidemiología, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Antonio Portolés
- Servicio de Farmacología Clínica, Hospital Clínico San Carlos, IdISSC, Madrid, Spain
- Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Spanish Clinical Research Network – SCReN – ISCIII, Madrid, Spain
| | - David Lora
- Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Facultad de Medicina, Universidad Complutense de Madrid (UCM)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Spanish Clinical Research Network – SCReN – ISCIII, Madrid, Spain
- Facultad de Estudios Estadísticos, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Mercedes Bermejo
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Patricia Conde
- Laboratorio de Referencia en Inmunología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Lourdes Hernández-Gutierrez
- Laboratorio de Serología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Antonio Carcas
- Servicio de Farmacología Clínica, Departamento de Farmacología y Terapéutica, Facultad de Medicina, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Eunate Arana-Arri
- Biocruces Bizkaia, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, UPV-EHU, Barakaldo, Spain
| | - Marta Tortajada
- Servicio de Prevención de Riesgos Laborales, Salud Laboral, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Inmaculada Fuentes
- Unidad de Soporte a la Investigación Clínica, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Ana Ascaso
- Servicio de Farmacología Clínica, Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - María Teresa García-Morales
- Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Facultad de Medicina, Universidad Complutense de Madrid (UCM)
- Spanish Clinical Research Network – SCReN – ISCIII, Madrid, Spain
| | | | - José-Ramón Arribas
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Servicio de Medicina Interna, Departamento de Medicina, Facultad de Medicina, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Natale Imaz-Ayo
- Biocruces Bizkaia, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, UPV-EHU, Barakaldo, Spain
| | - Eugènia Mellado-Pau
- Servicio de Medicina Preventiva y Epidemiologia, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Antonia Agustí
- Servicio de Farmacología Clínica, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Departament de Farmacologia, Terapèutica i Toxicologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Carla Pérez-Ingidua
- Servicio de Farmacología Clínica, Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Agustín Gómez de la Cámara
- Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Facultad de Medicina, Universidad Complutense de Madrid (UCM)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Facultad de Medicina, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Spanish Clinical Research Network – SCReN – ISCIII, Madrid, Spain
| | - Jordi Ochando
- Laboratorio de Referencia en Inmunología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | | | - Jesús Frías
- Servicio de Farmacología Clínica, Departamento de Farmacología y Terapéutica, Facultad de Medicina, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - José Alcamí
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Corresponding author at: Unidad de Inmunopatología del SIDA Instituto de Salud Carlos III, 28220 Majadahonda, Spain.
| | - Mayte Pérez-Olmeda
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Laboratorio de Serología, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Corresponding author at: Laboratorio de Serología, Instituto de salud Carlos III, 28220 Majadahonda, Spain.
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