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Chaudhary P, Gulati N, Gupta V, Garg R, Walia S, Dhawan I, Thakur B. COVID-19 pandemic - Cocktail of variants, a study from Northern India. J Family Med Prim Care 2024; 13:2449-2454. [PMID: 39027869 PMCID: PMC11254030 DOI: 10.4103/jfmpc.jfmpc_1107_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/08/2023] [Accepted: 02/02/2024] [Indexed: 07/20/2024] Open
Abstract
Context The aim of the study was to identify and monitor the circulating strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the samples received at our center and update the existing national and international genomic surveillance data. Introduction SARS-CoV-2 is no exception to the basic nature of the viruses ability to change and evolve. Since its first report in December 2019 from Wuhan, China, multiple variants of the virus have emerged and been reported. Five variants of concern have been recognized and reported by the Centers for Disease Control and Prevention, which are associated with variable degrees of transmissibility and mortality. Materials and Methods Nasopharyngeal and oropharyngeal swabs received in viral transport medium at the Viral Research Diagnostic Laboratory were processed for reverse transcription-polymerase chain reaction for SARS-CoV-2. Whole genome sequencing (WGS) was performed for selective positive samples using Oxford Nanopore sequencing technology, using MinKNOW software for data acquisition. Statistical Analysis The clades were assigned using Nextclade v2.4.1 software. The statistical analysis was calculated using OpenEpi version 3, an open-source calculator, and two by two. Results Variants reported over the study period included Alpha, Kappa, Delta, and Omicron. Delta dominated in the year 2021, while Omicron was the dominant variant in 2022. In both the dominant variants, asymptomatics contributed to around 30-40% of positives. Intensive care unit admissions and mortality were higher in the Delta variant, while vaccination history and travel history were higher in the patients with Omicron variant. Conclusion The trend tracking of these variants has been important in view of public health, enabling early interventions to control the spread of the disease and foresight in preparation for the situation.
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Affiliation(s)
- Preeti Chaudhary
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Neelam Gulati
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Varsha Gupta
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Rajni Garg
- CSIR Pool Scientist, IMTECH, Chandigarh, India
| | - Sohini Walia
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Isha Dhawan
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
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Chakraborty C, Bhattacharya M, Islam MA, Zayed H, Ohimain EI, Lee SS, Bhattacharya P, Dhama K. Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review. J Microbiol 2024; 62:337-354. [PMID: 38777985 DOI: 10.1007/s12275-024-00138-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, VyasaVihar, Balasore, 756020, Odisha, India
| | - Md Aminul Islam
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, Bangladesh
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - Elijah Ige Ohimain
- Microbiology Department, Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 24252, Republic of Korea.
| | - Prosun Bhattacharya
- COVID-19 Research, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
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3
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Chen L, He Y, Liu H, Shang Y, Guo G. Potential immune evasion of the severe acute respiratory syndrome coronavirus 2 Omicron variants. Front Immunol 2024; 15:1339660. [PMID: 38464527 PMCID: PMC10924305 DOI: 10.3389/fimmu.2024.1339660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic. The Omicron variant (B.1.1.529) was first discovered in November 2021 in specimens collected from Botswana, South Africa. Omicron has become the dominant variant worldwide, and several sublineages or subvariants have been identified recently. Compared to those of other mutants, the Omicron variant has the most highly expressed amino acid mutations, with almost 60 mutations throughout the genome, most of which are in the spike (S) protein, especially in the receptor-binding domain (RBD). These mutations increase the binding affinity of Omicron variants for the ACE2 receptor, and Omicron variants may also lead to immune escape. Despite causing milder symptoms, epidemiological evidence suggests that Omicron variants have exceptionally higher transmissibility, higher rates of reinfection and greater spread than the prototype strain as well as other preceding variants. Additionally, overwhelming amounts of data suggest that the levels of specific neutralization antibodies against Omicron variants decrease in most vaccinated populations, although CD4+ and CD8+ T-cell responses are maintained. Therefore, the mechanisms underlying Omicron variant evasion are still unclear. In this review, we surveyed the current epidemic status and potential immune escape mechanisms of Omicron variants. Especially, we focused on the potential roles of viral epitope mutations, antigenic drift, hybrid immunity, and "original antigenic sin" in mediating immune evasion. These insights might supply more valuable concise information for us to understand the spreading of Omicron variants.
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Affiliation(s)
- Luyi Chen
- Chongqing Nankai Secondary School, Chongqing, China
| | - Ying He
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Hongye Liu
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Yongjun Shang
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Guoning Guo
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
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4
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Yeh YJ, Chao TL, Chang YJ, Chang SY, Lu CH, Chao CH, Su WC, Tseng CP, Lai MM, Cheng JC. Dual Effects of 3- epi-betulin from Daphniphyllum glaucescens in Suppressing SARS-CoV-2-Induced Inflammation and Inhibiting Virus Entry. Int J Mol Sci 2023; 24:17040. [PMID: 38069363 PMCID: PMC10707724 DOI: 10.3390/ijms242317040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The continuous emergence of SARS-CoV-2 variants has led to a protracted global COVID-19 pandemic with significant impacts on public health and global economy. While there are currently available SARS-CoV-2 vaccines and therapeutics, most of the FDA-approved antiviral agents directly target viral proteins. However, inflammation is the initial immune pathogenesis induced by SARS-CoV-2 infection, there is still a need to find additional agents that can control the virus in the early stages of infection to alleviate disease progression for the next pandemic. Here, we find that both the spike protein and its receptor CD147 are crucial for inducing inflammation by SARS-CoV-2 in THP-1 monocytic cells. Moreover, we find that 3-epi-betulin, isolated from Daphniphyllum glaucescens, reduces the level of proinflammatory cytokines induced by SARS-CoV-2, consequently resulting in a decreased viral RNA accumulation and plaque formation. In addition, 3-epi-betulin displays a broad-spectrum inhibition of entry of SARS-CoV-2 pseudoviruses, including Alpha (B.1.1.7), Eplison (B.1.429), Gamma (P1), Delta (B.1.617.2) and Omicron (BA.1). Moreover, 3-epi-betulin potently inhibits SARS-CoV-2 infection with an EC50 of <20 μM in Calu-3 lung epithelial cells. Bioinformatic analysis reveals the chemical interaction between the 3-epi-betulin and the spike protein, along with the critical amino acid residues in the spike protein that contribute to the inhibitory activity of 3-epi-betulin against virus entry. Taken together, our results suggest that 3-epi-betulin exhibits dual effect: it reduces SARS-CoV-2-induced inflammation and inhibits virus entry, positioning it as a potential antiviral agent against SARS-CoV-2.
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Affiliation(s)
- Yung-Ju Yeh
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404328, Taiwan
- Research Center for Emerging Viruses, China Medical University Hospital, Taichung 404328, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 100229, Taiwan
| | - Yu-Jen Chang
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 404328, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 100229, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College Medicine, Taipei 100229, Taiwan
| | - Chih-Hao Lu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Chih-Hua Chao
- School of Pharmacy, China Medical University, Taichung 4060404, Taiwan
| | - Wen-Chi Su
- Research Center for Emerging Viruses, China Medical University Hospital, Taichung 404328, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung 404328, Taiwan
| | - Ching-Ping Tseng
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan 33302, Taiwan
| | - Michael M.C. Lai
- Research Center for Emerging Viruses, China Medical University Hospital, Taichung 404328, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
| | - Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404328, Taiwan
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Li T, Chen Y, Chen Z, Hao Y, Liang M, Liu Y, Ou G, Zhang H, Tang Y, Hao Y, Wageh S, Al-Hartomy OA, Kalam A, Zhang B, Shi X, Li X, Zhang H. Early and Sensitive Detection of Pathogens for Public Health and Biosafety: An Example of Surveillance and Genotyping of SARS-CoV-2 in Sewage Water by Cas12a-Facilitated Portable Plasmonic Biosensor. RESEARCH (WASHINGTON, D.C.) 2023; 6:0205. [PMID: 37521328 PMCID: PMC10380551 DOI: 10.34133/research.0205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023]
Abstract
Infectious diseases severely threaten public health and global biosafety. In addition to transmission through the air, pathogenic microorganisms have also been detected in environmental liquid samples, such as sewage water. Conventional biochemical detection methodologies are time-consuming and cost-ineffective, and their detection limits hinder early diagnosis. In the present study, ultrafine plasmonic fiber probes with a diameter of 125 μm are fabricated for clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-12a-mediated sensing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Single-stranded DNA exposed on the fiber surface is trans-cleaved by the Cas12a enzyme to release gold nanoparticles that are immobilized onto the fiber surface, causing a sharp reduction in the surface plasmon resonance (SPR) wavelength. The proposed fiber probe is virus-specific with the limit of detection of ~2,300 copies/ml, and genomic copy numbers can be reflected as shifts in wavelengths. A total of 21 sewage water samples have been examined, and the data obtained are consistent with those of quantitative polymerase chain reaction (qPCR). In addition, the Omicron variant and its mutation sites have been fast detected using S gene-specific Cas12a. This study provides an accurate and convenient approach for the real-time surveillance of microbial contamination in sewage water.
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Affiliation(s)
- Tianzhong Li
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yuzhi Chen
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Sensor Technology, Shenzhen 518060, China
| | - Zhi Chen
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, China
| | - Yuan Hao
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Sensor Technology, Shenzhen 518060, China
| | - Minyi Liang
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Sensor Technology, Shenzhen 518060, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital,
Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Guanyong Ou
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital,
Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
- School of Medicine,
Southern University of Science and Technology, Shenzhen 518055, China
| | - Huanian Zhang
- School of Physics and Optoelectronic Engineering,
Shandong University of Technology, Zibo 255049, China
| | - Yuxuan Tang
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yabing Hao
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Swelm Wageh
- Department of Physics, Faculty of Science,
King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Omar A. Al-Hartomy
- Department of Physics, Faculty of Science,
King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abul Kalam
- Research Center for Advanced Materials Science (RCAMS),
King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry,
College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Bin Zhang
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Xin Shi
- Health Sciences Institute,
China Medical University, Shenyang 110000, China
| | - Xuejin Li
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Sensor Technology, Shenzhen 518060, China
- The Chinese University of Hong Kong, Shenzhen 518060, China
| | - Han Zhang
- College of Physics and Optoelectronic Engineering, Institute of Translational Medicine, Department of Otolaryngology, Shenzhen Second People’s Hospital,
First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518060, China
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Arefinia N, Yaghobi R, Ramezani A, Sarvari J. Sequence Analysis of Hot Spot Regions of Spike and RNA-dependent-RNA polymerase (RdRp) Genes of SARS-CoV-2 in Kerman, Iran. Mediterr J Hematol Infect Dis 2023; 15:e2023042. [PMID: 37435034 PMCID: PMC10332355 DOI: 10.4084/mjhid.2023.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/18/2023] [Indexed: 07/13/2023] Open
Abstract
Background Mutations in the SARS-CoV-2 genome might influence pathogenicity, transmission rate, and evasion of the host immune system. Therefore, the purpose of the present study was to investigate the genetic alteration as well as assess their effects on the receptor binding domain (RBD) of the spike and the putative RNA binding site of the RdRp genes of SARS-CoV-2 using bioinformatics tools. Materials and Method In this cross-sectional study, 45 confirmed COVID-19 patients using qRT-PCR were included and divided into mild, severe, and critical groups based on the severity of the disease. RNA was extracted from nasopharyngeal swab samples using a commercial kit. RT-PCR was performed to amplify the target sequences of the spike and RdRp genes and sequence them by the Sanger method. Clustal OMEGA, MEGA 11 software, I-mutant tools, SWISS-MODEL, and HDOCK web servers were used for bioinformatics analyses. Results The mean age of the patients was 50.68±2.73. The results showed that four of six mutations (L452R, T478K, N501Y, and D614G) in RBD and three of eight in the putative RNA binding site (P314L, E1084D, V1883T) were missense. In the putative RNA binding site, another deletion was discovered. Among missense mutations, N501Y and V1883T were responsible for increasing structural stability, while others were responsible for decreasing it. The various homology models designed showed that these homologies were like the Wuhan model. The molecular docking analysis revealed that the T478K mutation in RBD had the highest binding affinity. In addition, 35 RBD samples (89.7%) and 33 putative RNA binding site samples (84.6%) were similar to the Delta variant. Conclusion Our results indicated that double mutations (T478K and N501Y) in the S protein might increase the binding affinity of SARS-CoV-2 to human ACE2 compared to the wild-type (WT) strain. Moreover, variations in the spike and RdRp genes might influence the stability of encoded proteins.
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Affiliation(s)
- Nasir Arefinia
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Sarvari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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7
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Yu Q, Tong X, Zuo L, Tao X, Xu Z, Li X, Liu H, Guan W, Liu D, Liu H, Huang F, Jia L. Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022. Viruses 2023; 15:1355. [PMID: 37376654 DOI: 10.3390/v15061355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The continuously emerging new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made the global coronavirus disease 2019 (COVID-19) pandemic unpredictable. Since the beginning of the pandemic, densely populated South and Southeast Asia have suffered great losses due to multiple COVID-19 surges because of vaccine and other medical resource shortages. Therefore, it is crucial to closely monitor the SARS-CoV-2 epidemic and to understand the evolutionary and transmission characteristics of SARS-CoV-2 in these regions. Here, we document the evolution of epidemic strains in the Philippines, Pakistan, and Malaysia from late 2021 to early 2022. Our results confirmed the circulation of at least five SARS-CoV-2 genotypes in these countries in January 2022, when Omicron BA.2, with a detection rate of 69.11%, replaced Delta B.1.617 as the dominant strain. Single-nucleotide polymorphism analysis indicated the distinct evolutionary directions of the Omicron and Delta isolates, with S, Nsp1, and Nsp6 genes potentially playing a significant role in the host adaptation of the Omicron strain. These findings are able to provide insights for predicting the evolutionary direction of SARS-CoV-2 in terms of variant competition, developing multi-part vaccines, and to support the evaluation and adjustment of current surveillance, prevention, and control strategies in South and Southeast Asia.
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Affiliation(s)
- Qiong Yu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100045, China
| | - Xi Tong
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100045, China
| | - Li Zuo
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100045, China
| | - Xinyu Tao
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100045, China
| | | | | | - Haizhou Liu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Wuxiang Guan
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Di Liu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Haibin Liu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Fang Huang
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Lijia Jia
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100045, China
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8
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Jalal D, Samir O, Elzayat MG, El-Shqanqery HE, Diab AA, ElKaialy L, Mohammed AM, Hamdy D, Matar IK, Amer K, Elnakib M, Hassan W, Mansour T, Soliman S, Hassan R, Al-Toukhy GM, Hammad M, Abdo I, Sayed AA. Genomic characterization of SARS-CoV-2 in Egypt: insights into spike protein thermodynamic stability. Front Microbiol 2023; 14:1190133. [PMID: 37333655 PMCID: PMC10273679 DOI: 10.3389/fmicb.2023.1190133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
The overall pattern of the SARS-CoV-2 pandemic so far has been a series of waves; surges in new cases followed by declines. The appearance of novel mutations and variants underlie the rises in infections, making surveillance of SARS-CoV-2 mutations and prediction of variant evolution of utmost importance. In this study, we sequenced 320 SARS-CoV-2 viral genomes isolated from patients from the outpatient COVID-19 clinic in the Children's Cancer Hospital Egypt 57357 (CCHE 57357) and the Egypt Center for Research and Regenerative Medicine (ECRRM). The samples were collected between March and December 2021, covering the third and fourth waves of the pandemic. The third wave was found to be dominated by Nextclade 20D in our samples, with a small number of alpha variants. The delta variant was found to dominate the fourth wave samples, with the appearance of omicron variants late in 2021. Phylogenetic analysis reveals that the omicron variants are closest genetically to early pandemic variants. Mutation analysis shows SNPs, stop codon mutation gain, and deletion/insertion mutations, with distinct patterns of mutations governed by Nextclade or WHO variant. Finally, we observed a large number of highly correlated mutations, and some negatively correlated mutations, and identified a general inclination toward mutations that lead to enhanced thermodynamic stability of the spike protein. Overall, this study contributes genetic and phylogenetic data, as well as provides insights into SARS-CoV-2 viral evolution that may eventually help in the prediction of evolving mutations for better vaccine development and drug targets.
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Affiliation(s)
- Deena Jalal
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Omar Samir
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Mariam G. Elzayat
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Hend E. El-Shqanqery
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Aya A. Diab
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Lamiaa ElKaialy
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Aya M. Mohammed
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Donia Hamdy
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Islam K. Matar
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
- Department of Chemistry, Saint Mary’s University, Halifax, NS, Canada
| | - Khaled Amer
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Mostafa Elnakib
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Wael Hassan
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Tarek Mansour
- Department of Virology and Immunology, National Cancer Institute, Cairo University, Cairo, Egypt
- Department of Clinical Pathology, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Sonia Soliman
- Department of Clinical Pathology, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Reem Hassan
- Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt
- Molecular Microbiology Unit, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Ghada M. Al-Toukhy
- Department of Virology and Immunology, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Mahmoud Hammad
- Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
- Department of Pediatric Oncology, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Ibrahim Abdo
- Department of Clinical Pharmacy, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Ahmed A. Sayed
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
- Faculty of Science, Department of Biochemistry, Ain Shams University, Cairo, Egypt
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9
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Bhattacharya M, Alshammari A, Alharbi M, Dhama K, Lee SS, Chakraborty C. A novel mutation-proof, next-generation vaccine to fight against upcoming SARS-CoV-2 variants and subvariants, designed through AI enabled approaches and tools, along with the machine learning based immune simulation: A vaccine breakthrough. Int J Biol Macromol 2023; 242:124893. [PMID: 37207746 DOI: 10.1016/j.ijbiomac.2023.124893] [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: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023]
Abstract
Emerging SARS-CoV-2 variants and subvariants are great concerns for their significant mutations, which are also responsible for vaccine escape. Therefore, the study was undertaken to develop a mutation-proof, next-generation vaccine to protect against all upcoming SARS-CoV-2 variants. We used advanced computational and bioinformatics approaches to develop a multi-epitopic vaccine, especially the AI model for mutation selection and machine learning (ML) strategies for immune simulation. AI-enabled and the top-ranked antigenic selection approaches were used to select nine mutations from 835 RBD mutations. We selected twelve common antigenic B cell and T cell epitopes (CTL and HTL) containing the nine RBD mutations and joined them with the adjuvants, PADRE sequence, and suitable linkers. The constructs' binding affinity was confirmed through docking with TLR4/MD2 complex and showed significant binding free energy (-96.67 kcal mol-1) with positive binding affinity. Similarly, the calculated eigenvalue (2.428517e-05) from the NMA of the complex reveals proper molecular motion and superior residues' flexibility. Immune simulation shows that the candidate can induce a robust immune response. The designed mutation-proof, multi-epitopic vaccine could be a remarkable candidate for upcoming SARS-CoV-2 variants and subvariants. The study method might guide researchers in developing AI-ML and immunoinformatics-based vaccines for infectious disease.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
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10
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Ciuoderis K, Perez L, Alvarez C, Usuga J, Carvajal L, Cardona A, Maya MA, Cloherty G, Hernandez-Ortiz JP, Osorio JE. Urticaria after breakthrough Omicron BA.5.1 severe acute respiratory syndrome coronavirus 2 infection in a triple-vaccinated (Pfizer) patient: a case report. J Med Case Rep 2023; 17:177. [PMID: 37138300 PMCID: PMC10156422 DOI: 10.1186/s13256-023-03904-2] [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: 09/02/2022] [Accepted: 03/22/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 continues to threaten public health. The virus is causing breakthrough infections in vaccinated individuals. Also, scarce information is available about cutaneous manifestations after severe acute respiratory syndrome coronavirus 2 infection. CASE PRESENTATION AND FINDINGS A case of a triple-vaccinated (Pfizer) 37-year-old Hispanic American (Colombian) male who developed urticaria after Omicron BA.5.1 severe acute respiratory syndrome coronavirus 2 breakthrough infection is described. Virus isolation and whole genome sequencing along with immune and molecular assays were performed. Dermatological manifestations (skin rash and urticaria) after Omicron BA.5.1 infection were observed. Sequence analysis of the Omicron BA.5.1 isolate also revealed several important mutations. Hemogram analysis revealed leukocytosis and neutrophilia. Serology testing revealed anti-spike immunoglobulin G serum titers but negative detection of immunoglobulin M at 10 days after symptom onset. Anti-nucleocapsid, anti-spike 1 immunoglobulin G, anti-spike trimer, and anti-receptor-binding-domain immunoglobulin G and immunoglobulin E sera were detected at different titers 10 days after symptom onset. Several serum levels of chemokines/cytokines (Interferon-α, interferon-γ, interleukin-12/interleukin-23p40, interleukin-18, interferon gamma-induced protein-10, monocyte chemoattractant protein-1, monokine induced by gamma, macrophage inflammatory protein-1α, chemokine (C-C motif) ligand-5 , tumor necrosis factor-β1, Tumor necrosis factor-α) were detected, but interleukin-2, interleukin-4, interleukin-6, interleukin-8, and interleukin-17A were below the limit of detection. INTERPRETATION AND CONCLUSIONS To our knowledge, this is the first study describing skin effects of a severe acute respiratory syndrome coronavirus 2 Omicron BA.5 variant breakthrough infection in a triple-vaccinated patient in Colombia. Several important mutations were found in the spike glycoprotein of the virus isolated; these mutations are associated with immune evasion and changes in antigenic properties of the virus. Physicians overseeing coronavirus disease 2019 cases should be aware of the potential skin effects of the infection. Pathogenesis of severe acute respiratory syndrome coronavirus 2 infection and its association with proinflammatory cytokines and chemokines may enhance the development of urticaria and other skin manifestations in immunized individuals. However, further studies are needed to better understand the complexity of coronavirus disease in such situations.
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Affiliation(s)
- Karl Ciuoderis
- Laboratorio Genómico One Health, UW-GHI One Health Colombia, Universidad Nacional de Colombia, Cll 75#79A-51, Bloque M15, 050034, Medellin, Colombia.
| | - Laura Perez
- Laboratorio Genómico One Health, UW-GHI One Health Colombia, Universidad Nacional de Colombia, Cll 75#79A-51, Bloque M15, 050034, Medellin, Colombia
| | - Catalina Alvarez
- Laboratorio Genómico One Health, UW-GHI One Health Colombia, Universidad Nacional de Colombia, Cll 75#79A-51, Bloque M15, 050034, Medellin, Colombia
| | - Jaime Usuga
- Laboratorio Genómico One Health, UW-GHI One Health Colombia, Universidad Nacional de Colombia, Cll 75#79A-51, Bloque M15, 050034, Medellin, Colombia
| | - Leidi Carvajal
- Laboratorio Genómico One Health, UW-GHI One Health Colombia, Universidad Nacional de Colombia, Cll 75#79A-51, Bloque M15, 050034, Medellin, Colombia
| | - Andrés Cardona
- Laboratorio Genómico One Health, UW-GHI One Health Colombia, Universidad Nacional de Colombia, Cll 75#79A-51, Bloque M15, 050034, Medellin, Colombia
| | - Maria A Maya
- Division of Infectious Diseases, San Vicente Fundación Hospital, Medellín, Colombia
| | | | - Juan P Hernandez-Ortiz
- Laboratorio Genómico One Health, UW-GHI One Health Colombia, Universidad Nacional de Colombia, Cll 75#79A-51, Bloque M15, 050034, Medellin, Colombia
| | - Jorge E Osorio
- Global Health Institute, University of Wisconsin-Madison, Madison, USA
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11
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Cai X, Lan T, Ping P, Oliver B, Li J. Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search. Viruses 2023; 15:v15051065. [PMID: 37243151 DOI: 10.3390/v15051065] [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: 01/28/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method aimed at identifying co-existing intra-host strains of the virus from RNA-sequencing data of short reads that were used to assemble the original reference genome. Our method consisted of five key steps: extraction of relevant reads, error correction for the reads, identification of within-host diversity, phylogenetic study, and protein binding affinity analysis. Our study revealed that multiple strains of SARS-CoV-2 can coexist in both the viral sample used to produce the reference sequence and a wastewater sample from California. Additionally, our workflow demonstrated its capability to identify within-host diversity in foot-and-mouth disease virus (FMDV). Through our research, we were able to shed light on the binding affinity and phylogenetic relationships of these strains with the published SARS-CoV-2 reference genome, SARS-CoV, variants of concern (VOC) of SARS-CoV-2, and some closely related coronaviruses. These insights have important implications for future research efforts aimed at identifying within-host diversity, understanding the evolution and spread of these viruses, as well as the development of effective treatments and vaccines against them.
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Affiliation(s)
- Xinhui Cai
- Data Science Institute and School of Computer Science, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tian Lan
- Data Science Institute and School of Computer Science, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Pengyao Ping
- Data Science Institute and School of Computer Science, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Brian Oliver
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Jinyan Li
- Data Science Institute and School of Computer Science, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China
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12
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Singh UB, Deb S, Rani L, Bhardwaj D, Gupta R, Kabra M, Bala K, Kumari L, Perumalla S, Shukla J, Nayer J, Aggarwal P, Ahuja V, Chaudhry R, Sinha S, Guleria R. Genomic surveillance of SARS-CoV-2 upsurge in India due to Omicron sub-lineages BA.2.74, BA.2.75 and BA.2.76. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 11:100148. [PMID: 36643851 PMCID: PMC9832050 DOI: 10.1016/j.lansea.2023.100148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/11/2022] [Accepted: 12/24/2022] [Indexed: 01/13/2023]
Affiliation(s)
- Urvashi B. Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India,Corresponding author. Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sushanta Deb
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Rani
- Central Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Deepika Bhardwaj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Kiran Bala
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Kumari
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sowjanya Perumalla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Shukla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jamshed Nayer
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care & Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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13
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SARS-CoV-2 Vaccines, Vaccine Development Technologies, and Significant Efforts in Vaccine Development during the Pandemic: The Lessons Learned Might Help to Fight against the Next Pandemic. Vaccines (Basel) 2023; 11:vaccines11030682. [PMID: 36992266 DOI: 10.3390/vaccines11030682] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
We are currently approaching three years since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 has caused extensive disruptions in everyday life, public health, and the global economy. Thus far, the vaccine has worked better than expected against the virus. During the pandemic, we experienced several things, such as the virus and its pathogenesis, clinical manifestations, and treatments; emerging variants; different vaccines; and the vaccine development processes. This review describes how each vaccine has been developed and approved with the help of modern technology. We also discuss critical milestones during the vaccine development process. Several lessons were learned from different countries during the two years of vaccine research, development, clinical trials, and vaccination. The lessons learned during the vaccine development process will help to fight the next pandemic.
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14
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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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15
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Li G, Ko CN, Wang Z, Chen F, Wang W, Ma DL, Leung CH. Interference reduction isothermal nucleic acid amplification strategy for COVID-19 variant detection. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 377:133006. [PMID: 36439053 PMCID: PMC9678234 DOI: 10.1016/j.snb.2022.133006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Common reference methods for COVID-19 variant diagnosis include viral sequencing and PCR-based methods. However, sequencing is tedious, expensive, and time-consuming, while PCR-based methods have high risk of insensitive detection in variant-prone regions and are susceptible to potential background signal interference in biological samples. Here, we report a loop-mediated interference reduction isothermal nucleic acid amplification (LM-IR-INA) strategy for highly sensitive single-base mutation detection in viral variants. This strategy exploits the advantages of nicking endonuclease-mediated isothermal amplification, luminescent iridium(III) probes, and time-resolved emission spectroscopy (TRES). Using the LM-IR-INA strategy, we established a luminescence platform for diagnosing COVID-19 D796Y single-base substitution detection with a detection limit of 2.01 × 105 copies/μL in a linear range of 6.01 × 105 to 3.76 × 108 copies/μL and an excellent specificity with a variant/wild-type ratio of significantly less than 0.0625%. The developed TRES-based method was also successfully applied to detect D796Y single-base substitution sequence in complicated biological samples, including throat and blood, and was a superior to steady-state technique. LM-IR-INA was also demonstrated for detecting the single-base substitution D614G as well as the multiple-base mutation H69/V70del without mutual interference, indicating that this approach has the potential to be used as a universal viral variant detection strategy.
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Affiliation(s)
- Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao Special Administrative Region of China
- Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
| | - Chung-Nga Ko
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Zikang Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao Special Administrative Region of China
| | - Feng Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao Special Administrative Region of China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao Special Administrative Region of China
- Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
- Macau Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao Special Administrative Region of China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao Special Administrative Region of China
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16
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Bhattacharya M, Chatterjee S, Sharma AR, Lee SS, Chakraborty C. Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape. Folia Microbiol (Praha) 2023; 68:17-28. [PMID: 35962276 PMCID: PMC9374302 DOI: 10.1007/s12223-022-01001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/07/2022] [Indexed: 12/01/2022]
Abstract
The Delta variant is one of the alarming variants of the SARS-CoV-2 virus that have been immensely detrimental and a significant cause of the prolonged pandemic (B.1.617.2). During the SARS-CoV-2 pandemic from December 2020 to October 2021, the Delta variant showed global dominance, and afterwards, the Omicron variant showed global dominance. Delta shows high infectivity rate which accounted for nearly 70% of the cases after December 2020. This review discusses the additional attributes that make the Delta variant so infectious and transmissible. The study also focuses on the significant mutations, namely the L452R and T478K present on the receptor-binding domain of spike (S)-glycoprotein, which confers specific alterations to the Delta variant. Considerably, we have also highlighted other notable factors such as the immune escape, infectivity and re-infectivity, vaccine escape, Ro number, S-glycoprotein stability, cleavage pattern, and its binding affinity with the host cell receptor protein. We have also emphasized clinical manifestations, symptomatology, morbidity, and mortality for the Delta variant compared with other significant SARS-CoV-2 variants. This review will help the researchers to get an elucidative view of the Delta variant to adopt some practical strategies to minimize the escalating spread of the SARS-CoV-2 Delta variant.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore-756020, Odisha, India
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
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17
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Widyasari K, Kim J. A Review of the Currently Available Antibody Therapy for the Treatment of Coronavirus Disease 2019 (COVID-19). Antibodies (Basel) 2023; 12:5. [PMID: 36648889 PMCID: PMC9887598 DOI: 10.3390/antib12010005] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Monoclonal antibodies are a promising treatment for COVID-19. However, the emergence of SARS-CoV-2 variants raised concerns about these therapies' efficacy and long-term viability. Studies reported several antibodies, that received authorization for COVID-19 treatment, are not effective against new variants or subvariants of SARS-CoV-2, hence their distribution has to be paused. Here, the authors reviewed the status of the currently available monoclonal antibodies for COVID-19 treatment, their potential as a therapeutic agent, and the challenges ahead. To address these issues, the authors presented general information on SARS-CoV-2 and how monoclonal antibodies work against SARS-CoV-2. The authors then focus on the antibodies that have been deployed for COVID-19 treatment and their current status, as well as the evidence supporting their potential as an early intervention against COVID-19. Lastly, the authors discussed some leading obstacles that hinder the development and administration of monoclonal antibodies for the treatment of COVID-19.
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Affiliation(s)
- Kristin Widyasari
- Gyeongsang Institute of Health Sciences, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Jinnam Kim
- Major of Food Science & Nutrition, Pukyong National University, Busan 48513, Republic of Korea
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18
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Majed SO, Mustafa SA, Jalal PJ, Fatah MH, Miasko M, Jawhar Z, Karim AY. SARS-CoV-2 Omicron Variant Genomic and Phylogenetic Analysis in Iraqi Kurdistan Region. Genes (Basel) 2023; 14:173. [PMID: 36672914 PMCID: PMC9859166 DOI: 10.3390/genes14010173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Omicron variants have been classified as Variants of Concern (VOC) by the World Health Organization (WHO) ever since they first emerged as a result of a significant mutation in this variant, which showed to have an impact on transmissibility and virulence of the virus, as evidenced by the ongoing modifications in the SARS-CoV-2 virus. As a global pandemic, the Omicron variant also spread among the Kurdish population. This study aimed to analyze different strains from different cities of the Kurdistan region of Iraq to show the risk of infection and the impact of the various mutations on immune responses and vaccination. A total of 175 nasopharyngeal/oropharyngeal specimens were collected at West Erbil Emergency Hospital and confirmed for SARS-CoV-2 infection by RT-PCR. The genomes of the samples were sequenced using the Illumina COVID-Seq Method. The genome analysis was established based on previously published data in the GISAID database and compared to previously detected mutations in the Omicron variants, and that they belong to the BA.1 lineage and include most variations determined in other studies related to transmissibility, high infectivity and immune escape. Most of the mutations were found in the RBD (receptor binding domain), the region related to the escape from humoral immunity. Remarkably, these point mutations (G339D, S371L, S373P, S375F, T547K, D614G, H655Y, N679K and N969K) were also determined in this study, which were unique, and their impact should be addressed more. Overall, the Omicron variants were more contagious than other variants. However, the mortality rate was low, and most infectious cases were asymptomatic. The next step should address the potential of Omicron variants to develop the next-generation COVID-19 vaccine.
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Affiliation(s)
- Sevan Omer Majed
- Biology Department, College of Education, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
| | - Suhad Asad Mustafa
- General Directorate of Scientific Research Center, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
| | - Paywast Jamal Jalal
- Biology Department, College of Science, University of Sulaimani, Sulaymaniyah 46001, Kurdistan Region, Iraq
| | - Mohammed Hassan Fatah
- Medical Lab., Technology Department, Kalar Technical College, Sulaimani Polytechnic University, Kalar 46021, Kurdistan Region, Iraq
| | - Monika Miasko
- Medical Analysis Department, Faculty of Applied Science, Tishk International University, Erbil 44001, Kurdistan Region, Iraq
| | - Zanko Jawhar
- Medical Laboratory Science, College of Health Sciences, Lebanese French University, Erbil 44001, Kurdistan Region, Iraq
| | - Abdulkarim Yasin Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
- Department of Medical Microbiology, College of Science, Cihan University, Erbil 44001,Kurdistan Region, Iraq
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19
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Chatterjee S, Bhattacharya M, Nag S, Dhama K, Chakraborty C. A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies. Viruses 2023; 15:167. [PMID: 36680207 PMCID: PMC9866114 DOI: 10.3390/v15010167] [Citation(s) in RCA: 92] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all the previously emerged variants. The numerous mutations in Omicron's viral genome and its sub-lineages attribute it a larger amount of viral fitness, owing to the alteration of the transmission and pathophysiology of the virus. With a rapid change to the viral structure, Omicron and its sub-variants, namely BA.1, BA.2, BA.3, BA.4, and BA.5, dominate the community with an ability to escape the neutralization efficiency induced by prior vaccination or infections. Similarly, several recombinant sub-variants of Omicron, namely XBB, XBD, and XBF, etc., have emerged, which a better understanding. This review mainly entails the changes to Omicron and its sub-lineages due to it having a higher number of mutations. The binding affinity, cellular entry, disease severity, infection rates, and most importantly, the immune evading potential of them are discussed in this review. A comparative analysis of the Delta variant and the other dominating variants that evolved before Omicron gives the readers an in-depth understanding of the landscape of Omicron's transmission and infection. Furthermore, this review discusses the range of neutralization abilities possessed by several approved antiviral therapeutic molecules and neutralizing antibodies which are functional against Omicron and its sub-variants. The rapid evolution of the sub-variants is causing infections, but the broader aspect of their transmission and neutralization has not been explored. Thus, the scientific community should adopt an elucidative approach to obtain a clear idea about the recently emerged sub-variants, including the recombinant variants, so that effective neutralization with vaccines and drugs can be achieved. This, in turn, will lead to a drop in the number of cases and, finally, an end to the pandemic.
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Affiliation(s)
- Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Sagnik Nag
- Department of Biotechnology, School of Biosciences & Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India
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20
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Bai H, Ata G, Sun Q, Rahman SU, Tao S. Natural selection pressure exerted on "Silent" mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure. Virus Res 2023; 323:198966. [PMID: 36244617 PMCID: PMC9561399 DOI: 10.1016/j.virusres.2022.198966] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023]
Abstract
From the first emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) till now, multiple mutations that caused synonymous and nonsynonymous substitutions have accumulated. Among them, synonymous substitutions were regarded as "silent" mutations that received less attention than nonsynonymous substitutions that cause amino acid variations. However, the importance of synonymous substitutions can not be neglected. This research focuses on synonymous substitutions on SARS-CoV-2 and proves that synonymous substitutions were under purifying selection in its evolution. The evidence of purifying selection is provided by comparing the mutation number per site in coding and non-coding regions. We then study the two forces of purifying selection: synonymous codon usage and RNA secondary structure. Results show that the codon usage optimization leads to an adapted codon usage towards humans. Furthermore, our results show that the maintenance of RNA secondary structure causes the purifying of synonymous substitutions in the structural region. These results explain the selection pressure on synonymous substitutions during the evolution of SARS-CoV-2.
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Affiliation(s)
- Haoxiang Bai
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Galal Ata
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Qing Sun
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa, Pakistan
| | - Shiheng Tao
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China.
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21
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Molina-Mora JA, Reales-González J, Camacho E, Duarte-Martínez F, Tsukayama P, Soto-Garita C, Brenes H, Cordero-Laurent E, Ribeiro dos Santos A, Guedes Salgado C, Santos Silva C, Santana de Souza J, Nunes G, Negri T, Vidal A, Oliveira R, Oliveira G, Muñoz-Medina JE, Salas-Lais AG, Mireles-Rivera G, Sosa E, Turjanski A, Monzani MC, Carobene MG, Remes Lenicov F, Schottlender G, Fernández Do Porto DA, Kreuze JF, Sacristán L, Guevara-Suarez M, Cristancho M, Campos-Sánchez R, Herrera-Estrella A. Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021. Front Public Health 2023; 11:1095202. [PMID: 36935725 PMCID: PMC10018007 DOI: 10.3389/fpubh.2023.1095202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- *Correspondence: Jose Arturo Molina-Mora
| | | | - Erwin Camacho
- Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, Colombia
| | - Francisco Duarte-Martínez
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Pablo Tsukayama
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Claudio Soto-Garita
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Hebleen Brenes
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Estela Cordero-Laurent
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | | | | | - Caio Santos Silva
- Instituto de Ciências Biológica, Universidade Federal do Pará, Belém, Brazil
| | | | - Gisele Nunes
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Tatianne Negri
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Amanda Vidal
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Renato Oliveira
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Guilherme Oliveira
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Guadalupe Mireles-Rivera
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Ezequiel Sosa
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Adrián Turjanski
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Cecilia Monzani
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauricio G. Carobene
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Remes Lenicov
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gustavo Schottlender
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Luisa Sacristán
- Vicerrectoria de Investigación y Creación, Universidad de Los Andes, Bogotá, Colombia
| | | | - Marco Cristancho
- Vicerrectoria de Investigación y Creación, Universidad de Los Andes, Bogotá, Colombia
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
- Alfredo Herrera-Estrella
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22
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Zapata-Cardona MI, Flórez-Álvarez L, Lopera TJ, Chvatal-Medina M, Zapata-Builes W, Diaz FJ, Aguilar-Jimenez W, Taborda N, Hernandez JC, Rugeles MT. Neutralizing antibody titers to Omicron six months after vaccination with BNT162b2 in Colombia. Front Immunol 2022; 13:1102384. [PMID: 36618393 PMCID: PMC9811190 DOI: 10.3389/fimmu.2022.1102384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of the Omicron variant has generated concerns about the efficacy of COVID-19 vaccines. We evaluated the serum neutralizing activity of antibodies against the Omicron (lineage BA.1.1) by plaque reduction neutralizing test, as well as its correlation with age and gender, in a Colombian cohort six months after being vaccinated with BNT162b2 (Pfizer/BioNTech). Compared to all other variants analyzed, a significantly lower neutralizing activity (p<0.001) was observed against Omicron. Interestingly, older individuals exhibited lower titers against Omicron than those younger than 40. No statistical differences in neutralizing activity were observed according to gender. Our results showed that two doses of BNT162b2 might not provide robust protection against the Omicron variant over time. It is necessary to consider including changes in the composition of the vaccines to protect against new emerging variants of SARS-CoV-2 and campaigns to implement additional booster vaccinations.
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Affiliation(s)
- María I. Zapata-Cardona
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tulio J. Lopera
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia., Medellín, Colombia
| | - Francisco J. Diaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Natalia Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
| | - Juan C. Hernandez
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia., Medellín, Colombia
| | - Maria T. Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,*Correspondence: Maria T. Rugeles,
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Xiong D, Zhang X, Yu J, Wei H. Distribution of intra-host variations and mutations in the genomes of SARS-CoV-2 and their implications on detection and therapeutics. MedComm (Beijing) 2022; 3:e186. [PMID: 36474856 PMCID: PMC9717708 DOI: 10.1002/mco2.186] [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: 08/05/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 12/03/2022] Open
Abstract
The ongoing circulation of SARS-CoV-2 variants of concern (VOCs) has caused global concerns, because VOCs could escape current vaccines, antiviral drugs, and diagnosis. Analyzing mutations and intra-host diversities in different and widespread VOCs can provide important insights to virus adaptive evolution and validity of vaccines, antiviral drugs, and diagnosis. In this study, by analyzing 1744 high-throughput sequencing data for intra-host single-nucleotide variations (iSNVs) and 3,668,205 genome sequences for mutations in different VOCs, it was found that Omicron variant is still evolving at high speed, especially having high iSNVs frequency in its S and N genes. The efficacies of antibodies or detection primers targeting these two genes are at high risks to be invalid. Instead, highly conserved regions such as NSP8 gene could be better therapeutic and detection targets. Furthermore, mutations in later VOCs could be traced to the minor alleles in the previous variant samples such as Alpha and Delta in different countries. Finally, it was found that mutations C14408T in RdRp and A18163G in NSP14 gene might be associated with the higher genetic diversity in Omicron. Our findings not only contribute to understanding the adaptive evolution of SARS-CoV-2 VOCs, but also provide useful information for both drugs and diagnostic kits development.
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Affiliation(s)
- Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and BiosafetyCenter for Biosafety Mega‐ScienceWuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- CAS Key Laboratory of Special Pathogens and BiosafetyUniversity of Chinese Academy of SciencesBeijingChina
| | - Xiaoxu Zhang
- CAS Key Laboratory of Special Pathogens and BiosafetyCenter for Biosafety Mega‐ScienceWuhan Institute of VirologyChinese Academy of SciencesWuhanChina
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and BiosafetyCenter for Biosafety Mega‐ScienceWuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- CAS Key Laboratory of Special Pathogens and BiosafetyUniversity of Chinese Academy of SciencesBeijingChina
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and BiosafetyCenter for Biosafety Mega‐ScienceWuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- CAS Key Laboratory of Special Pathogens and BiosafetyUniversity of Chinese Academy of SciencesBeijingChina
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Dhawan M, Sharma A, Priyanka, Thakur N, Rajkhowa TK, Choudhary OP. Delta variant (B.1.617.2) of SARS-CoV-2: Mutations, impact, challenges and possible solutions. Hum Vaccin Immunother 2022; 18:2068883. [PMID: 35507895 PMCID: PMC9359381 DOI: 10.1080/21645515.2022.2068883] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/04/2022] [Accepted: 04/18/2022] [Indexed: 12/24/2022] Open
Abstract
Since commencement of COVID-19 pandemic, several SARS-CoV-2 variants have emerged amid containment efforts via vaccination. The Delta variant (B.1.617.2), discovered in October 2020, was designated as a VOC by the WHO on May 11, 2021. The enhanced transmissibility of Delta variant has been associated with critical mutations such as D614G, L452R, P681R, and T478K in the S-protein. The increased affinity of the S-protein and ACE2 has been postulated as a key reason for decreased vaccine efficacy. As per evidence, the Delta variant possesses increased transmissibility and decreased vaccine efficacy compared to other VOCs like Alpha and Beta. This has led to concerns regarding the acquisition of novel mutations in the Delta variant and outbreaks in vulnerable communities, including vaccinated people. In this mini-review of Delta variant, we have explained its evolution and characteristics, the impact of spike mutations on infectivity and immune evasion, and measures to combat future outbreaks.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, India
- Trafford College, Altrincham, Manchester, UK
| | - Abhilasha Sharma
- Department of Life Science, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Priyanka
- Independent Researcher, 07, Type IV Quarter, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
| | - Nanamika Thakur
- Department of Medical Lab Technology, Faculty of Allied and Healthcare Sciences, GNA University, Phagwara, Punjab, India
| | - Tridib Kumar Rajkhowa
- Department of Veterinary Pathology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Lee SS. The rapid emergence of multiple sublineages of Omicron (B.1.1.529) variant: Dynamic profiling via molecular phylogenetics and mutational landscape studies. J Infect Public Health 2022; 15:1234-1258. [PMID: 36270226 DOI: 10.1016/j.jiph.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022] Open
Abstract
PURPOSE The recent Omicron (B.1.1.529) variant poses a significant threat to global health. This variant has spread worldwide, and several sublineages have rapidly emerged. Study tried to analyze the microevolution of this variant. METHODS We studied the molecular phylogenetics, divergence, geographical distributions, frequencies, risk mutations for antibody affinity, and mutational landscape for Omicron sublineages using in silico analysis and statistical models. The risk mutation of spike for nAb affinity was analyzed and illustrated by statistical plots. Finally, the mutational properties of the spike mutations and their stability were predicted and demonstrated. RESULTS First, we studied the microevolutionary Omicron sublineages using molecular phylogenetics. Simultaneously, we revealed divergence events of the Omicron sublineages and observed the lowest minimum divergence of 51 in clade 21K and the highest maximum divergence of 90 in clade 21L. We have demonstrated cluster analyses, geographical distributions, frequencies of Omicron and its sublineages. Finally, we evaluated the mutational landscape of the Omicron sublineages. In this mutational study, we performed a genome-wide analysis of general mutations, mutations in the non-spike genome, and spike mutations of Omicron sublineages. The risk mutation of S-glycoprotein for nAb affinity has been analyzed for Omicron sublineages. Here, we found that some sublineages have all four significant highly destabilizing mutations. Such sublineages are BA.1 (G446S, E484A, T95I, and D614G), BA.2 (H655Y, Q493R, G493S, and D614G), BA.4 (N501Y, Y505H, N969K, and D614G), and BA.2.75 (Q454H, T547K, N764K, D614G and G446S). Finally, from the mutation stability prediction through ΔΔG, we observed that BA.1 and BA.4 had two destabilizing and two stabilizing mutations. Similarly, BA.2, BA.5, and BA.2.12.1 have one destabilizing and three stabilizing mutations. However, all four mutations in BA.2.75 are stabilizing mutations. CONCLUSIONS Our molecular phylogenetic studies provided a deeper understanding of the microevolution of sublineages and the creation of Omicron. Similarly, this study might help scientists develop pan-coronavirus vaccines that consider their mutational properties.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging &Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging &Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea.
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26
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Chakraborty C. Cases of BA.2.75 and recent BA.2.75.2 subvariant of Omicron are increasing in India: Is it alarming at the global level? Ann Med Surg (Lond) 2022; 84:104963. [PMCID: PMC9671875 DOI: 10.1016/j.amsu.2022.104963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Chiranjib Chakraborty
- Corresponding author. Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
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27
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G. A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs. GeroScience 2022; 44:2393-2425. [PMID: 35989365 PMCID: PMC9393103 DOI: 10.1007/s11357-022-00631-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/20/2022] [Indexed: 01/18/2023] Open
Abstract
The Omicron variant is spreading rapidly throughout several countries. Thus, we comprehensively analyzed Omicron's mutational landscape and compared mutations with VOC/VOI. We analyzed SNVs throughout the genome, and AA variants (NSP and SP) in VOC/VOI, including Omicron. We generated heat maps to illustrate the AA variants with high mutation prevalence (> 75% frequency) of Omicron, which demonstrated eight mutations with > 90% prevalence in ORF1a and 29 mutations with > 75% prevalence in S-glycoprotein. A scatter plot for Omicron and VOC/VOI's cluster evaluation was computed. We performed a risk analysis of the antibody-binding risk among four mutations (L452, F490, P681, D614) and observed three mutations (L452R, F490S, D614G) destabilized antibody interactions. Our comparative study evaluated the properties of 28 emerging mutations of the S-glycoprotein of Omicron, and the ΔΔG values. Our results showed K417N with minimum and Q954H with maximum ΔΔG value. Furthermore, six important RBD mutations (G339D, S371L, N440K, G446S, T478K, Q498R) were chosen for comprehensive analysis for stabilizing/destabilizing properties and molecular flexibility. The G339D, S371L, N440K, and T478K were noted as stable mutations with 0.019 kcal/mol, 0.127 kcal/mol, 0.064 kcal/mol, and 1.009 kcal/mol. While, G446S and Q498R mutations showed destabilizing results. Simultaneously, among six RBD mutations, G339D, G446S, and Q498R mutations increased the molecular flexibility of S-glycoprotein. This study depicts the comparative mutational pattern of Omicron and other VOC/VOI, which will help researchers to design and deploy novel vaccines and therapeutic antibodies to fight against VOC/VOI, including Omicron.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020, Odisha, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
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Solanki K, Rajpoot S, Kumar A, J Zhang KY, Ohishi T, Hirani N, Wadhonkar K, Patidar P, Pan Q, Baig MS. Structural analysis of spike proteins from SARS-CoV-2 variants of concern highlighting their functional alterations. Future Virol 2022. [PMID: 35935449 PMCID: PMC9345306 DOI: 10.2217/fvl-2022-0003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/22/2022] [Indexed: 12/15/2022]
Abstract
Aim: Mutations in the SARS-CoV-2 spike (S) protein have dramatically changed the transmissibility and pathogenicity of the virus. Therefore, we studied the binding affinity of Omicron spike-receptor binding domain (S-RBD) with human ACE2 receptor. Materials & methods: We used pyDockWEB and HADDOCK 2.4 docking for our study. Results: Computational docking indicated higher binding affinity of Omicron S-RBD as compared with wild-type SARS-CoV-2 and Delta S-RBD with ACE2. Interface analysis suggested four mutated residues of Omicron S-RBD for its enhanced binding. We also showed decreased binding affinity of Omicron and Delta S-RBDs with monoclonal antibodies. Conclusion: Compared with wild-type SARS-CoV-2, Omicron S-RBD exhibit higher binding with ACE2 and lower affinity against monoclonal antibodies.
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Affiliation(s)
- Kundan Solanki
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Sajjan Rajpoot
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomokazu Ohishi
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Numazu-Shi, Shizuoka, 410-0301, Japan
| | - Nik Hirani
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH164TJ, UK
| | - Khandu Wadhonkar
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Pramod Patidar
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Qiuwei Pan
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Mirza S Baig
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
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Characterization of SARS-CoV-2 Escape Mutants to a Pair of Neutralizing Antibodies Targeting the RBD and the NTD. Int J Mol Sci 2022; 23:ijms23158177. [PMID: 35897753 PMCID: PMC9332373 DOI: 10.3390/ijms23158177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 01/27/2023] Open
Abstract
Mutations in the spike protein of SARS-CoV-2 can lead to evasion from neutralizing antibodies and affect the efficacy of passive and active immunization strategies. Immunization of mice harboring an entire set of human immunoglobulin variable region gene segments allowed to identify nine neutralizing monoclonal antibodies, which either belong to a cluster of clonally related RBD or NTD binding antibodies. To better understand the genetic barrier to emergence of SARS-CoV-2 variants resistant to these antibodies, escape mutants were selected in cell culture to one antibody from each cluster and a combination of the two antibodies. Three independently derived escape mutants to the RBD antibody harbored mutations in the RBD at the position T478 or S477. These mutations impaired the binding of the RBD antibodies to the spike protein and conferred resistance in a pseudotype neutralization assay. Although the binding of the NTD cluster antibodies were not affected by the RBD mutations, the RBD mutations also reduced the neutralization efficacy of the NTD cluster antibodies. The mutations found in the escape variants to the NTD antibody conferred resistance to the NTD, but not to the RBD cluster antibodies. A variant resistant to both antibodies was more difficult to select and only emerged after longer passages and higher inoculation volumes. VOC carrying the same mutations as the ones identified in the escape variants were also resistant to neutralization. This study further underlines the rapid emergence of escape mutants to neutralizing monoclonal antibodies in cell culture and indicates the need for thorough investigation of escape mutations to select the most potent combination of monoclonal antibodies for clinical use.
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Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105282. [PMID: 35427787 PMCID: PMC9005225 DOI: 10.1016/j.meegid.2022.105282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
Abstract
Background The massive increase in COVID-19 infection had generated a second wave in India during May–June 2021 with a critical pandemic situation. The Delta variant (B.1.617.2) was a significant factor during the second wave. Conversely, the UK had passed through the crucial phase of the pandemic from November to December 2020 due to B.1.1.7. The study tried to comprehend the pandemic response in the UK and India to the spread of the B.1.1.7 (Alpha, UK) variant and B.1.617.2 (Delta, India) variant. Methods This study was performed in three directions to understand the pandemic response of the two emerging variants. First, we served comparative genomics, such as genome sequence submission patterns, mutational landscapes, and structural landscapes of significant mutations (N501Y, D614G, L452R, E484Q, and P681R). Second, we performed evolutionary epidemiology using molecular phylogenetics, scatter plots of the cluster evaluation, country-wise transmission pattern, and frequency pattern. Third, the receptor binding pattern was analyzed using the Wuhan reference strain and the other two variants. Results The study analyzed the country-wise and region-wise genome sequences and their submission pattern, molecular phylogenetics, scatter plot of the cluster evaluation, country-wise geographical distribution and transmission pattern, frequency pattern, entropy diversity, and mutational landscape of the two variants. The structural pattern was analyzed in the N501Y, D614G L452R, E484Q, and P681R mutations. The study found increased molecular interactivity between hACE2-RBD binding of B.1.1.7 and B.1.617.2 compared to the Wuhan reference strain. Our receptor binding analysis showed a similar indication pattern for hACE2-RBD of these two variants. However, B.1.617.2 offers slightly better stability in the hACE2-RBD binding pattern through MD simulation than B.1.1.7. Conclusion The increased hACE2-RBD binding pattern of B.1.1.7 and B.1.617.2 might help to increase the infectivity compared to the Wuhan reference strain.
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Tahsin A, Ahmed R, Bhattacharjee P, Adiba M, Al Saba A, Yasmin T, Chakraborty S, Hasan AM, Nabi AN. Most frequently harboured missense variants of hACE2 across different populations exhibit varying patterns of binding interaction with spike glycoproteins of emerging SARS-CoV-2 of different lineages. Comput Biol Med 2022; 148:105903. [PMID: 35932731 PMCID: PMC9296255 DOI: 10.1016/j.compbiomed.2022.105903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/03/2022] [Accepted: 07/16/2022] [Indexed: 11/22/2022]
Abstract
Since the emergence of SARS-CoV-2 at Wuhan in the Hubei province of China in 2019, the virus has accumulated various mutations, giving rise to many variants. According to the combinations of mutations acquired, these variants are classified into lineages and greatly differ in infectivity and transmissibility. In 2021 alone, a variant of interest (VoI) Mu (B.1.621), as well as, variants of concern (VoC) Delta (B.1.617.2) and Omicron (BA.1, BA.2) and later in 2022, BA.4, BA.5, and BA.2.12.1 have emerged. Since then, the world has seen prominent surges in the rate of infection during short periods of time. However, not all populations have suffered equally, which suggests a possible role of host genetic factors. Here, we investigated the strength of binding of the spike glycoprotein receptor-binding domain (RBD) of the SARS-CoV-2 variants: Mu, Delta, Delta Plus (AY.1), Omicron sub-variants BA.1, BA.2, BA.4, BA.5, and BA.2.12.1 with the human angiotensin-converting enzyme 2 (hACE2) missense variants prevalent in major populations. In this purpose, molecular docking analysis, as well as, molecular dynamics simulation was performed of the above-mentioned SARS-CoV-2 RBD variants with the hACE2 containing the single amino acid substitutions prevalent in African (E37K), Latin American (F40L), non-Finnish European (D355 N), and South Asian (P84T) populations, in order to predict the effects of the lineage-defining mutations of the viral variants on receptor binding. The effects of these mutations on protein stability were also explored. The protein-protein docking and molecular dynamics simulation analyses have revealed variable strength of attachment and exhibited altered interactions in the case of different hACE2-RBD complexes. In vitro studies are warranted to confirm these findings which may enable early prediction regarding the risk of transmissibility of newly emerging variants across different populations in the future.
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32
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Lino A, Cardoso MA, Martins‐Lopes P, Gonçalves HMR. Omicron - The new SARS-CoV-2 challenge? Rev Med Virol 2022; 32:e2358. [PMID: 35445774 PMCID: PMC9111063 DOI: 10.1002/rmv.2358] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 01/05/2023]
Abstract
SARS-CoV-2 virus has infected nearly 300 M people worldwide and has been associated with over 6 M deaths by March 2022. Since the virus emergence in December 2019 in Wuhan, several new mutations have been described. The World Health Organization has developed a working name for these emerging variants according to their impact on the worldwide population. In this context a high alert has been paid to variants of concern (VOC) due to their high infectiousness and transmissibility patterns. The most recent VOC, Omicron (B.1.1.529), has become dominant in the shortest time ever and has placed Europe under an overwhelming and unprecedented number of new cases. This variant has numerous mutations in regions that are associated with higher transmissibility, stronger viral binding, affinity and antibody escape. Moreover, the mutations and deletions present in the spike protein suggest that the SARS-CoV-2 specific attachment inhibitors may not be the best option for Omicron therapy. Omicron is the dominant variant circulating worldwide and, at the end of February 2022, it was responsible for nearly all sequences reported to GISAID. Omicron is made up of several sublineages, where the most common are BA.1 and BA.2 (or Nextstrain clade 21K and 21L, respectively). At a global level, it is possible to say that the proportion of BA.2 has been increasing relative to BA.1 and in some countries it has been replacing it at high rates. In order to better assess the Omicron effectiveness on antibody escape, spread and infectious ability it is of the highest relevance to maintain a worldwide tight surveillance. Even though this variant has been associated with a lower death rate, it is important to highlight that the number of people becoming infected is concerning and that further unpredictable mutations may emerge as the number of infected people rises.
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Affiliation(s)
- A. Lino
- BioISI ‐ Biosystems & Integrative Sciences InstituteFaculty of SciencesUniversity of LisbonLisbonPortugal
| | - M. A. Cardoso
- REQUIMTEInstituto Superior de Engenharia do PortoPortoPortugal
| | - P. Martins‐Lopes
- BioISI ‐ Biosystems & Integrative Sciences InstituteFaculty of SciencesUniversity of LisbonLisbonPortugal
- Department of Genetics and Biotechnology (DGB)University of Trás‐os‐Montes e Alto Douro (UTAD)Vila RealPortugal
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33
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Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther 2022; 7:202. [PMID: 35764603 PMCID: PMC9240077 DOI: 10.1038/s41392-022-01039-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lan-Yi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Guangdong-Hong Kong Joint Laboratory for RNA Medicine, 510060, Guangzhou, China.
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Chavda VP, Hanuma Kumar Ghali EN, Yallapu MM, Apostolopoulos V. Therapeutics to tackle Omicron outbreak. Immunotherapy 2022; 14:833-838. [PMID: 35678049 PMCID: PMC9180252 DOI: 10.2217/imt-2022-0064] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In this commentary, the authors have focused on the mutational impact of the Omicron variant on the current therapeutics to manage #COVID19.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics & Pharmaceutical Technology, LM College of Pharmacy, Ahmedabad, Gujarat, 380008, India
| | - Eswara Naga Hanuma Kumar Ghali
- Department of Immunology & Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA.,South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Murali M Yallapu
- Department of Immunology & Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA.,South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Vasso Apostolopoulos
- Institute for Health & Sport, Victoria University, Melbourne, Victoria, 3030, Australia.,Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, Victoria, 3021, Australia
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