1
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Jiang RM, Xie ZD, Jiang Y, Lu XX, Jin RM, Zheng YJ, Shang YX, Xu BP, Liu ZS, Lu G, Deng JK, Liu GH, Wang XC, Wang JS, Feng LZ, Liu W, Zheng Y, Shu SN, Lu M, Luo WJ, Liu M, Cui YX, Ye LP, Shen AD, Liu G, Gao LW, Xiong LJ, Bai Y, Lin LK, Wei Z, Xue FX, Wang TY, Zhao DC, Shao JB, Ng DKK, Wong GWK, Zhao ZY, Li XW, Yang YH, Shen KL. Diagnosis, treatment and prevention of severe acute respiratory syndrome coronavirus 2 infection in children: experts' consensus statement updated for the Omicron variant. World J Pediatr 2024; 20:272-286. [PMID: 37676610 DOI: 10.1007/s12519-023-00745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/29/2023] [Indexed: 09/08/2023]
Affiliation(s)
- Rong-Meng Jiang
- Diagnosis and Treatment Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Zheng-De Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Yi Jiang
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xiao-Xia Lu
- Department of Respiratory, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Run-Ming Jin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yue-Jie Zheng
- Department of Respiratory, Shenzhen Children's Hospital, Shenzhen, 518038, China
| | - Yun-Xiao Shang
- Department of Pediatric Respiratory, Shengjing Hospital Affiliated to China Medical University, Shenyang, 110004, China
| | - Bao-Ping Xu
- Department of Respiratory, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, 100045, China
| | - Zhi-Sheng Liu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Gen Lu
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Ji-Kui Deng
- Department of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, 518038, China
| | - Guang-Hua Liu
- Department of Pediatrics, Fujian Branch of Shanghai Children's Medical Center, Fujian Children's Hospital, Fuzhou, 350005, China
| | - Xiao-Chuan Wang
- Department of Clinical Immunology and Allergy, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China
| | - Jian-She Wang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China
| | - Lu-Zhao Feng
- School of Population Medicine and Public Health, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, 100730, China
| | - Wei Liu
- Children's Hospital of Tianjin University, Tianjin Children's Hospital, Tianjin, 300134, China
| | - Yi Zheng
- Beijing Key Laboratory of Diagnosis and Treatment of Mental Disorders, National Clinical Research Center for Mental and Psychological Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
| | - Sai-Nan Shu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Min Lu
- Department of Respiratory, Shanghai Children's Hospital, Shanghai, 200062, China
| | - Wan-Jun Luo
- Office of Infection Management, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Miao Liu
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yu-Xia Cui
- Department of Pediatrics, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Le-Ping Ye
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - A-Dong Shen
- Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, 100045, China
| | - Gang Liu
- Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Li-Wei Gao
- Department of Respiratory, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, 100045, China
| | - Li-Juan Xiong
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yan Bai
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Li-Kai Lin
- Hospital Management Institute of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zhuang Wei
- Children's Health Care Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Feng-Xia Xue
- Department of Respiratory, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, 100045, China
| | - Tian-You Wang
- Hematology and Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Dong-Chi Zhao
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jian-Bo Shao
- Department of Radiology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Daniel Kwok-Keung Ng
- Department of Pediatrics, Hong Kong Sanatorium & Hospital, Hong Kong, 999077, China
| | - Gary Wing-Kin Wong
- Department of Pediatrics, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Zheng-Yan Zhao
- Department of Developmental Behavior, Children's Hospital, Zhejiang University College of Medicine, Hangzhou, 310051, China.
| | - Xing-Wang Li
- Diagnosis and Treatment Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
| | - Yong-Hong Yang
- Department of Respiratory, Shenzhen Children's Hospital, Shenzhen, 518038, China.
- Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, 100045, China.
| | - Kun-Ling Shen
- Department of Respiratory, Shenzhen Children's Hospital, Shenzhen, 518038, China.
- Department of Respiratory, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, 100045, China.
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2
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Sun J, Liu X, Zhang S, Li M, Zhang Q, Chen J. Molecular insights and optimization strategies for the competitive binding of engineered ACE2 proteins: a multiple replica molecular dynamics study. Phys Chem Chem Phys 2023; 25:28479-28496. [PMID: 37846774 DOI: 10.1039/d3cp03392a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally, and rapid viral evolution and the emergence of new variants pose challenges to pandemic control. During infection, the spike protein of SARS-CoV-2 interacts with the human ACE2 protein via its receptor binding domain (RBD), and it is known that engineered forms of ACE2 can compete with wild-type (WT) ACE2 for binding to inhibit infection. Here, we conducted multiple replica molecular dynamics (MRMD) simulations to study the mechanisms of the engineered ACE2 variants 3N39 and 3N94 and provide directions for optimization. Our findings reveal that engineered ACE2 is notably more efficacious in systems that show weaker binding to WT ACE2 (i.e., WT and BA.1 RBD), but also faces immune escape as the virus evolves. Moreover, by modifying residue types near the binding interface, engineered ACE2 alters the electrostatic potential distribution and reconfigures the hydrogen bonding network, which results in modified binding to the RBD. However, this structural rearrangement does not occur in all RBD variants. In addition, we identified potentially engineerable beneficial residues and potentially engineerable detrimental residues in both ACE2 and RBD. Functional conservation can thus enable the optimization of these residues and improve the binding competitiveness of engineered ACE2, which therefore provides additional immune escape prevention. Finally, we conclude that these findings have implications for understanding the mechanisms responsible for engineered ACE2 and can help us to develop engineered ACE2 proteins that show superior performance.
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Affiliation(s)
- Jiahao Sun
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Meng Li
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
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3
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Yassi A, Barker S, Lockhart K, Taylor D, Harris D, Hundal H, Grant JM, Okpan AI, Pollock S, Sprague S, Sing CK. Urban-rural divide in COVID-19 infection and vaccination rates in healthcare workers in British Columbia, Canada. CANADIAN JOURNAL OF RURAL MEDICINE 2023; 28:47-58. [PMID: 37005988 DOI: 10.4103/cjrm.cjrm_24_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Introduction Healthcare workers (HCWs) play a critical role in responding to the COVID-19 pandemic. Early in the pandemic, urban centres were hit hardest globally; rural areas gradually became more impacted. We compared COVID-19 infection and vaccine uptake in HCWs living in urban versus rural locations within, and between, two health regions in British Columbia (BC), Canada. We also analysed the impact of a vaccine mandate for HCWs. Methods We tracked laboratory-confirmed SARS-CoV-2 infections, positivity rates and vaccine uptake in all 29,021 HCWs in Interior Health (IH) and all 24,634 HCWs in Vancouver Coastal Health (VCH), by occupation, age and home location, comparing to the general population in that region. We then evaluated the impact of infection rates as well as the mandate on vaccination uptake. Results While we found an association between vaccine uptake by HCWs and HCW COVID-19 rates in the preceding 2-week period, the higher rates of COVID-19 infection in some occupational groups did not lead to increased vaccination in these groups. By 27 October 2021, the date that unvaccinated HCWs were prohibited from providing healthcare, only 1.6% in VCH compared with 6.5% in IH remained unvaccinated. Rural workers in both areas had significantly higher unvaccinated rates compared with urban dwellers. Over 1800 workers, comprising 6.7% of rural HCWs and 3.6% of urban HCWs, remained unvaccinated and set to be terminated from their employment. While the mandate prompted a significant increase in uptake of second doses, the impact on the unvaccinated was less clear. Conclusions As rural areas often suffer from under-staffing, loss of HCWs could have serious impacts on healthcare provision as well as on the livelihoods of unvaccinated HCWs. Greater efforts are needed to understand how to better address the drivers of rural-related vaccine hesitancy.
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Affiliation(s)
- Annalee Yassi
- School of Population and Public Health, University of British Columbia; Medical Practitioners Occupational Safety and Health (mPOSH), Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Stephen Barker
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Lockhart
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Devin Harris
- Interior Health, Kelowna, British Columbia; Department of Emergency Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harsh Hundal
- Interior Health, Kelowna, British Columbia, Canada
| | - Jennifer M Grant
- Medical Practitioners Occupational Safety and Health (mPOSH), Vancouver Coastal Health; Department of Pathology and Laboratory Medicine, Vancouver Coastal Health; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arnold Ikedichi Okpan
- School of Population and Public Health, University of British Columbia; Medical Practitioners Occupational Safety and Health (mPOSH), Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Sue Pollock
- School of Population and Public Health, University of British Columbia, Vancouver; Interior Health, Kelowna, British Columbia, Canada
| | - Stacy Sprague
- Employee Safety, Health and Wellness, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Chad Kim Sing
- Department of Emergency Medicine, Faculty of Medicine, University of British Columbia; Medicine, Quality and Safety, Vancouver Coastal Health, Vancouver, British Columbia, Canada
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4
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Mohapatra RK, Verma S, Kandi V, Sarangi AK, Seidel V, Das SN, Behera A, Tuli HS, Sharma AK, Dhama K. The SARS‐CoV‐2 Omicron Variant and its Multiple Sub‐lineages: Transmissibility, Vaccine Development, Antiviral Drugs, Monoclonal Antibodies, and Strategies for Infection Control – a Review. ChemistrySelect 2023. [DOI: 10.1002/slct.202201380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Ranjan K. Mohapatra
- Department of Chemistry Government College of Engineering Keonjhar 758002 Odisha India
| | - Sarika Verma
- Council of Scientific and Industrial Research-Advanced Materials and Processes Research Institute Bhopal MP 462026 India
- Academy of council Scientific and Industrial Research - Advanced Materials and Processes Research Institute (AMPRI) Hoshangabad Road Bhopal (M.P) 462026 India
| | - Venkataramana Kandi
- Department of Microbiology Prathima Institute of Medical Sciences Karimnagar 505417 Telangana India
| | - Ashish K. Sarangi
- Department of Chemistry School of Applied Sciences Centurion University of Technology and Management Odisha India
| | - Veronique Seidel
- Strathclyde Institute of Pharmacy and Biomedical Sciences University of Strathclyde Glasgow G4 0RE United Kingdom
| | - Subrata Narayan Das
- Department of Mining Engineering Government College of Engineering Keonjhar 758002 Odisha India
| | - Ajit Behera
- Department of Metallurgical & Materials Engineering National Institute of Technology Rourkela 769008 India
| | - Hardeep Singh Tuli
- Department of Biotechnology Maharishi MarkandeshwarEngineering College Maharishi MarkandeshwarDeemed to be University, Mullana Ambala, 133207 Haryana India
| | - Ashwani K. Sharma
- Department of Chemistry Government Digvijay (Autonomous) Post-Graduate College Rajnandgaon (C.G. India
| | - Kuldeep Dhama
- Division of Pathology ICAR-Indian Veterinary Research Institute Bareilly
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5
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Cox M, Peacock TP, Harvey WT, Hughes J, Wright DW, Willett BJ, Thomson E, Gupta RK, Peacock SJ, Robertson DL, Carabelli AM. SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nat Rev Microbiol 2023; 21:112-124. [PMID: 36307535 PMCID: PMC9616429 DOI: 10.1038/s41579-022-00809-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 01/20/2023]
Abstract
Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in vitro neutralization data for mAbs against live variants and viral constructs containing spike mutations of interest. Unfortunately, evasion of mAb-induced protection is being reported with new SARS-CoV-2 variants. The magnitude of neutralization reduction varied greatly among mAb-variant pairs. For example, sotrovimab retained its neutralization capacity against Omicron BA.1 but showed reduced efficacy against BA.2, BA.4 and BA.5, and BA.2.12.1. At present, only bebtelovimab has been reported to retain its efficacy against all SARS-CoV-2 variants considered here. Resistance to mAb neutralization was dominated by the action of epitope single amino acid substitutions in the spike protein. Although not all observed epitope mutations result in increased mAb evasion, amino acid substitutions at non-epitope positions and combinations of mutations also contribute to evasion of neutralization. This Review highlights the implications for the rational design of viral genomic surveillance and factors to consider for the development of novel mAb therapies.
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Affiliation(s)
- MacGregor Cox
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Derek W Wright
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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6
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Simple Wastewater Preparation Protocol Applied to Monitor the Emergence of the Omicron 21L/BA.2 Variant by Genome Sequencing. Viruses 2023; 15:v15020268. [PMID: 36851484 PMCID: PMC9965846 DOI: 10.3390/v15020268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/22/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Detecting and monitoring viruses in wastewater samples have been reported as useful ways of tracking SARS-CoV-2 epidemic trends. However, there is currently no unanimously recognised method of processing samples to identify and quantify SARS-CoV-2 variants in wastewater. We aimed to implement a method that was as simple as possible in order to be used universally. In a study performed between January 2022 and June 2022 in the city of Marseille, France, we first evaluated the impact of the sample preservation strategy. We then compared ultracentrifugation to ultrafiltration and several steps of filtration to determine the optimal approach for virus concentration. As a proof-of-concept, the definitive protocol was applied to next-generation sequencing of SARS-CoV-2 in wastewater to monitor the emergence of the Omicron variant in the city. For sewage water to be processed in the week following the sampling, storage at +4 °C is sufficient, with less than 1 Ct loss. Filtration with a 5 µm syringe filter, then with a 0.8 µm filtration unit, followed by ultrafiltration was the optimal protocol, leading to an average increase of 3.24 Ct when the starting Ct was on average 38 in the wastewater. This made it possible to observe the emergence of the Omicron 21L/BA.2 variant after Omicron 21K/BA.1 by genome sequencing over a period ranging from 20 February to 10 April 2022 in agreement with observations based on patient data. To conclude, by using a simple method requiring only basic filters and a centrifuge as equipment, it is possible to accurately track the relative incidence rates and the emergence of SARS-CoV-2 variants based on sewage samples.
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7
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Suardana IBK, Mahardika BK, Pharmawati M, Sudipa PH, Sari TK, Mahendra NB, Mahardika GN. Whole-Genome Comparison of Representatives of All Variants of SARS-CoV-2, Including Subvariant BA.2 and the GKA Clade. Adv Virol 2023; 2023:6476626. [PMID: 36938489 PMCID: PMC10019969 DOI: 10.1155/2023/6476626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 12/10/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
Since its discovery at the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into many variants, including the subvariant BA.2 and the GKA clade. Genomic clarification is needed for better management of the current pandemic as well as the possible reemergence of novel variants. The sequence of the reference genome Wuhan-Hu-1 and approximately 20 representatives of each variant were downloaded from GenBank and GISAID. Two representatives with no track of in-definitive nucleotides were selected. The sequences were aligned using muscle. The location of insertion/deletion (indel) in the genome was mapped following the open reading frame (ORF) of Wuhan-Hu-1. The phylogeny of the spike protein coding region was constructed using the maximum likelihood method. Amino acid substitutions in all ORFs were analyzed separately. There are two indel sites in ORF1AB, eight in spike, and one each in ORF3A, matrix (MA), nucleoprotein (NP), and the 3'-untranslated regions (3'UTR). Some indel sites and residues/substitutions are not unique, and some are variant-specific. The phylogeny shows that Omicron, Deltacron, and BA2 are clustered together and separated from other variants with 100% bootstrap support. In conclusion, whole-genome comparison of representatives of all variants revealed indel patterns that are specific to SARS-CoV-2 variants or subvariants. Polymorphic amino acid comparison across all coding regions also showed amino acid residues shared by specific groups of variants. Finally, the higher transmissibility of BA.2 might be due at least in part to the 48 nucleotide deletions in the 3'UTR, while the seem-to-be extinction of GKA clade is due to the lack of genetic advantages as a consequence of amino acid substitutions in various genes.
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Affiliation(s)
- Ida B. K. Suardana
- 1Virology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Bayu K. Mahardika
- 2The Animal Biomedical and Molecular Biology Laboratory, Udayana University, Jl. Sesetan-Markisa 6A, Denpasar 80223, Bali, Indonesia
| | - Made Pharmawati
- 3The Biology Study Program, The Faculty of Mathematic and Natural Science, Udayana University, Kampus Bukit Jimbaran, Badung, Bali, Indonesia
| | - Putu H. Sudipa
- 4Veterinary Bacteriology and Mycology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Tri K. Sari
- 1Virology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Nyoman B. Mahendra
- 5The Department of Obstetrics and Genecology, The Faculty of Medicine, Udayana University, Kuta Selatan, Bali, Indonesia
| | - Gusti N. Mahardika
- 1Virology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia
- 2The Animal Biomedical and Molecular Biology Laboratory, Udayana University, Jl. Sesetan-Markisa 6A, Denpasar 80223, Bali, Indonesia
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8
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Dhama K, Nainu F, Frediansyah A, Yatoo MI, Mohapatra RK, Chakraborty S, Zhou H, Islam MR, Mamada SS, Kusuma HI, Rabaan AA, Alhumaid S, Mutair AA, Iqhrammullah M, Al-Tawfiq JA, Mohaini MA, Alsalman AJ, Tuli HS, Chakraborty C, Harapan H. Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies. J Infect Public Health 2023; 16:4-14. [PMID: 36446204 PMCID: PMC9675435 DOI: 10.1016/j.jiph.2022.11.024] [Citation(s) in RCA: 99] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/06/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022] Open
Abstract
Newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuously posing high global public health concerns and panic resulting in waves of coronavirus disease 2019 (COVID-19) pandemic. Depending on the extent of genomic variations, mutations and adaptation, few of the variants gain the ability to spread quickly across many countries, acquire higher virulency and ability to cause severe disease, morbidity and mortality. These variants have been implicated in lessening the efficacy of the current COVID-19 vaccines and immunotherapies resulting in break-through viral infections in vaccinated individuals and recovered patients. Altogether, these could hinder the protective herd immunity to be achieved through the ongoing progressive COVID-19 vaccination. Currently, the only variant of interest of SARS-CoV-2 is Omicron that was first identified in South Africa. In this review, we present the overview on the emerging SARS-CoV-2 variants with a special focus on the Omicron variant, its lineages and hybrid variants. We discuss the hypotheses of the origin, genetic change and underlying molecular mechanism behind higher transmissibility and immune escape of Omicron variant. Major concerns related to Omicron including the efficacy of the current available immunotherapeutics and vaccines, transmissibility, disease severity, and mortality are discussed. In the last part, challenges and strategies to counter Omicron variant, its lineages and hybrid variants amid the ongoing COVID-19 pandemic are presented.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India.
| | - Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Andri Frediansyah
- Research Division for Natural Product Technology (BPTBA), National Research and Innovation Agency (BRIN), Gunungkidul, Yogyakarta 55861, Indonesia
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190006, India
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, Odisha, India
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, R.K. Nagar, West Tripura, Tripura, India
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Microbiology, NYU Grossman School of Medicine, New York 10016, USA
| | - Md Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, 74/A Green Road, Farmgate, Dhaka 1205, Bangladesh
| | - Sukamto S Mamada
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Hendrix Indra Kusuma
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia; Biology Education Department, Faculty of Tarbiyah and Teacher Training, Universitas Islam Negeri Ar-Raniry, Jl. Syeikh Abdur Rauf, Kopelma Darussalaml, Banda Aceh 23111, Indonesia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia; College of Nursing, Prince Nora University, Riyadh 11564, Saudi Arabia; School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia; Nursing Department, Prince Sultan Military College of Health Sciences, Dhahran 33048, Saudi Arabia
| | - Muhammad Iqhrammullah
- Graduate School of Mathematics and Applied Sciences, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine and Quality Department, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Infectious Disease Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mohammed Al Mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Al-Ahsa 31982, Saudi Arabia; King Abdullah International Medical Research Center, Al-Ahsa 31982, Saudi Arabia
| | - Abdulkhaliq J Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar University, Mullana, Ambala 133207, Haryana, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126, India
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Tropical Diseases Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia.
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9
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Roohani J, Keikha M. Global challenge with the SARS-CoV-2 omicron BA.2 (B.1.1.529.2) subvariant: Should we be concerned? World J Virol 2022; 11:496-501. [PMID: 36483099 PMCID: PMC9724199 DOI: 10.5501/wjv.v11.i6.496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/23/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
BA.2 is a novel omicron offshoot of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has gone viral. There is limited knowledge regarding this variant of concern. Current evidence suggests that this variant is more contagious but less severe than previous SARS-CoV-2 variants. However, there is concern regarding the virus mutations that could influence pathogenicity, transmissibility, and immune evasion.
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Affiliation(s)
- Jalil Roohani
- Department of Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 13131-99137, Iran
| | - Masoud Keikha
- Department of Medical Microbiology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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10
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Phan T, Boes S, McCullough M, Gribschaw J, Wells A. Mini-evaluation of the Lyra SARS-CoV-2 assay to detect Omicron BA.1 and BA.2 in nasopharyngeal swabs. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100118. [PMID: 36277996 PMCID: PMC9578329 DOI: 10.1016/j.jcvp.2022.100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Stephanie Boes
- Clinical Microbiology Laboratory, UPMC Hospital System, Pittsburgh, PA 15261, United States
| | - Melissa McCullough
- Clinical Microbiology Laboratory, UPMC Hospital System, Pittsburgh, PA 15261, United States
| | - Jamie Gribschaw
- Clinical Microbiology Laboratory, UPMC Hospital System, Pittsburgh, PA 15261, United States
| | - Alan Wells
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, United States
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11
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Rahman S, Hossain MJ, Nahar Z, Shahriar M, Bhuiyan MA, Islam MR. Emerging SARS-CoV-2 Variants and Subvariants: Challenges and Opportunities in the Context of COVID-19 Pandemic. ENVIRONMENTAL HEALTH INSIGHTS 2022; 16:11786302221129396. [PMID: 36299441 PMCID: PMC9585367 DOI: 10.1177/11786302221129396] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/09/2022] [Indexed: 05/30/2023]
Abstract
The COVID-19 pandemic has become the most devastating pandemic of the 21st century since its appearance in December 2019. Like other RNA viruses, continuous mutation is common for coronavirus to create several variants and subvariants. The main reason behind this mutation and evolvement of SARS-CoV-2 was its structural spike (S) glycoprotein. Coronavirus has become a threat to global public health due to its high mutation capability and antibody neutralizing capacity. According to the World Health Organization (WHO), there are 5 major variants of concern (VOC) are Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529). Recently, different Omicron subvariants have gained worldwide dominance, such as BA.1, BA.2, BA.3, BA.4, and BA.5. However, there is a discernible drop in this symptomatic sickness globally due to the success of numerous monoclonal antibodies and vaccinations. Here we also discussed the currently dominant Omicron subvariants and the effectiveness of antiviral agents and vaccines. Based on the available data and our knowledge, we can suggest that the global healthcare organizations can decide on the declaration of the end of the pandemic phase of COVID-19 soon; however, the covid-19 will continue.
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Affiliation(s)
- Smaranika Rahman
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | - Md. Jamal Hossain
- Department of Pharmacy, State
University of Bangladesh, Dhanmondi, Dhaka, Bangladesh
| | - Zabun Nahar
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | - Mohammad Shahriar
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | | | - Md. Rabiul Islam
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
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12
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Bedada FB, Gorfu G, Teng S, Neita ME. Insight into genomic organization of pathogenic coronaviruses, SARS-CoV-2: Implication for emergence of new variants, laboratory diagnosis and treatment options. FRONTIERS IN MOLECULAR MEDICINE 2022; 2:917201. [PMID: 39157715 PMCID: PMC11328875 DOI: 10.3389/fmmed.2022.917201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/13/2022] [Indexed: 08/20/2024]
Abstract
SARS-CoV-2 is a novel zoonotic positive-sense RNA virus (ssRNA+) belonging to the genus beta coronaviruses (CoVs) in the Coronaviridae family. It is the causative agent for the outbreak of the disease, COVID-19. It is the third CoV causing pneumonia around the world in the past 2 decades. To date, it has caused significant deaths worldwide. Notably, the emergence of new genetic variants conferring efficient transmission and immune evasion remained a challenge, despite the reduction in the number of death cases, owing to effective vaccination regimen (boosting) and safety protocols. Thus, information harnessed from SARS-CoV-2 genomic organization is indispensable for seeking laboratory diagnosis and treatment options. Here in, we review previously circulating variants of SARS-CoV-2 designated variant of concern (VOC) including the Alpha (United Kingdom), Beta (South Africa), Gamma (Brazil), Delta (India), and recently circulating VOC, Omicron (South Africa) and its divergent subvariants (BA.1, BA.2, BA.3, BA.2.12.1, BA.4 and BA.5) with BA.5 currently becoming dominant and prolonging the COVID pandemic. In addition, we address the role of computational models for mutagenesis analysis which can predict important residues that contribute to transmissibility, virulence, immune evasion, and molecular detections of SARS-CoV-2. Concomitantly, the importance of harnessing the immunobiology of SARS-CoV-2 and host interaction for therapeutic purpose; and use of an in slilico based biocomputational approaches to achieve this purpose via predicting novel therapeutic agents targeting PRR such as toll like receptor, design of universal vaccine and chimeric antibodies tailored to the emergent variant have been highlighted.
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Affiliation(s)
- Fikru B. Bedada
- Department of Clinical Laboratory Science, College of Nursing and Allied Health Sciences, Howard University, Washington, DC, United States
| | - Gezahegn Gorfu
- Department of Clinical Laboratory Science, College of Nursing and Allied Health Sciences, Howard University, Washington, DC, United States
- Department of Pathology, College of Medicine, Howard University, Washington, DC, United States
| | - Shaolei Teng
- Department of Biology, College of Arts and Sciences, Howard University, Washington, DC, United States
| | - Marguerite E. Neita
- Department of Clinical Laboratory Science, College of Nursing and Allied Health Sciences, Howard University, Washington, DC, United States
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13
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Chadeau-Hyam M, Tang D, Eales O, Bodinier B, Wang H, Jonnerby J, Whitaker M, Elliott J, Haw D, Walters CE, Atchison C, Diggle PJ, Page AJ, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Donnelly CA, Elliott P. Omicron SARS-CoV-2 epidemic in England during February 2022: A series of cross-sectional community surveys. THE LANCET REGIONAL HEALTH. EUROPE 2022; 21:100462. [PMID: 35915784 PMCID: PMC9330654 DOI: 10.1016/j.lanepe.2022.100462] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Background The Omicron wave of COVID-19 in England peaked in January 2022 resulting from the rapid transmission of the Omicron BA.1 variant. We investigate the spread and dynamics of the SARS-CoV-2 epidemic in the population of England during February 2022, by region, age and main SARS-CoV-2 sub-lineage. Methods In the REal-time Assessment of Community Transmission-1 (REACT-1) study we obtained data from a random sample of 94,950 participants with valid throat and nose swab results by RT-PCR during round 18 (8 February to 1 March 2022). Findings We estimated a weighted mean SARS-CoV-2 prevalence of 2.88% (95% credible interval [CrI] 2.76-3.00), with a within-round effective reproduction number (R) overall of 0.94 (0·91-0.96). While within-round weighted prevalence fell among children (aged 5 to 17 years) and adults aged 18 to 54 years, we observed a level or increasing weighted prevalence among those aged 55 years and older with an R of 1.04 (1.00-1.09). Among 1,616 positive samples with sublineages determined, one (0.1% [0.0-0.3]) corresponded to XE BA.1/BA.2 recombinant and the remainder were Omicron: N=1047, 64.8% (62.4-67.2) were BA.1; N=568, 35.2% (32.8-37.6) were BA.2. We estimated an R additive advantage for BA.2 (vs BA.1) of 0.38 (0.34-0.41). The highest proportion of BA.2 among positives was found in London. Interpretation In February 2022, infection prevalence in England remained high with level or increasing rates of infection in older people and an uptick in hospitalisations. Ongoing surveillance of both survey and hospitalisations data is required. Funding Department of Health and Social Care, England.
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Affiliation(s)
- Marc Chadeau-Hyam
- School of Public Health, Imperial College London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK
| | - David Tang
- School of Public Health, Imperial College London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK
| | - Oliver Eales
- School of Public Health, Imperial College London, UK
- MRC Centre for Global infectious Disease Analysis
- Jameel Institute, Imperial College London, UK
| | - Barbara Bodinier
- School of Public Health, Imperial College London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK
| | - Haowei Wang
- School of Public Health, Imperial College London, UK
- MRC Centre for Global infectious Disease Analysis
- Jameel Institute, Imperial College London, UK
| | - Jakob Jonnerby
- School of Public Health, Imperial College London, UK
- MRC Centre for Global infectious Disease Analysis
- Jameel Institute, Imperial College London, UK
| | - Matthew Whitaker
- School of Public Health, Imperial College London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK
| | | | - David Haw
- School of Public Health, Imperial College London, UK
- MRC Centre for Global infectious Disease Analysis
- Jameel Institute, Imperial College London, UK
| | - Caroline E. Walters
- School of Public Health, Imperial College London, UK
- MRC Centre for Global infectious Disease Analysis
- Jameel Institute, Imperial College London, UK
| | | | - Peter J. Diggle
- CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK
| | | | - Deborah Ashby
- School of Public Health, Imperial College London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, UK
| | - Graham Taylor
- Department of Infectious Disease, Imperial College London, UK
| | - Graham Cooke
- Imperial College Healthcare NHS Trust, UK
- National Institute for Health Research Imperial Biomedical Research Centre, UK
| | - Helen Ward
- School of Public Health, Imperial College London, UK
- Imperial College Healthcare NHS Trust, UK
- National Institute for Health Research Imperial Biomedical Research Centre, UK
| | - Ara Darzi
- Imperial College Healthcare NHS Trust, UK
- Institute of Global Health Innovation, Imperial College London, UK
| | - Christl A. Donnelly
- School of Public Health, Imperial College London, UK
- MRC Centre for Global infectious Disease Analysis
- Jameel Institute, Imperial College London, UK
- Department of Statistics, University of Oxford, UK
| | - Paul Elliott
- School of Public Health, Imperial College London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Imperial College Healthcare NHS Trust, UK
- National Institute for Health Research Imperial Biomedical Research Centre, UK
- Health Data Research (HDR) UK, Imperial College London, UK
- UK Dementia Research Institute, Imperial College London, UK
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14
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Laine L, Skön M, Väisänen E, Julkunen I, Österlund P. SARS-CoV-2 variants Alpha, Beta, Delta and Omicron show a slower host cell interferon response compared to an early pandemic variant. Front Immunol 2022; 13:1016108. [PMID: 36248817 PMCID: PMC9561549 DOI: 10.3389/fimmu.2022.1016108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/15/2022] [Indexed: 11/15/2022] Open
Abstract
Since the start of the pandemic at the end of 2019, arising mutations in SARS-CoV-2 have improved its transmission and ability to circumvent the immunity induced by vaccination and previous COVID-19 infection. Studies on the effects of SARS-CoV-2 genomic mutations on replication and innate immunity will give us valuable insight into the evolution of the virus which can aid in further development of vaccines and new treatment modalities. Here we systematically analyzed the kinetics of virus replication, innate immune activation, and host cell antiviral response patterns in Alpha, Beta, Delta, Kappa, Omicron and two early pandemic SARS-CoV-2 variant-infected human lung epithelial Calu-3 cells. We observed overall comparable replication patterns for these variants with modest variations. Particularly, the sublineages of Omicron BA.1, BA.2 and a recombinant sublineage, XJ, all showed attenuated replication in Calu-3 cells compared to Alpha and Delta. Furthermore, there was relatively weak activation of primary innate immune signaling pathways, however, all variants produced enough interferons to induce the activation of STAT2 and production of interferon stimulated genes (ISGs). While interferon mRNA expression and STAT2 activation correlated with cellular viral RNA levels, ISG production did not. Although clear cut effects of specific SARS-CoV-2 genomic mutations could not be concluded, the variants of concern, including Omicron, showed a lower replication efficiency and a slower interferon response compared to an early pandemic variant in the study.
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Affiliation(s)
- Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- *Correspondence: Larissa Laine,
| | - Marika Skön
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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15
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Hirotsu Y, Maejima M, Shibusawa M, Natori Y, Nagakubo Y, Hosaka K, Sueki H, Mochizuki H, Tsutsui T, Kakizaki Y, Miyashita Y, Omata M. Classification of Omicron BA.1, BA.1.1, and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data. Int J Infect Dis 2022; 122:486-491. [PMID: 35760380 PMCID: PMC9233878 DOI: 10.1016/j.ijid.2022.06.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES Recently, the Omicron strain of SARS-CoV-2 has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1, and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants. METHODS A TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages with 171 samples. We analyzed three characteristic mutations of the spike gene, Δ69-70, G339D, and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis. RESULTS A total of 171 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for Δ69-70, G339D and Q493R by TaqMan assay. A total of 42 samples, determined as BA.2 by WGS, were negative for Δ69-70 but positive for G339D and Q493R by TaqMan. Two samples with G339N were determined to be inconclusive by the TaqMan method. Except for these two samples, the concordance rate between WGS and the TaqMan assay was 100% (169/169). CONCLUSION TaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
| | - Makoto Maejima
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Masahiro Shibusawa
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yume Natori
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yuki Nagakubo
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Kazuhiro Hosaka
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Hitomi Sueki
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Central Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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16
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Li J, Gao Z, Chen J, Cheng R, Niu J, Zhang J, Yang Y, Yuan X, Xia J, Mao G, Liu H, Dong Y, Wu C. Development of a panel of three multiplex allele-specific qRT-PCR assays for quick differentiation of recombinant variants and Omicron subvariants of SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:953027. [PMID: 36061868 PMCID: PMC9433905 DOI: 10.3389/fcimb.2022.953027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Quick differentiation of the circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmission. However, the widely used gene sequencing method is time-consuming and costly when facing the viral recombinant variants, because partial or whole genome sequencing is required. Allele-specific real time RT-PCR (qRT-PCR) represents a quick and cost-effective method in SNP genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 3 multiplex allele-specific qRT-PCR assays targeting 12 key differential mutations for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2). Two parallel multiplex qRT-PCR reactions were designed to separately target the protype allele and the mutated allele of the four mutations in each allele-specific qRT-PCR assay. The variation of Cp values (ΔCp) between the two multiplex qRT-PCR reactions was applied for mutation determination. The developed multiplex allele-specific qRT-PCR assays exhibited outstanding analytical sensitivities (with limits of detection [LoDs] of 2.97-27.43 copies per reaction), wide linear detection ranges (107-100 copies per reaction), good amplification efficiencies (82% to 95%), good reproducibility (Coefficient of Variations (CVs) < 5% in both intra-assay and inter-assay tests) and clinical performances (99.5%-100% consistency with Sanger sequencing). The developed multiplex allele-specific qRT-PCR assays in this study provide an alternative tool for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2).
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Affiliation(s)
- Jianguo Li
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- *Correspondence: Jianguo Li, ; Changxin Wu,
| | - Zefeng Gao
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jing Chen
- Shanxi Provincial Key Laboratory for Major Infectious Disease Response, Shanxi Provincial Center for Disease Control and Prevention, Taiyuan, China
| | - Ruiling Cheng
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jiahui Niu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jialei Zhang
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - You Yang
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - Ximei Yuan
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - Juan Xia
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Guoli Mao
- Laboratory, Shanxi Guoxin Caregeno Biotechnology Co., Ltd, Taiyuan, China
| | - Hulong Liu
- Laboratory, Shanxi Guoxin Caregeno Biotechnology Co., Ltd, Taiyuan, China
| | - Yongkang Dong
- Administrative Office, the Fourth People's Hospital of Taiyuan, Taiyuan, China
| | - Changxin Wu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- *Correspondence: Jianguo Li, ; Changxin Wu,
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17
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Sánchez-Morales L, Sánchez-Vizcaíno JM, Pérez-Sancho M, Domínguez L, Barroso-Arévalo S. The Omicron (B.1.1.529) SARS-CoV-2 variant of concern also affects companion animals. Front Vet Sci 2022; 9:940710. [PMID: 36032286 PMCID: PMC9411866 DOI: 10.3389/fvets.2022.940710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/27/2022] [Indexed: 12/02/2022] Open
Abstract
The emergence of the Omicron variant (B.1. 1.529) has brought with it an increase in the incidence of SARS-CoV-2 disease. However, there is hardly any data on its incidence in companion animals. We have detected the presence of this new variant in domestic animals (dogs and cats) living with infected owners in Spain. None of the RT-qPCR positive animals (10.13%) presented any clinical signs and the viral loads detected were low. In addition, the shedding of viral RNA lasted a short period of time in the positive animals. Infection with this variant of concern (VOC) was confirmed by RT-qPCR and sequencing. These outcomes suggest a lower virulence of this variant in infected cats and dogs. They also demonstrate the transmission from infected humans to domestic animals and highlight the importance of active surveillance as well as genomic research to detect the presence of VOCs or mutations associated with animal hosts.
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Affiliation(s)
- Lidia Sánchez-Morales
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - José M. Sánchez-Vizcaíno
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Marta Pérez-Sancho
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Sandra Barroso-Arévalo
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
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18
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Gautret P, Hoang VT, Jimeno MT, Lagier J, Rossi P, Fournier PE, Colson P, Raoult D. The severity of the first 207 infections with the SARS-CoV-2 Omicron BA.2 variant, in Marseille, France, December 2021-February 2022. J Med Virol 2022; 94:3494-3497. [PMID: 35365865 PMCID: PMC9088598 DOI: 10.1002/jmv.27760] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Philippe Gautret
- IHU Méditerranée InfectionMarseilleFrance
- Aix Marseille UniversityIRD, AP‐HM, SSA, VITROMEMarseilleFrance
| | - Van T. Hoang
- Department of Family MedicineThai Binh University of Medicine and PharmacyThai BinhVietnam
| | - Marie T. Jimeno
- Department of Internal MedicineAssistance Publique – Hôpitaux de MarseilleMarseilleFrance
| | - Jean‐Christophe Lagier
- IHU Méditerranée InfectionMarseilleFrance
- Aix Marseille UniversityIRD, AP‐HM, MEPHIMarseilleFrance
| | - Pascal Rossi
- Department of Internal MedicineAssistance Publique – Hôpitaux de MarseilleMarseilleFrance
| | - Pierre E. Fournier
- IHU Méditerranée InfectionMarseilleFrance
- Aix Marseille UniversityIRD, AP‐HM, SSA, VITROMEMarseilleFrance
| | - Philippe Colson
- IHU Méditerranée InfectionMarseilleFrance
- Aix Marseille UniversityIRD, AP‐HM, MEPHIMarseilleFrance
| | - Didier Raoult
- IHU Méditerranée InfectionMarseilleFrance
- Aix Marseille UniversityIRD, AP‐HM, MEPHIMarseilleFrance
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19
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Discrimination of SARS-CoV-2 Omicron Sublineages BA.1 and BA.2 Using a High-Resolution Melting-Based Assay: a Pilot Study. Microbiol Spectr 2022; 10:e0136722. [PMID: 35861527 PMCID: PMC9430517 DOI: 10.1128/spectrum.01367-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. As of March 2022, Omicron variant BA.2 is rapidly replacing variant BA.1. As variant BA.2 may cause more severe disease than variant BA.1, variant BA.2 requires continuous monitoring. The current study aimed to develop a novel high-resolution melting (HRM) assay for variants BA.1 and BA.2 and to determine the sensitivity and specificity of our method using clinical samples. Here, we focused on the mutational spectra at three regions in the spike receptor-binding domain (RBD; R408, G446/L452, and S477/T478) for the variant-selective HRM analysis. Each variant was identified based on the mutational spectra as follows: no mutations (Alpha variant); L452R and T478K (Delta variant); G446S and S477N/T478K (Omicron variant BA.1); and R408S and S477N/T478K (Omicron variant BA.2). Upon analysis of mutation-coding RNA fragments, the melting curves of the wild-type fragments were distinct from those of the mutant fragments. The sensitivity and specificity of this method were determined as 100% and more than 97.5%, respectively, based on 128 clinical samples (40 Alpha, 40 Delta, 40 Omicron variant BA.1/BA.1.1, and 8 Omicron variant BA.2). These results suggest that this HRM-based assay is a promising screening method for monitoring the transmission of Omicron variants BA.1 and BA.2. IMPORTANCE This study seeks to apply a novel high-resolution melting (HRM) assay to identify and discriminate BA.1 and BA.2 sublineages of the SARS-CoV-2 Omicron variant. Variant BA.2 may cause more severe disease than variant BA.1, meaning that identifying this variant is an important step toward improving the care of patients suffering from COVID-19. However, screening for these variants remains difficult, as current methods mostly rely on next-generation sequencing, which is significantly costlier and more time-consuming than other methods. We believe that our study makes a significant contribution to the literature because we show that this method was 100% sensitive and over 97.5% specific in our confirmation of 128 clinical samples.
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20
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What we recognize about omicron sub-lineage BA.2 as a global new challenge? - Correspondence. Int J Surg 2022; 103:106704. [PMID: 35697323 DOI: 10.1016/j.ijsu.2022.106704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/20/2022] [Accepted: 06/02/2022] [Indexed: 11/20/2022]
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21
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Colson P, Delerce J, Beye M, Levasseur A, Boschi C, Houhamdi L, Tissot‐Dupont H, Yahi N, Million M, La Scola B, Fantini J, Raoult D, Fournier P. First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France. J Med Virol 2022; 94:3421-3430. [PMID: 35243660 PMCID: PMC9088623 DOI: 10.1002/jmv.27695] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/22/2022]
Abstract
The SARS-CoV-2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here, we describe the first cases diagnosed with this variant in south-eastern France. We identified 13 cases using variant-specific qPCR and next-generation sequencing between 28/11/2021 and 31/01/2022, the first two cases being diagnosed in travelers returning from Tanzania. Overall, viral genomes displayed a mean (±standard deviation) number of 65.9 ± 2.5 (range, 61-69) nucleotide substitutions and 31.0 ± 8.3 (27-50) nucleotide deletions, resulting in 49.6 ± 2.2 (45-52) amino acid substitutions (including 28 in the spike protein) and 12.4 ± 1.1 (12-15) amino acid deletions. Phylogeny showed the distribution in three different clusters of these genomes, which were most closely related to genomes from England and South Africa, from Singapore and Nepal, or from France and Denmark. Structural predictions highlighted a significant enlargement and flattening of the surface of the 21L/BA.2 N-terminal domain of the spike protein compared to that of the 21K/BA.1 Omicron variant, which may facilitate initial viral interactions with lipid rafts. Close surveillance is needed at global, country, and center scales to monitor the incidence and clinical outcome of the 21L/BA.2 Omicron variant.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée InfectionMarseilleFrance
- Institut de Recherche pour le Développement, Microbes Evolution Phylogeny and InfectionsAix‐Marseille UniversitéMarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
| | | | | | - Anthony Levasseur
- IHU Méditerranée InfectionMarseilleFrance
- Institut de Recherche pour le Développement, Microbes Evolution Phylogeny and InfectionsAix‐Marseille UniversitéMarseilleFrance
| | - Céline Boschi
- IHU Méditerranée InfectionMarseilleFrance
- Institut de Recherche pour le Développement, Microbes Evolution Phylogeny and InfectionsAix‐Marseille UniversitéMarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
| | - Linda Houhamdi
- IHU Méditerranée InfectionMarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
| | - Hervé Tissot‐Dupont
- IHU Méditerranée InfectionMarseilleFrance
- Institut de Recherche pour le Développement, Microbes Evolution Phylogeny and InfectionsAix‐Marseille UniversitéMarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
| | - Nouara Yahi
- Aix‐Marseille Université, INSERM UMR S 1072MarseilleFrance
| | - Matthieu Million
- IHU Méditerranée InfectionMarseilleFrance
- Institut de Recherche pour le Développement, Microbes Evolution Phylogeny and InfectionsAix‐Marseille UniversitéMarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
| | - Bernard La Scola
- IHU Méditerranée InfectionMarseilleFrance
- Institut de Recherche pour le Développement, Microbes Evolution Phylogeny and InfectionsAix‐Marseille UniversitéMarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
| | | | - Didier Raoult
- IHU Méditerranée InfectionMarseilleFrance
- Institut de Recherche pour le Développement, Microbes Evolution Phylogeny and InfectionsAix‐Marseille UniversitéMarseilleFrance
| | - Pierre‐Edouard Fournier
- IHU Méditerranée InfectionMarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
- Institut de Recherche pour le Développement, Vecteurs–Infections Tropicales et MéditerranéennesAix‐Marseille UniversitéMarseilleFrance
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22
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Ito K, Piantham C, Nishiura H. Estimating relative generation times and reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta variant in Denmark. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:9005-9017. [PMID: 35942746 DOI: 10.3934/mbe.2022418] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The Omicron variant spreads fastest as ever among the severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) we had so far. The BA.1 and BA.2 sublineages of Omicron are circulating worldwide and it is urgent to evaluate the transmission advantages of these sublineages. Using a mathematical model describing trajectories of variant frequencies that assumes a constant ratio in mean generation times and a constant ratio in effective reproduction numbers among variants, trajectories of variant frequencies in Denmark from November 22, 2021 to February 26, 2022 were analyzed. We found that the mean generation time of Omicron BA.1 is 0.44-0.46 times that of Delta and the effective reproduction number of Omicron BA.1 is 1.88-2.19 times larger than Delta under the epidemiological conditions at the time. We also found that the mean generation time of Omicron BA.2 is 0.76-0.80 times that of BA.1 and the effective reproduction number of Omicron BA.2 is 1.25-1.27 times larger than Omicron BA.1. These estimates on the ratio of mean generation times and the ratio of effective reproduction numbers have epidemiologically important implications. The contact tracing for Omicron BA.2 infections must be done more quickly than that for BA.1 to stop further infections by quarantine. In the Danish population, the control measures against Omicron BA.2 need to reduce 20-21% of additional contacts compared to that against BA.1.
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Affiliation(s)
- Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Chayada Piantham
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
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23
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Affiliation(s)
- Rok Hrzic
- Department of International Health, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, the Netherlands
- ASPHER Young Professional, Brussels, Belgium
- ASPHER COVID-19 Task Force
| | - Vasco Ricoca Peixoto
- ASPHER COVID-19 Task Force
- NOVA National School of Public Health, Public Health Research Centre, Universida de NOVA de Lisboa
- Comprehensive Health Research Centre - Universidade Nova de Lisboa
| | - Amanda J Mason-Jones
- ASPHER COVID-19 Task Force
- Department of Health Sciences, University of York, York, UK
| | - Alison McCallum
- ASPHER COVID-19 Task Force
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
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24
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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25
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Loconsole D, Centrone F, Sallustio A, Accogli M, Casulli D, Sacco D, Zagaria R, Morcavallo C, Chironna M. Characteristics of the First 284 Patients Infected with the SARS-CoV-2 Omicron BA.2 Subvariant at a Single Center in the Apulia Region of Italy, January-March 2022. Vaccines (Basel) 2022; 10:674. [PMID: 35632430 PMCID: PMC9146056 DOI: 10.3390/vaccines10050674] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 02/05/2023] Open
Abstract
Since its initial detection, the SARS-CoV-2 Omicron sublineage BA.2 has been spreading rapidly worldwide. The aims of this study were to describe the first 284 patients infected with the Omicron BA.2 variant of concern (VOC) in the Apulia region of southern Italy and to assess the differences in the demographic and clinical characteristics of patients infected with the SARS-CoV-2 BA.1 and BA.2 variants. The demographic characteristics of patients, as well as information about symptoms, vaccinations and hospitalizations for COVID-19, were collected. A subset of samples from patients infected with the BA.2 variant was subjected to whole-genome sequencing. The characteristics of the first 284 patients infected with Omicron BA.2 and the first 175 patients infected with Omicron BA.1 were compared. The proportion of patients infected with the BA.2 variant rapidly increased, from 0.5% during the third week of 2022 to 29.6% during the tenth week of 2022. Ten isolates (out of 34 BA.2 isolates) contain the substitutional mutation, H78K in ORF3a, and four isolates include two mutations, A2909V in ORF1a and L140F in ORDF3a. Compared with patients infected with BA.1, those infected with BA.2 were more likely to be symptomatic and booster-vaccinated, and showed a shorter time from the last dose of vaccine to infection. The high transmissibility and immune-evasive properties of Omicron BA.2, which will become the leading SARS-CoV-2 VOC, suggest that short-term public health measures should not be discontinued in Italy.
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Affiliation(s)
- Daniela Loconsole
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy; (D.L.); (D.S.); (R.Z.)
| | - Francesca Centrone
- Hygiene Section, Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (F.C.); (M.A.); (C.M.)
| | - Anna Sallustio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy; (A.S.); (D.C.)
| | - Marisa Accogli
- Hygiene Section, Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (F.C.); (M.A.); (C.M.)
| | - Daniele Casulli
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy; (A.S.); (D.C.)
| | - Davide Sacco
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy; (D.L.); (D.S.); (R.Z.)
| | - Riccardo Zagaria
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy; (D.L.); (D.S.); (R.Z.)
| | - Caterina Morcavallo
- Hygiene Section, Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (F.C.); (M.A.); (C.M.)
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy; (D.L.); (D.S.); (R.Z.)
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26
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Barre A, Klonjkowski B, Benoist H, Rougé P. How Do Point Mutations Enhancing the Basic Character of the RBDs of SARS-CoV-2 Variants Affect Their Transmissibility and Infectivity Capacities? Viruses 2022; 14:783. [PMID: 35458513 PMCID: PMC9031512 DOI: 10.3390/v14040783] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022] Open
Abstract
The spread of SARS-CoV-2 variants in the population depends on their ability to anchor the ACE2 receptor in the host cells. Differences in the electrostatic potentials of the spike protein RBD (electropositive/basic) and ACE2 receptor (electronegative/acidic) play a key role in both the rapprochement and the recognition of the coronavirus by the cell receptors. Accordingly, point mutations that result in an increase in electropositively charged residues, e.g., arginine and lysine, especially in the RBD of spike proteins in the SARS-CoV-2 variants, could contribute to their spreading capacity by favoring their recognition by the electronegatively charged ACE2 receptors. All SARS-CoV-2 variants that have been recognized as being highly transmissible, such as the kappa (κ), delta (δ) and omicron (o) variants, which display an enhanced electropositive character in their RBDs associated with a higher number of lysine- or arginine-generating point mutations. Lysine and arginine residues also participate in the enhanced RBD-ACE2 binding affinity of the omicron variant, by creating additional salt bridges with aspartic and glutamic acid residues from ACE2. However, the effects of lysine- and arginine-generating point mutations on infectivity is more contrasted, since the overall binding affinity of omicron RBD for ACE2 apparently results from some epistasis among the whole set of point mutations.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
| | - Bernard Klonjkowski
- UMR Virologie, INRA, ANSES, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France;
| | - Hervé Benoist
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
| | - Pierre Rougé
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
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