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Yazdani Z, Rafiei A, Momenizadeh M, Abediankenari S, Yazdani M, Lagzian M. Designing novel peptides for detecting the Omicron variant, specifying SARS-CoV-2, and simultaneously screening coronavirus infections. J Biomol Struct Dyn 2024; 42:4759-4768. [PMID: 37306566 DOI: 10.1080/07391102.2023.2222821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
In this study in silico a candidate diagnostic peptide-based tool was designed in four stages including diagnosis of coronavirus diseases, simultaneously identifying of COVID-19 and SARS from other members of this family, specific identification of SARS-CoV2, and diagnosis of COVID-19 Omicron. Designed candidate peptides consist of four immunodominant peptides from the proteins of the SARS-CoV-2 spike (S) and membrane (M). The tertiary structure of each peptide was predicted. The stimulation ability of the humoral immunity for each peptide was evaluated. Finally, in silico cloning was performed to develop an expression strategy for each peptide. These four peptides have suitable immunogenicity, appropriate construct, and the ability to be expressed in E.coli. These results must be experimentally validated in vitro and in vivo to ensure the immunogenicity of the kit.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Yazdani
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Rafiei
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Momenizadeh
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saeid Abediankenari
- Immunogenetics Research Center, Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Milad Lagzian
- Department of Biology, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
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Abd-Elshafy DN, Nadeem R, Nasraa MH, Bahgat MM. Analysis of the SARS-CoV-2 nsp12 P323L/A529V mutations: coeffect in the transiently peaking lineage C.36.3 on protein structure and response to treatment in Egyptian records. Z NATURFORSCH C 2024; 79:13-24. [PMID: 38265042 DOI: 10.1515/znc-2023-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
SARS-CoV-2 nsp12, the RNA-dependent RNA-polymerase plays a crucial role in virus replication. Monitoring the effect of its emerging mutants on viral replication and response to antiviral drugs is important. Nsp12 of two Egyptian isolates circulating in 2020 and 2021 were sequenced. Both isolates included P323L, one included the A529V. Tracking A529V mutant frequency, it relates to the transience peaked C.36.3 variant and its parent C.36, both peaked worldwide on February-August 2021, enlisted as high transmissible variants under investigation (VUI) on May 2021. Both Mutants were reported to originate from Egypt and showed an abrupt low frequency upon screening, we analyzed all 1104 nsp12 Egyptian sequences. A529V mutation was in 36 records with an abrupt low frequency on June 2021. As its possible reappearance might obligate actions for a candidate VUI, we analyzed the predicted co-effect of P323L and A529V mutations on protein stability and dynamics through protein structure simulations. Three available structures for drug-nsp12 interaction were used representing remdesivir, suramin and favipiravir drugs. Remdesivir and suramin showed an increase in structure stability and considerable change in flexibility while favipiravir showed an extreme interaction. Results predict a favored efficiency of the drugs except for favipiravir in case of the reported mutations.
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Affiliation(s)
- Dina N Abd-Elshafy
- Department of Water Pollution Research, Environmental and Climate Change Research Institute, The National Research Centre, Dokki, Cairo, Egypt
- Immune- and Bio-markers for Infection Research Group, The Center of Excellence for Advanced Sciences, The National Research Centre, Dokki, Cairo, Egypt
| | - Rola Nadeem
- Department of Therapeutic Chemistry, Pharmaceutical and Drug Industries Research Institute, The National Research Centre, Dokki, Cairo, Egypt
- Immune- and Bio-markers for Infection Research Group, The Center of Excellence for Advanced Sciences, The National Research Centre, Dokki, Cairo, Egypt
| | - Mohamed H Nasraa
- Department of Therapeutic Chemistry, Pharmaceutical and Drug Industries Research Institute, The National Research Centre, Dokki, Cairo, Egypt
- Immune- and Bio-markers for Infection Research Group, The Center of Excellence for Advanced Sciences, The National Research Centre, Dokki, Cairo, Egypt
| | - Mahmoud M Bahgat
- Department of Therapeutic Chemistry, Pharmaceutical and Drug Industries Research Institute, The National Research Centre, Dokki, Cairo, Egypt
- Immune- and Bio-markers for Infection Research Group, The Center of Excellence for Advanced Sciences, The National Research Centre, Dokki, Cairo, Egypt
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3
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Liu X, Zhang P, Chen M, Zhou H, Yue T, Xu M, Cai T, Huang J, Yue X, Li G, Zhou Z. Epidemiological and clinical features of COVID-19 inpatients in Changsha, China: A retrospective study from 2020 to 2022. Heliyon 2023; 9:e22873. [PMID: 38125480 PMCID: PMC10731055 DOI: 10.1016/j.heliyon.2023.e22873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Objectives The spread of SARS-Cov-2 remains a global concern along with the emergence of variants. This study aims to characterize the epidemiological and clinical features of hospitalized patients who were dragonized with five different variants of SARS-CoV-2 during the past 3 years. Methods This retrospective study recruited 432 COVID-19 patients who were hospitalized in the First Hospital of Changsha from January 2020 to August 2022. Clinical records on clinical symptoms, laboratory profiles, and chest CT images was collected. The epidemiological and clinical features were compared between COVID-19 patients infected with either the wild-type, Omicron variant or pre- Omicron variants (e.g., Alpha, Beta, Delta). Results A total of 432 laboratory-confirmed COVID-19 inpatients were dialogized during three waves, including 247 cases during the wild-type transmission period, 65 cases during the transmission period of pre-Omicron variants, and 119 cases during the transmission period of Omicron variants. The proportion of moderately or severely ill inpatients showed a gradual decline from the wild-type transmission period to the Omicron transmission period. The common symptoms of inpatients infected with SARS-CoV-2 wildtype strains included fever (67.61 %), cough (57.89 %), fatigue (33.60 %), and shortness of breath (12.15 %). In contrast, patients infected with other variants mostly showed upper respiratory symptoms. Based on chest CT images, a lower degree of acute pulmonary infection was observed among inpatients infected with the Omicron variants than those infected with the wild-type strain (31.09 % vs 93.12 %, p-value<0.01). Conclusions Compared with the wild-type strain, SARS-CoV-2 variants of concern, especially the Omicron variant, mostly caused a lower degree of acute pulmonary infection, indicating the reduced disease severity and mortality among hospitalized COVID-19 patients.
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Affiliation(s)
- Xiaofang Liu
- Department of Medical Administration, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha) Changsha 410000, China
| | - Pan Zhang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Meiping Chen
- Department of Infectious Diseases, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, China
| | - Haibo Zhou
- Department of Respiratory and Critical Care Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, China
| | - Tingting Yue
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ming Xu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ting Cai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Juan Huang
- Department of Pediatrics, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University(The First Hospital of Changsha), Changsha, 410000, China
| | - Xiaoyang Yue
- Department of General Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University(The First Hospital of Changsha), Changsha, 410000, China
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zhiguo Zhou
- Department of Respiratory and Critical Care Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, China
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4
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Xu M, Cai T, Yue T, Zhang P, Huang J, Liu Q, Wang Y, Luo R, Li Z, Luo L, Ji C, Tan X, Zheng Y, Whitley R, De Clercq E, Yin Q, Li G. Comparative effectiveness of oseltamivir versus peramivir for hospitalized children (aged 0-5 years) with influenza infection. Int J Infect Dis 2023; 128:157-165. [PMID: 36608788 DOI: 10.1016/j.ijid.2022.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES The effectiveness of oseltamivir versus peramivir in children infected with influenza remains unclear. This study aimed to evaluate their effectiveness in young children (aged 0-5 years) infected with severe influenza A virus (IAV) or influenza B virus (IBV). METHODS We analyzed a cohort of 1662 young children with either IAV (N = 1095) or IBV (N = 567) who received oseltamivir or peramivir treatment from January 1, 2018 to March 31, 2022. Propensity score matching methods were applied to match children who were oseltamivir-treated versus peramivir-treated. RESULTS Children who were IAV-infected and IBV-infected shared similar features, such as influenza-associated symptoms and comorbidities at baseline. Among children infected with IAV with bacterial coinfection, the recovery rate was significantly greater in children treated with oseltamivir than in children treated with peramivir (15.6% vs 4.4%, P = 0.01). The median duration of hospitalization was also shorter in children treated with oseltamivir. Among children infected with IAV without bacterial coinfection, the recovery rate was greater in children treated with oseltamivir than in children treated with peramivir (21.1% vs 3.7%, P = 0.002). However, oseltamivir and peramivir offered similar recovery rates and duration of hospitalization (P >0.05 for both) among children infected with IBV. CONCLUSION Oseltamivir and peramivir exhibit similar effectiveness in young children with severe influenza B, whereas oseltamivir demonstrated improved recovery and shorter hospitalization in the treatment of severe influenza A in hospitalized children.
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Affiliation(s)
- Ming Xu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China; Hunan Children's Hospital, Changsha, China
| | - Ting Cai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Tingting Yue
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Pan Zhang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jie Huang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Qi Liu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Yue Wang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ruping Luo
- Hunan Children's Hospital, Changsha, China
| | | | - Linli Luo
- Hunan Children's Hospital, Changsha, China
| | - Chunyi Ji
- Hunan Children's Hospital, Changsha, China
| | - Xinrui Tan
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yanling Zheng
- College of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, People's Republic of China
| | - Richard Whitley
- Department of Pediatrics, Microbiology, Medicine and Neurosurgery, University of Alabama at Birmingham, Birmingham, USA
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Qiang Yin
- Hunan Children's Hospital, Changsha, China.
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China; Hunan Children's Hospital, Changsha, China.
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5
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Jia C, Zhou Z, Pan W, Zhang P, Yang M, Zhao M, Li B, Liu P, Zhang Q, Kong X, Li K, Yue T, Cai T, Wang Z, De Clercq E, Li S, Li G, Liu J, Wu H, Lu Q. Immune repertoire sequencing reveals an abnormal adaptive immune system in COVID-19 survivors. J Med Virol 2023; 95:e28340. [PMID: 36420584 PMCID: PMC10107439 DOI: 10.1002/jmv.28340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Accumulating evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impairs the adaptive immune system during acute infection. Still, it remains largely unclear whether the frequency and functions of T and B cells return to normal after the recovery of Coronavirus Disease 2019 (COVID-19). Here, we analyzed immune repertoires and SARS-CoV-2-specific neutralization antibodies in a prospective cohort of 40 COVID-19 survivors with a 6-month follow-up after hospital discharge. Immune repertoire sequencing revealed abnormal T- and B-cell expression and function with large T cell receptor/B cell receptor clones, decreased diversity, abnormal class-switch recombination, and somatic hypermutation. A decreased number of B cells but an increased proportion of CD19+ CD138+ B cells were found in COVID-19 survivors. The proportion of CD4+ T cells, especially circulating follicular helper T (cTfh) cells, was increased, whereas the frequency of CD3+ CD4- T cells was decreased. SARS-CoV-2-specific neutralization IgG and IgM antibodies were identified in all survivors, especially those recorded with severe COVID-19 who showed a higher inhibition rate of neutralization antibodies. All severe cases complained of more than one COVID-19 sequelae after 6 months of recovery. Overall, our findings indicate that SARS-CoV-2-specific antibodies remain detectable even after 6 months of recovery. Because of their abnormal adaptive immune system with a low number of CD3+ CD4- T cells and high susceptibility to infections, COVID-19 patients might need more time and medical care to fully recover from immune abnormalities and tissue damage.
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Affiliation(s)
- Chen Jia
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiguo Zhou
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Wenjing Pan
- Nanjing ARP Biotechnology Co., Ltd., Nanjing, Jiangsu, China
| | - Pan Zhang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ming Yang
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bo Li
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Ping Liu
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Qianqian Zhang
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Xianglong Kong
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Keyu Li
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Tingting Yue
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ting Cai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zijun Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan, China
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jiyang Liu
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Haijing Wu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
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6
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Chang MR, Tomasovic L, Kuzmina NA, Ronk AJ, Byrne PO, Johnson R, Storm N, Olmedillas E, Hou YJ, Schäfer A, Leist SR, Tse LV, Ke H, Coherd C, Nguyen K, Kamkaew M, Honko A, Zhu Q, Alter G, Saphire EO, McLellan JS, Griffiths A, Baric RS, Bukreyev A, Marasco WA. IgG-like bispecific antibodies with potent and synergistic neutralization against circulating SARS-CoV-2 variants of concern. Nat Commun 2022; 13:5814. [PMID: 36192374 PMCID: PMC9528872 DOI: 10.1038/s41467-022-33030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Monoclonal antibodies are a promising approach to treat COVID-19, however the emergence of SARS-CoV-2 variants has challenged the efficacy and future of these therapies. Antibody cocktails are being employed to mitigate these challenges, but neutralization escape remains a major challenge and alternative strategies are needed. Here we present two anti-SARS-CoV-2 spike binding antibodies, one Class 1 and one Class 4, selected from our non-immune human single-chain variable fragment (scFv) phage library, that are engineered into four, fully-human IgG-like bispecific antibodies (BsAb). Prophylaxis of hACE2 mice and post-infection treatment of golden hamsters demonstrates the efficacy of the monospecific antibodies against the original Wuhan strain, while promising in vitro results with the BsAbs demonstrate enhanced binding and distinct synergistic effects on neutralizing activity against circulating variants of concern. In particular, one BsAb engineered in a tandem scFv-Fc configuration shows synergistic neutralization activity against several variants of concern including B.1.617.2. This work provides evidence that synergistic neutralization can be achieved using a BsAb scaffold, and serves as a foundation for the future development of broadly reactive BsAbs against emerging variants of concern. COVID-19 can be treated with monoclonal antibodies against SARS-CoV-2, but emerging new variants might show resistance towards existing therapy. Here authors show that anti-SARS-CoV-2 spike human single-chain antibody fragments could gain neutralizing activity against variants of concern upon engineering into a human bispecific antibody.
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Affiliation(s)
- Matthew R Chang
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Luke Tomasovic
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Natalia A Kuzmina
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Galveston National Laboratory, Galveston, TX, 77555, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Adam J Ronk
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Galveston National Laboratory, Galveston, TX, 77555, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Rebecca Johnson
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, 02118, USA
| | - Nadia Storm
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, 02118, USA
| | | | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hanzhong Ke
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Christian Coherd
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Katrina Nguyen
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Maliwan Kamkaew
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Anna Honko
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, 02118, USA
| | - Quan Zhu
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, 02118, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Galveston National Laboratory, Galveston, TX, 77555, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Wayne A Marasco
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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7
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Leducq V, Couturier J, Granger B, Jolivet S, Morand-Joubert L, Robert J, Denis M, Salauze B, Goldstein V, Zafilaza K, Rufat P, Marcelin AG, Jary A, Barbut F. Investigation of healthcare-associated COVID-19 in a large French hospital group by whole-genome sequencing. Microbiol Res 2022; 263:127133. [PMID: 35901580 PMCID: PMC9306220 DOI: 10.1016/j.micres.2022.127133] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022]
Abstract
OBJECTIVES Despite the quick implementation of infection prevention and control procedures and the use of personal protective equipment within healthcare facilities, many cases of nosocomial COVID-19 transmission have been reported. We aimed to estimate the frequency and impact of healthcare-associated COVID-19 (HA-COVID-19) and evaluate the contribution of whole-genome sequencing (WGS) in cluster investigation. METHODS We estimated the frequency and mortality of HA-COVID-19 infections from September 1 to November 30, 2020, with a focus on the evolution of hospitalized community-associated COVID-19 (CA-COVID-19) cases and cases detected among healthcare workers (HCWs) within the Sorbonne University Hospital Group (Paris, France). We thoroughly examined 12 clusters through epidemiological investigations and WGS. RESULTS Overall, 209 cases of HA-COVID-19 were reported. Evolution of HA-COVID-19 incidence closely correlated with the incidence of CA-COVID-19 and COVID-19 among HCWs. During the study period, 13.9 % of hospitalized patients with COVID-19 were infected in the hospital and the 30-day mortality rate of HA-COVID-19 was 31.5 %. Nosocomial transmission of SARS-CoV-2 led to clusters involving both patients and HCWs. WGS allowed the exclusion of one-third of cases initially assigned to a cluster. CONCLUSIONS WGS analysis combined with comprehensive epidemiological investigations is essential to understand transmission routes and adapt the IPC response to protect both patients and HCWs.
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Affiliation(s)
- Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
| | - Jeanne Couturier
- Unité de Prévention du Risque Infectieux, Hôpital Saint-Antoine, GH Sorbonne Université, AP-HP, Paris, France
| | - Benjamin Granger
- Département de Santé Publique, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France
| | - Sarah Jolivet
- Unité de Prévention du Risque Infectieux, Hôpital Saint-Antoine, GH Sorbonne Université, AP-HP, Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, APHP, Hôpital Saint-Antoine, Département de Virologie, Paris, France
| | - Jérôme Robert
- Equipe Opérationnelle d'Hygiène, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France
| | - Michel Denis
- Equipe Opérationnelle d'Hygiène, Hôpital Tenon, GH Sorbonne Université, AP-HP, Paris, France
| | - Beatrice Salauze
- Equipe Opérationnelle d'Hygiène, Hôpitaux Trousseau et Rothschild, GH Sorbonne Université, AP-HP, Paris, France
| | - Valérie Goldstein
- Equipe Opérationnelle d'Hygiène Hôpital Charles Foix, GH Sorbonne Université, AP-HP, Ivry, France
| | - Karen Zafilaza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Pierre Rufat
- Département d'Information Médicale, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Frédéric Barbut
- Unité de Prévention du Risque Infectieux, Hôpital Saint-Antoine, GH Sorbonne Université, AP-HP, Paris, France
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8
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Miao M, De Clercq E, Li G. Towards Efficient and Accurate SARS-CoV-2 Genome Sequence Typing Based on Supervised Learning Approaches. Microorganisms 2022; 10:microorganisms10091785. [PMID: 36144387 PMCID: PMC9505117 DOI: 10.3390/microorganisms10091785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the active development of SARS-CoV-2 surveillance methods (e.g., Nextstrain, GISAID, Pangolin), the global emergence of various SARS-CoV-2 viral lineages that potentially cause antiviral and vaccine failure has driven the need for accurate and efficient SARS-CoV-2 genome sequence classifiers. This study presents an optimized method that accurately identifies the viral lineages of SARS-CoV-2 genome sequences using existing schemes. For Nextstrain and GISAID clades, a template matching-based method is proposed to quantify the differences between viral clades and to play an important role in classification evaluation. Furthermore, to improve the typing accuracy of SARS-CoV-2 genome sequences, an ensemble model that integrates a combination of machine learning-based methods (such as Random Forest and Catboost) with optimized weights is proposed for Nextstrain, Pangolin, and GISAID clades. Cross-validation is applied to optimize the parameters of the machine learning-based method and the weight settings of the ensemble model. To improve the efficiency of the model, in addition to the one-hot encoding method, we have proposed a nucleotide site mutation-based data structure that requires less computational resources and performs better in SARS-CoV-2 genome sequence typing. Based on an accumulated database of >1 million SARS-CoV-2 genome sequences, performance evaluations show that the proposed system has a typing accuracy of 99.879%, 97.732%, and 96.291% for Nextstrain, Pangolin, and GISAID clades, respectively. A single prediction only takes an average of <20 ms on a portable laptop. Overall, this study provides an efficient and accurate SARS-CoV-2 genome sequence typing system that benefits current and future surveillance of SARS-CoV-2 variants.
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Affiliation(s)
- Miao Miao
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
- Hunan Children’s Hospital, Changsha 410007, China
- Correspondence: ; Tel.: +86-731-8480-5414
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9
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Madi N, Safar HA, Mustafa AS, Chehadeh W, Asadzadeh M, Sadeq M, Alawadhi E, Al-Muhaini A, Benthani FA. Molecular epidemiology and genetic characterization of SARS-CoV-2 in Kuwait: A descriptive study. Front Microbiol 2022; 13:858770. [PMID: 36090111 PMCID: PMC9459148 DOI: 10.3389/fmicb.2022.858770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been fatal to human health, affecting almost the entire world. Here we reported, for the first time, characterization of the genetic variants of SARS-CoV-2 circulating in Kuwait to understand their genetic diversity and monitor the accumulation of mutations over time. This study randomly enrolled 209 COVID-19 patients whose nasopharyngeal swabs were positive for SARS-CoV-2 between February 2020 and June 2021 using RT-PCR. The whole genomes of SARS-CoV-2 from the nasopharyngeal swabs were sequenced using the Oxford Nanopore sequencing technology following the ARTIC network protocol. Whole-genome sequencing has identified different clades/sub-clades circulating in Kuwait, mimicking the virus’s global spread. Clade 20A was dominant from February 2020 until January 2021, and then clade 20I (Alpha, V1) emerged and dominated. In June 2021, the number of cases infected with clades 21I, 21A, and 21 J (Delta) increased and dominated. We detected several known clade-defining missense and synonymous mutations and other missense mutations in the genes encoding important viral proteins, including ORF1a, S, ORF3a, ORF8 regions and a novel mutation in the N region. ORF1ab region harbored more mutations and deletions (n = 62, 49.2%) compared to the other 12 gene regions, and the most prevalent missense mutations were P314L (97%) in ORF1b and D614G (97%) in the S glycoprotein regions. Detecting and analyzing mutations and monitoring the evolution of SARS-CoV-2 over time is essential to help better understand the spread of various clades/strains of SARS-CoV-2 and their implications for pathogenesis. In addition, knowledge of the circulating variants and genome sequence variability of SARS-CoV-2 may potentially influence the development of vaccines and antiviral drugs to control the COVID-19 pandemic.
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Affiliation(s)
- Nada Madi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
- *Correspondence: Nada Madi,
| | - Hussain A. Safar
- OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Wassim Chehadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | | | - Ebaa Alawadhi
- Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait, Kuwait
| | - Ali Al-Muhaini
- Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait, Kuwait
| | - Fahad A. Benthani
- Research Institute for Developmental Medicine, Johannes Kepler University of Linz, Linz, Austria
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10
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Yue T, Zhang Q, Cai T, Xu M, Zhu H, Pourkarim MR, De Clercq E, Li G. Trends in the disease burden of HBV and HCV infection in China from 1990 to 2019. Int J Infect Dis 2022; 122:476-485. [PMID: 35724827 DOI: 10.1016/j.ijid.2022.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES This study aims to reveal the 30-year dynamics of HBV and HCV disease burden in China from 1990 to 2019. METHODS HBV/HCV data were retrieved from the Global Burden of Disease database. Joinpoint regression was used to examine temporal trends. Age-period-cohort models were applied to evaluate effects of patient age, period, and cohort on HBV/HCV-associated mortality and incidences. RESULTS A dramatic decrease in the disease burden of HBV was found from 1990 to 2019, but the disease burden of HCV has remained stable since 2000. Patient age, period, and cohort exerted a significant effect on the diseases burden of HBV and HCV infection. Compared with females, males had a higher risk of HBV/HCV infections as well as HBV/HCV-associated mortality and liver cancer. Overweight, alcohol, tobacco and drug use were important risk factors associated with HBV/HCV-associated liver cancer. The incidences of HBV- and HCV-associated liver cancer from 2019 to 2044 are expected to decrease by 39.4% and 33.3%, respectively. CONCLUSIONS The disease burden of HBV/HCV infection has decreased in China over the past 30 years, but HBV incidences remain high, especially in males. Effective management of HBV and HCV infections is still needed for high-risk populations.
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Affiliation(s)
- Tingting Yue
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Quanquan Zhang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Ting Cai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Ming Xu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082 Hunan, China
| | - Mahmoud Reza Pourkarim
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran; Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Hemmat Exp. Way, 14665-1157, Tehran, Iran
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China; Hunan Children's Hospital, Changsha 410007, Hunan, China.
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11
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Kolawole DB, Okeke MI. Phylogenetic and genome-wide mutational analysis of SARS-CoV-2 strains circulating in Nigeria: no implications for attenuated COVID-19 outcomes. Osong Public Health Res Perspect 2022; 13:101-113. [PMID: 35538682 PMCID: PMC9091640 DOI: 10.24171/j.phrp.2021.0329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/27/2022] [Accepted: 03/28/2022] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVES Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The COVID-19 incidence and mortality rates are low in Nigeria compared to global trends. This research mapped the evolution of SARS-CoV-2 circulating in Nigeria and globally to determine whether the Nigerian isolates are genetically distinct from strains circulating in regions of the world with a high disease burden. METHODS Bayesian phylogenetics using BEAST 2.0, genetic similarity analyses, and genomewide mutational analyses were used to characterize the strains of SARS-CoV-2 isolated in Nigeria. RESULTS SARS-CoV-2 strains isolated in Nigeria showed multiple lineages and possible introductions from Europe and Asia. Phylogenetic clustering and sequence similarity analyses demonstrated that Nigerian isolates were not genetically distinct from strains isolated in other parts of the globe. Mutational analysis demonstrated that the D614G mutation in the spike protein, the P323L mutation in open reading frame 1b (and more specifically in NSP12), and the R203K/ G204R mutation pair in the nucleocapsid protein were most prevalent in the Nigerian isolates. CONCLUSION The SARS-CoV-2 strains in Nigeria were neither phylogenetically nor genetically distinct from virus strains circulating in other countries of the world. Thus, differences in SARS-CoV-2 genomes are not a plausible explanation for the attenuated COVID-19 outcomes in Nigeria.
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Affiliation(s)
- Daniel B. Kolawole
- Department of Natural and Environmental Sciences, Biomedical Science Concentration, School of Arts and Sciences, American University of Nigeria, Yola, Nigeria
| | - Malachy I. Okeke
- Department of Natural and Environmental Sciences, Biomedical Science Concentration, School of Arts and Sciences, American University of Nigeria, Yola, Nigeria
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12
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Li G, Wang Y, De Clercq E. Approved HIV reverse transcriptase inhibitors in the past decade. Acta Pharm Sin B 2022; 12:1567-1590. [PMID: 35847492 PMCID: PMC9279714 DOI: 10.1016/j.apsb.2021.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 01/09/2023] Open
Abstract
HIV reverse transcriptase (RT) inhibitors are the important components of highly active antiretroviral therapies (HAARTs) for anti-HIV treatment and pre-exposure prophylaxis in clinical practice. Many RT inhibitors and their combination regimens have been approved in the past ten years, but a review on their drug discovery, pharmacology, and clinical efficacy is lacking. Here, we provide a comprehensive review of RT inhibitors (tenofovir alafenamide, rilpivirine, doravirine, dapivirine, azvudine and elsulfavirine) approved in the past decade, regarding their drug discovery, pharmacology, and clinical efficacy in randomized controlled trials. Novel RT inhibitors such as islatravir, MK-8504, MK-8507, MK8583, IQP-0528, and MIV-150 will be also highlighted. Future development may focus on the new generation of novel antiretroviral inhibitors with higher bioavailability, longer elimination half-life, more favorable side-effect profiles, fewer drug-drug interactions, and higher activities against circulating drug-resistant strains.
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Key Words
- 3TC, (−)-2′,3′-dideoxy-3′-thiacytidine (common name, lamivudine)
- ABC, abacavir
- ATV, atazanavir
- AZT, 3′-azido-3′-deoxy-thymidine (common name, zidovudine)
- BIC, bictegravir
- CAB, cabotegravir
- CC50, the 50% cytotoxic concentration
- COBI, cobicistat
- Clinical efficacy
- DOR, doravirine
- DPV, dapivirine
- DRV, darunavir
- DTG, dolutegravir
- EACS, European AIDS Clinical Society
- EC50, half maximal effective concentration
- EFV, efavirenz
- ESV, elsulfavirine
- EVG, elvitegravir
- F, bioavailability
- FDA, US Food and Drug Administration
- FTC, (−)-2′,3′-dideoxy-5-fluoro-3′-thiacytidine (common name, emtricitabine)
- HAART
- HAART, highly active antiretroviral therapy
- HIV treatment
- HIV, human immunodeficiency virus
- IAS-USA, International Antiviral Society-USA
- IC50, half maximal inhibitory concentration
- MSM, men who have sex with men
- NNRTI
- NNRTI, non-nucleoside reverse transcriptase inhibitor
- NRTI
- NRTI, nucleoside/nucleotide reverse transcriptase inhibitor
- RPV, rilpivirine
- TAF, tenofovir alafenamide
- TDF, tenofovir disoproxil fumarate
- t1/2, elimination half-life
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Affiliation(s)
- Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Yali Wang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Erik De Clercq
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven B-3000, Belgium
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13
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Jing X, Xu M, Song D, Yue T, Wang Y, Zhang P, Zhong Y, Zhang M, Lam TTY, Faria NR, De Clercq E, Li G. Association between inflammatory cytokines and anti-SARS-CoV-2 antibodies in hospitalized patients with COVID-19. Immun Ageing 2022; 19:12. [PMID: 35248063 PMCID: PMC8897556 DOI: 10.1186/s12979-022-00271-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND COVID-19 patients may experience "cytokine storm" when human immune system produces excessive cytokines/chemokines. However, it remains unclear whether early responses of inflammatory cytokines would lead to high or low titers of anti-SARS-CoV-2 antibodies. METHODS This retrospective study enrolled a cohort of 272 hospitalized patients with laboratory-confirmed SARS-CoV-2. Laboratory assessments of serum cytokines (IL-2R, IL-6, IL-8, IL-10, TNF-α), anti-SARS-CoV-2 IgG/IgM antibodies, and peripheral blood biomarkers were conducted during hospitalization. RESULTS At hospital admission, 36.4% patients were severely ill, 51.5% patients were ≥ 65 years, and 60.3% patients had comorbidities. Higher levels of IL-2R and IL-6 were observed in older patients (≥65 years). Significant differences of IL-2R (week 2 to week ≥5 from symptom onset), IL-6 (week 1 to week ≥5), IL-8 (week 2 to week ≥5), and IL-10 (week 1 to week 3) were observed between moderately-ill and severely ill patients. Anti-SARS-CoV-2 IgG titers were significantly higher in severely ill patients than in moderately ill patients, but such difference was not observed for IgM. High titers of early-stage IL-6, IL-8, and TNF-α (≤2 weeks after symptom onset) were positively correlated with high titers of late-stage IgG (≥5 weeks after symptom onset). Deaths were mostly observed in severely ill older patients (45.9%). Survival analyses revealed risk factors of patient age, baseline COVID-19 severity, and baseline IL-6 that affected survival time, especially in severely ill older patients. CONCLUSION Early responses of elevated cytokines such as IL-6 reflect the active immune responses, leading to high titers of IgG antibodies against COVID-19.
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Affiliation(s)
- Xixi Jing
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Min Xu
- grid.452708.c0000 0004 1803 0208Department of Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Deye Song
- grid.452708.c0000 0004 1803 0208Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Tingting Yue
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Yali Wang
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Pan Zhang
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Yanjun Zhong
- grid.452708.c0000 0004 1803 0208Department of Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Min Zhang
- grid.216417.70000 0001 0379 7164Institute of Hepatology and Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Tommy Tsan-Yuk Lam
- grid.194645.b0000000121742757State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, SAR China
| | - Nuno Rodrigues Faria
- grid.7445.20000 0001 2113 8111Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK ,grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Erik De Clercq
- grid.415751.3Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078, China.
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14
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Cao Y, Wu D, Zeng K, Chen L, Yu J, He W, Chen L, Ren W, Gao F, Chen W, Wang H, Gale RP, Chen Z, Li Q. COVID-19 in China and the US: Differences in Hospital Admission Co-Variates and Outcomes. Vaccines (Basel) 2022; 10:vaccines10020326. [PMID: 35214784 PMCID: PMC8878315 DOI: 10.3390/vaccines10020326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 02/01/2023] Open
Abstract
(1) Background: Although there are extensive data on admission co-variates and outcomes of persons with coronavirus infectious disease-2019 (COVID-19) at diverse geographic sites, there are few, if any, subject-level comparisons between sites in regions and countries. We investigated differences in hospital admission co-variates and outcomes of hospitalized people with COVID-19 between Wuhan City, China and the New York City region, USA. (2) Methods: We retrospectively analyzed clinical data on 1859 hospitalized subjects with COVID-19 in Wuhan City, China, from 20 January to 4 April 2020. Data on 5700 hospitalized subjects with COVID-19 in the New York City region, USA, from 1 March to 4 April 2020 were extracted from an article by Richardson et al. Hospital admission co-variates (epidemiological, demographic, and laboratory co-variates) and outcomes (rate of intensive care unit [ICU] admission, invasive mechanical ventilation [IMV], major organ failure and death, and length of hospital stay) were compared between the cohorts. (3) Results: Wuhan subjects were younger, more likely female, less likely to have co-morbidities and fever, more likely to have a blood lymphocyte concentration > 1 × 109/L, and less likely to have abnormal liver and cardiac function tests compared with New York subjects. There were outcomes data on all Wuhan subjects and 2634 New York subjects. Wuhan subjects had higher blood nadir median lymphocyte concentrations and longer hospitalizations, and were less likely to receive IMV, ICU hospitalization, and interventions for kidney failure. Amongst subjects not receiving IMV, those in Wuhan were less likely to die compared with New York subjects. In contrast, risk of death was similar in subjects receiving IMV at both sites. (4) Conclusions: We found different hospital admission co-variates and outcomes between hospitalized persons with COVID-19 between Wuhan City and the New York region, which should be useful developing a comprehensive global understanding of the SARS-CoV-2 pandemic and COVID-19.
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Affiliation(s)
- Yulin Cao
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Di Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Kuo Zeng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, China;
| | - Lei Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Jianming Yu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Wenjuan He
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Li Chen
- Department of Hematology, Wuhan Central Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China; (L.C.); (H.W.)
| | - Wenxiang Ren
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Fei Gao
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Wenlan Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Hongxiang Wang
- Department of Hematology, Wuhan Central Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China; (L.C.); (H.W.)
| | - Robert Peter Gale
- Center for Hematology Research, Department of Immunology and Inflammation, Imperial College London, London W12 0NM, UK;
| | - Zhichao Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
| | - Qiubai Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.C.); (D.W.); (L.C.); (J.Y.); (W.H.); (W.R.); (F.G.); (W.C.); (Z.C.)
- Hubei Engineering Research Center for Application of Extracelluar Vesicles, Hubei University of Science and Technology, Xianning 437100, China
- Correspondence: ; Tel.: +86-27-8572-6387
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15
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Nosocomial transmission clusters and lineage diversity characterized by SARS-CoV-2 genomes from two large hospitals in Paris, France, in 2020. Sci Rep 2022; 12:1094. [PMID: 35058525 PMCID: PMC8776803 DOI: 10.1038/s41598-022-05085-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
France went through three deadly epidemic waves due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing major public health and socioeconomic issues. We proposed to study the course of the pandemic along 2020 from the outlook of two major Parisian hospitals earliest involved in the fight against COVID-19. Genome sequencing and phylogenetic analysis were performed on samples from patients and health care workers (HCWs) from Bichat (BCB) and Pitié-Salpêtrière (PSL) hospitals. A tree-based phylogenetic clustering method and epidemiological data were used to investigate suspected nosocomial transmission clusters. Clades 20A, 20B and 20C were prevalent during the spring wave and, following summer, clades 20A.EU2 and 20E.EU1 emerged and took over. Phylogenetic clustering identified 57 potential transmission clusters. Epidemiological connections between participants were found for 17 of these, with a higher proportion of HCWs. The joint presence of HCWs and patients suggest viral contaminations between these two groups. We provide an enhanced overview of SARS-CoV-2 phylogenetic changes over 2020 in the Paris area, one of the regions with highest incidence in France. Despite the low genetic diversity displayed by the SARS-CoV-2, we showed that phylogenetic analysis, along with comprehensive epidemiological data, helps to identify and investigate healthcare associated clusters.
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16
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Peisahovics F, Rohaim MA, Munir M. Structural topological analysis of spike proteins of SARS-CoV-2 variants of concern highlight distinctive amino acid substitution patterns. Eur J Cell Biol 2022; 101:151275. [PMID: 36156414 PMCID: PMC9484102 DOI: 10.1016/j.ejcb.2022.151275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 02/08/2023] Open
Abstract
Since the onset of pandemic in 2019, SARS-CoV-2 has diverged into numerous variants driven by antigenic and infectivity-oriented selection. Some variants have accumulated fitness-enhancing mutations, evaded immunity and spread despite global vaccination campaigns. The spike (S) glycoprotein of SARS-CoV-2 demonstrated the greatest immunogenicity and amino acid substitution diversity owing to its importance in the interaction with human angiotensin receptor 2 (hACE2). The S protein consistently emerges as an amino acid substitution (AAS) hotspot in all six lineages, however, in Omicron this enrichment is significantly higher. This study attempts to design and validate a method of mapping S-protein substitution profile across variants to identify the conserved and AAS regions. A substitution matrix was created based on publicly available databases, and the substitution localization was illustrated on a cryo-electron microscopy generated S-protein model. Our analyses indicated that the diversity of N-terminal (NTD) and receptor-binding (RBD) domains exceeded that of any other regions but still contained extended low substitution density regions particularly considering significantly broader substitution profiles of Omicron BA.2 and BA.4/5. Finally, the substitution matrix was compared to a random sample alignment of variant sequences, revealing discrepancies. Therefore, it was suggested to improve matrix accuracy by processing a large number of S-protein sequences using an automated algorithm. Several critical immunogenic and receptor-interacting residues were identified in the conserved regions within NTD and RBD. In conclusion, the structural and topological analysis of S proteins of SARS-CoV-2 variants highlight distinctive amino acid substitution patterns which may be foundational in predicting future variants.
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Affiliation(s)
| | | | - Muhammad Munir
- Correspondence to: Lancaster University, Lancaster, United Kingdom
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17
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The importance of accessory protein variants in the pathogenicity of SARS-CoV-2. Arch Biochem Biophys 2022; 717:109124. [PMID: 35085577 PMCID: PMC8785432 DOI: 10.1016/j.abb.2022.109124] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 01/16/2023]
Abstract
The coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2) with an estimated fatality rate of less than 1%. The SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 possess putative functions to manipulate host immune mechanisms. These involve interferons, which appear as a consensus function, immune signaling receptor NLRP3 (NLR family pyrin domain-containing 3) inflammasome, and inflammatory cytokines such as interleukin 1β (IL-1β) and are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins were observed across six continents of all complete SARS-CoV-2 proteomes based on the data reported before November 2020. A decreasing order of percentage of unique variations in the accessory proteins was determined as ORF3a > ORF8 > ORF7a > ORF6 > ORF10 > ORF7b across all continents. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. These findings suggest that the wide variations in accessory proteins seem to affect the pathogenicity of SARS-CoV-2.
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18
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Nemr WA, Radwan NK. TYPING OF ALPHA AND BETA CORONAVIRUSES BY DNA BAR CODING OF NSP12 GENE. J Med Virol 2021; 94:1926-1934. [PMID: 34952969 PMCID: PMC9015621 DOI: 10.1002/jmv.27550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/09/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022]
Abstract
Since the spread of the COVID‐19 pandemic, the world paid attention to coronaviruses (CoVs) evolution and their diverged lineages because many researches studies supposed that the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is evolutionarily developed from a lineage of bats CoVs. This is due to the ability of some mutant CoVs to transmit from a host to different hosts. For this reason, there are many fears about the pathogenicity of the upcoming variants of CoVs. Thus, it is important to get a rapid and economic technique for typing a wide range of human and animal CoVs species for following up their mutant transmission. Therefore, the present study aims at approaching a simple design of DNA barcoding of a wide range of mammals' CoVs (including alpha and beta CoVs), by universal amplification of a species‐specific sequence inside a conserved gene (NSP12) followed by amplicon sequencing. The in silico evaluation involved 96 nucleotide sequences of different CoVs (18 alpha CoVs and 78 beta CoVs), and was applied experimentally into the lab on 5 human CoVs isolates; 3 of them belong to beta CoVs (OC43, MERS, and SARS‐CoV‐2) and 2 are alpha CoVs (229E and NL63). The results indicated that the designed universal primers are able to amplify 332 bp of a taxonomic region inside the NSP12 coding sequence that facilitates the identification and classification of mammals' CoVs upon the resulting phylogenetic tree.
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Affiliation(s)
- Waleed A Nemr
- Department of Radiation Microbiology, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Egypt
| | - Nashwa K Radwan
- Health Radiation Research Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Egypt
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19
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Alemayehu DH, Adnew B, Alemu F, Tefera DA, Seyoum T, Beyene GT, Gelanew T, Negash AA, Abebe M, Mihret A, Bayih AG, Abdissa A, Mulu A. Whole-Genome Sequences of SARS-CoV-2 Isolates from Ethiopian Patients. Microbiol Resour Announc 2021; 10:e0072121. [PMID: 34554000 PMCID: PMC8459669 DOI: 10.1128/mra.00721-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/22/2021] [Indexed: 11/20/2022] Open
Abstract
Three complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Ethiopian patients were compared with deposited global genomes. Two genomes belonged to genetic group 20A/B.1/GH, and the other belonged to genetic group 20A/B.1.480/GH. Enhancing genomic capacity is important to investigate the transmission and to monitor the evolution and mutational patterns of SARS-CoV-2 in this country.
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Affiliation(s)
| | | | - Fekadu Alemu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | | | | | | | | | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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20
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Zeghbib S, Somogyi BA, Zana B, Kemenesi G, Herczeg R, Derrar F, Jakab F. The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Viruses 2021; 13:1525. [PMID: 34452390 PMCID: PMC8402747 DOI: 10.3390/v13081525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023] Open
Abstract
To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylogeographic, haplotype, and genomic analysis were effectively implemented. We estimated the Time to the Most Recent Common Ancestor (TMRCA) in reference to the Algerian pandemic and highlighted the multiple introductions of the disease and the missing data depicted in the transmission loop. In addition, we emphasized the significant role played by local and international travels in disease dissemination. Most importantly, we unveiled mutational patterns, the effect of unique mutations on corresponding proteins, and the relatedness regarding the Algerian sequences to other sequences worldwide. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Similarly, successful tracing could be established, such as Algeria/G37318-8849/2020|EPI_ISL_766863, which was imported from Saudi Arabia during the pilgrimage. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.
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Affiliation(s)
- Safia Zeghbib
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (B.A.S.); (B.Z.); (G.K.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
| | - Balázs A. Somogyi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (B.A.S.); (B.Z.); (G.K.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
| | - Brigitta Zana
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (B.A.S.); (B.Z.); (G.K.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (B.A.S.); (B.Z.); (G.K.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
| | - Róbert Herczeg
- Genomics and Bioinformatics Core Facility, Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary;
| | - Fawzi Derrar
- National Influenza Centre, Viral Respiratory Laboratory, Institut Pasteur d’Algérie, Algiers 16000, Algeria;
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (B.A.S.); (B.Z.); (G.K.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
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