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Liang L, Wang B, Zhang Q, Zhang S, Zhang S. Antibody drugs targeting SARS-CoV-2: Time for a rethink? Biomed Pharmacother 2024; 176:116900. [PMID: 38861858 DOI: 10.1016/j.biopha.2024.116900] [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: 02/14/2024] [Revised: 04/20/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) heavily burdens human health. Multiple neutralizing antibodies (nAbs) have been issued for emergency use or tested for treating infected patients in the clinic. However, SARS-CoV-2 variants of concern (VOC) carrying mutations reduce the effectiveness of nAbs by preventing neutralization. Uncoding the mutation profile and immune evasion mechanism of SARS-CoV-2 can improve the outcome of Ab-mediated therapies. In this review, we first outline the development status of anti-SARS-CoV-2 Ab drugs and provide an overview of SARS-CoV-2 variants and their prevalence. We next focus on the failure causes of anti-SARS-CoV-2 Ab drugs and rethink the design strategy for developing new Ab drugs against COVID-19. This review provides updated information for the development of therapeutic Ab drugs against SARS-CoV-2 variants.
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Affiliation(s)
- Likeng Liang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Bo Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Qing Zhang
- Department of Laboratory Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China.
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2
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SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19. Vaccines (Basel) 2022; 10:vaccines10091538. [PMID: 36146616 PMCID: PMC9504858 DOI: 10.3390/vaccines10091538] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Over the past two years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused hundreds of millions of infections, resulting in an unprecedented pandemic of coronavirus disease 2019 (COVID-19). As the virus spreads through the population, ongoing mutations and adaptations are being discovered. There is now substantial clinical evidence that demonstrates the SARS-CoV-2 variants have stronger transmissibility and higher virulence compared to the wild-type strain of SARS-CoV-2. Hence, development of vaccines against SARS-CoV-2 variants to boost individual immunity has become essential. However, current treatment options are limited for COVID-19 caused by the SARS-CoV-2 variants. In this review, we describe current distribution, variation, biology, and clinical features of COVID-19 caused by SARS-CoV-2 variants (including Alpha (B.1.1.7 Lineage) variant, Beta (B.1.351 Lineage) variant, Gamma (P.1 Lineage) variant, Delta (B.1.617.2 Lineage) variant, and Omicron (B.1.1.529 Lineage) variant and others. In addition, we review currently employed vaccines in clinical or preclinical phases as well as potential targeted therapies in an attempt to provide better preventive and treatment strategies for COVID-19 caused by different SARS-CoV-2 variants.
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Araújo LPD, Dias MEC, Scodeler GC, Santos ADS, Soares LM, Corsetti PP, Padovan ACB, Silveira NJDF, de Almeida LA. Epitope identification of SARS-CoV-2 structural proteins using in silico approaches to obtain a conserved rational immunogenic peptide. IMMUNOINFORMATICS 2022; 7:100015. [PMID: 35721890 PMCID: PMC9188263 DOI: 10.1016/j.immuno.2022.100015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 04/08/2022] [Accepted: 06/10/2022] [Indexed: 10/29/2022]
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Jalal K, Khan K, Basharat Z, Abbas MN, Uddin R, Ali F, Khan SA, Hassan SSU. Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:60035-60053. [PMID: 35414157 PMCID: PMC9005162 DOI: 10.1007/s11356-022-19979-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/25/2022] [Indexed: 06/01/2023]
Abstract
The ongoing COVID-19 outbreak, initially identified in Wuhan, China, has impacted people all over the globe and new variants of concern continue to threaten hundreds of thousands of people. The delta variant (first reported in India) is currently classified as one of the most contagious variants of SARS-CoV-2. It is estimated that the transmission rate of delta variant is 225% times faster than the alpha variant, and it is causing havoc worldwide (especially in the USA, UK, and South Asia). The mutations found in the spike protein of delta variant make it more infective than other variants in addition to ruining the global efficacy of available vaccines. In the current study, an in silico reverse vaccinology approach was applied for multi-epitope vaccine construction against the spike protein of delta variant, which could induce an immune response against COVID-19 infection. Non-toxic, highly conserved, non-allergenic and highly antigenic B-cell, HTL, and CTL epitopes were identified to minimize adverse effects and maximize the efficacy of chimeric vaccines that could be developed from these epitopes. Finally, V1 vaccine construct model was shortlisted and 3D modeling was performed by refinement, docking against HLAs and TLR4 protein, simulation and in silico expression. In silico evaluation showed that the designed chimeric vaccine could elicit an immune response (i.e., cell-mediated and humoral) identified through immune simulation. This study could add to the efforts of overcoming global burden of COVID-19 particularly the variants of concern.
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Affiliation(s)
- Khurshid Jalal
- International Center for Chemical and Biological Sciences, HEJ Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS University of Karachi, Karachi, Pakistan
| | | | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
| | - Fawad Ali
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Saeed Ahmad Khan
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Syed Shams Ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
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5
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Fang ZG, Yang SQ, Lv CX, An SY, Wu W. Application of a data-driven XGBoost model for the prediction of COVID-19 in the USA: a time-series study. BMJ Open 2022; 12:e056685. [PMID: 35777884 PMCID: PMC9251895 DOI: 10.1136/bmjopen-2021-056685] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE The COVID-19 outbreak was first reported in Wuhan, China, and has been acknowledged as a pandemic due to its rapid spread worldwide. Predicting the trend of COVID-19 is of great significance for its prevention. A comparison between the autoregressive integrated moving average (ARIMA) model and the eXtreme Gradient Boosting (XGBoost) model was conducted to determine which was more accurate for anticipating the occurrence of COVID-19 in the USA. DESIGN Time-series study. SETTING The USA was the setting for this study. MAIN OUTCOME MEASURES Three accuracy metrics, mean absolute error (MAE), root mean square error (RMSE) and mean absolute percentage error (MAPE), were applied to evaluate the performance of the two models. RESULTS In our study, for the training set and the validation set, the MAE, RMSE and MAPE of the XGBoost model were less than those of the ARIMA model. CONCLUSIONS The XGBoost model can help improve prediction of COVID-19 cases in the USA over the ARIMA model.
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Affiliation(s)
- Zheng-Gang Fang
- Department of Epidemiology, China Medical University, Shenyang, China
| | - Shu-Qin Yang
- Department of Epidemiology, China Medical University, Shenyang, China
| | - Cai-Xia Lv
- Department of Epidemiology, China Medical University, Shenyang, China
| | - Shu-Yi An
- Department of Social Medicine and Health, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, China
| | - Wei Wu
- Department of Epidemiology, China Medical University, Shenyang, China
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6
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Jiang Y, Wu Q, Song P, You C. The Variation of SARS-CoV-2 and Advanced Research on Current Vaccines. Front Med (Lausanne) 2022; 8:806641. [PMID: 35118097 PMCID: PMC8804231 DOI: 10.3389/fmed.2021.806641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past 2 years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) and rapidly spread worldwide. In the process of evolution, new mutations of SARS-CoV-2 began to appear to be more adaptable to the diverse changes of various cellular environments and hosts. Generally, the emerging SARS-CoV-2 variants are characterized by high infectivity, augmented virulence, and fast transmissibility, posing a serious threat to the prevention and control of the global epidemic. At present, there is a paucity of effective measurements to cure COVID-19. It is extremely crucial to develop vaccines against SARS-CoV-2 and emerging variants to enhance individual immunity, but it is not yet known whether they are approved by the authority. Therefore, we systematically reviewed the main characteristics of the emerging various variants of SARS-CoV-2, including their distribution, mutations, transmissibility, severity, and susceptibility to immune responses, especially the Delta variant and the new emerging Omicron variant. Furthermore, we overviewed the suitable crowd, the efficacy, and adverse events (AEs) of current vaccines.
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Affiliation(s)
| | | | | | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, China
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7
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Singh DD, Parveen A, Yadav DK. SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines. Front Cell Infect Microbiol 2022; 11:777212. [PMID: 34970509 PMCID: PMC8713083 DOI: 10.3389/fcimb.2021.777212] [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: 09/15/2021] [Accepted: 11/09/2021] [Indexed: 01/14/2023] Open
Abstract
The emergence of SARS-CoV-2 variants may cause resistance at the immunity level against current vaccines. Some emergent new variants have increased transmissibility, infectivity, hospitalization, and mortality. Since the administration of the first SARS-CoV-2 vaccine to a human in March 2020, there is an ongoing global race against SARS-CoV-2 to control the current pandemic situation. Spike (S) glycoprotein of SARS-CoV-2 is the main target for current vaccine development, which can neutralize the infection. Companies and academic institutions have developed vaccines based on the S glycoprotein, as well as its antigenic domains and epitopes, which have been proven effective in generating neutralizing antibodies. The effectiveness of SARS-CoV-2 vaccines and other therapeutics developments are limited by the new emergent variants at the global level. We have discussed the emergent variants of SARS-CoV-2 on the efficacy of developed vaccines. Presently, most of the vaccines have been tremendously effective in severe diseases. However, there are still noteworthy challenges in certifying impartial vaccines; the stories of re-infections are generating more stressful conditions, and this needs further clinical evaluation.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Amna Parveen
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, South Korea
| | - Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, South Korea
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8
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Fan S, Xiao K, Li D, Zhao H, Zhang J, Yu L, Chang P, Zhu S, Xu X, Liao Y, Ji T, Jiang G, Yan D, Zeng F, Duan S, Xia B, Wang L, Yang F, He Z, Song Y, Cui P, Li X, Zhang Y, Zheng B, Zhang Y, Xu W, Li Q. Preclinical immunological evaluation of an intradermal heterologous vaccine against SARS-CoV-2 variants. Emerg Microbes Infect 2021; 11:212-226. [PMID: 34931939 PMCID: PMC8745378 DOI: 10.1080/22221751.2021.2021807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recent emergence of COVID-19 variants has necessitated the development of new vaccines that stimulate the formation of high levels of neutralizing antibodies against S antigen variants. A new strategy involves the intradermal administration of heterologous vaccines composed of one or two doses of inactivated vaccine and a booster dose with the mutated S1 protein (K-S). Such vaccines improve the immune efficacy by increasing the neutralizing antibody titers and promoting specific T cell responses against five variants of the RBD protein. A viral challenge test with the B.1.617.2 (Delta) variant confirmed that both administration schedules (i.e. “1 + 1” and “2 + 1”) ensured protection against this strain. These results suggest that the aforementioned strategy is effective for protecting against new variants and enhances the anamnestic immune response in the immunized population.
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Affiliation(s)
- Shengtao Fan
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Kang Xiao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Dandan Li
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Heng Zhao
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Jingjing Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Li Yu
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Penglan Chang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Shuangli Zhu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Xingli Xu
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Yun Liao
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Tianjiao Ji
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Guorun Jiang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Dongmei Yan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Fengyuan Zeng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Suqin Duan
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Baicheng Xia
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Lichun Wang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Fengmei Yang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Yang Song
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Pingfang Cui
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Xiaolei Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Yaxing Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Bangyi Zheng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Ying Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Qihan Li
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
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Wang Y, Chen R, Hu F, Lan Y, Yang Z, Zhan C, Shi J, Deng X, Jiang M, Zhong S, Liao B, Deng K, Tang J, Guo L, Jiang M, Fan Q, Li M, Liu J, Shi Y, Deng X, Xiao X, Kang M, Li Y, Guan W, Li Y, Li S, Li F, Zhong N, Tang X. Transmission, viral kinetics and clinical characteristics of the emergent SARS-CoV-2 Delta VOC in Guangzhou, China. EClinicalMedicine 2021; 40:101129. [PMID: 34541481 PMCID: PMC8435265 DOI: 10.1016/j.eclinm.2021.101129] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A novel variant of SARS-CoV-2, the Delta variant of concern (VOC, also known as lineage B.1.617.2), is fast becoming the dominant strain globally. We reported the epidemiological, viral, and clinical characteristics of hospitalized patients infected with the Delta VOC during the local outbreak in Guangzhou, China. METHODS We extracted the epidemiological and clinical information pertaining to the 159 cases infected with the Delta VOC across seven transmission generations between May 21 and June 18, 2021. The whole chain of the Delta VOC transmission was described. Kinetics of viral load and clinical characteristics were compared with a cohort of wild-type infection in 2020 admitted to the Guangzhou Eighth People's Hospital. FINDINGS There were four transmission generations within the first ten days. The Delta VOC yielded a significantly shorter incubation period (4.0 vs. 6.0 days), higher viral load (20.6 vs. 34.0, cycle threshold of the ORF1a/b gene), and a longer duration of viral shedding in pharyngeal swab samples (14.0 vs. 8.0 days) compared with the wild-type strain. In cases with critical illness, the proportion of patients over the age of 60 was higher in the Delta VOC group than in the wild-type strain (100.0% vs. 69.2%, p = 0.03). The Delta VOC had a higher risk than wild-type infection in deterioration to critical status (hazards ratio 2.98 [95%CI 1.29-6.86]; p = 0.01). INTERPRETATION Infection with the Delta VOC is characterized by markedly increased transmissibility, viral loads and risk of disease progression compared with the wild-type strain, calling for more intensive prevention and control measures to contain future outbreaks. FUNDING National Grand Program, National Natural Science Foundation of China, Guangdong Provincial Department of Science and Technology, Guangzhou Laboratory.
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Affiliation(s)
- Yaping Wang
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Ruchong Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
- Department of Allergy and Clinical Immunology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Fengyu Hu
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Yun Lan
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Zhaowei Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
- Department of Allergy and Clinical Immunology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Chen Zhan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
- Department of Allergy and Clinical Immunology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Jingrong Shi
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Xizi Deng
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Mei Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Shuxin Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Baolin Liao
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Kai Deng
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Jingyan Tang
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Liliangzi Guo
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Mengling Jiang
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Qinghong Fan
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Meiyu Li
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Jinxin Liu
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Yaling Shi
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Xilong Deng
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Xincai Xiao
- Guangzhou Chest Hospital, Guangzhou Medical University, Guangzhou 510095, China
| | - Min Kang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
| | - Weijie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Yimin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Shiyue Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Feng Li
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Laboratory, Bio-Island, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
- Guangzhou Laboratory, Bio-Island, Guangzhou 510320, China
| | - Xiaoping Tang
- Guangzhou Eighth People's Hospital , Guangzhou Medical University, Guangzhou, 510060, China
- Guangzhou Laboratory, Bio-Island, Guangzhou 510320, China
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10
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Wang S, Xu X, Wei C, Li S, Zhao J, Zheng Y, Liu X, Zeng X, Yuan W, Peng S. Molecular evolutionary characteristics of SARS-CoV-2 emerging in the United States. J Med Virol 2021; 94:310-317. [PMID: 34506640 PMCID: PMC8662038 DOI: 10.1002/jmv.27331] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022]
Abstract
SARS‐CoV‐2 is a newly discovered beta coronavirus at the end of 2019, which is highly pathogenic and poses a serious threat to human health. In this paper, 1875 SARS‐CoV‐2 whole genome sequences and the sequence coding spike protein (S gene) sampled from the United States were used for bioinformatics analysis to study the molecular evolutionary characteristics of its genome and spike protein. The MCMC method was used to calculate the evolution rate of the whole genome sequence and the nucleotide mutation rate of the S gene. The results showed that the nucleotide mutation rate of the whole genome was 6.677 × 10−4 substitution per site per year, and the nucleotide mutation rate of the S gene was 8.066 × 10−4 substitution per site per year, which was at a medium level compared with other RNA viruses. Our findings confirmed the scientific hypothesis that the rate of evolution of the virus gradually decreases over time. We also found 13 statistically significant positive selection sites in the SARS‐CoV‐2 genome. In addition, the results showed that there were 101 nonsynonymous mutation sites in the amino acid sequence of S protein, including seven putative harmful mutation sites. This paper has preliminarily clarified the evolutionary characteristics of SARS‐CoV‐2 in the United States, providing a scientific basis for future surveillance and prevention of virus variants.
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Affiliation(s)
- Shihang Wang
- Department of Virology, National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xuanyu Xu
- Department of Virology, National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Cai Wei
- Department of Virology, National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Sicong Li
- Department of Virology, National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jingying Zhao
- Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.,Department of Health Care, School of Physical Education & Health Care, East China Normal University, Shanghai, China
| | - Yin Zheng
- Department of Virology, National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xiaoyu Liu
- Department of Virology, National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xiaomin Zeng
- Department of Biostatistics, Central South University, Xiangya Public Health School, Changsha, China
| | - Wenliang Yuan
- Department of Mathematics, College of Mathematics and Information Engineering, Jiaxing University, Jiaxing, China
| | - Sihua Peng
- Department of Virology, National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
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11
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Shahraki AH, Vahed M, Mirsaeidi M. Mask-off policy in the shadow of emerging variants of SARS-COV-2. Eur J Intern Med 2021; 90:109-110. [PMID: 34193373 PMCID: PMC8236354 DOI: 10.1016/j.ejim.2021.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA; Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Majid Vahed
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA; Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mehdi Mirsaeidi
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA; Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL, USA.
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12
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Chakraborty C, Bhattacharya M, Sharma AR. Present variants of concern and variants of interest of severe acute respiratory syndrome coronavirus 2: Their significant mutations in S‐glycoprotein, infectivity, re‐infectivity, immune escape and vaccines activity. Rev Med Virol 2021. [PMCID: PMC8420283 DOI: 10.1002/rmv.2270] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Newly arising variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are now a threat to global public health and are creating COVID‐19 surges in different countries. At the same time, there is limited knowledge about these emerging variants. Even if research data are available, it is varyingly scattered. In this review, we have discussed the appearance of significant alarming SARS‐CoV‐2 variants in the entire world. The study also discusses the properties of the substantial variant of concern (VOC) variants such as B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.427 (Epsilon) and B.1.429 (Epsilon). At the same time, the characteristic properties of some significant variant of interest (VOI) variants like B.1.525 (Eta), B.1.526 (Iota) (sublineage B.1.526.1), B.1.617 (sublineages B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3), P.2 (Zeta), P.3 (Theta), B.1.616 and B.1.427 have also been discussed. Here, we have explained some essential mutations for the VOC and VOI variants such as K417T/N, L452R, E484K, N501Y, D614G and P681R. Consecutively, we also highlighted the crucial clinical characteristics of the variants, such as transmissibility, infectivity, re‐infectivity, immune escape, vaccine activity and vaccine escape. Our comprehensive review will provide updated information on the newly appearing variants of SARS‐CoV‐2 and help the researchers to formulate strategies to curtail the COVID‐19 pandemic.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology School of Life Science and Biotechnology Adamas University Kolkata West Bengal India
| | | | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery Hallym University‐Chuncheon Sacred Heart Hospital Chuncheon‐si Gangwon‐do South Korea
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