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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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Kohli M, Maschio M, Lee A, Igarashi A. Projections of the incidence of COVID-19 in Japan and the potential impact of a Fall 2023 COVID-19 vaccine. Vaccine 2024; 42:2282-2289. [PMID: 38429154 DOI: 10.1016/j.vaccine.2024.01.093] [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: 11/20/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND The study objective was to estimate the incidence of COVID-19 infection, hospitalization, and deaths in Japan from September 2023 to August 2024 and potential impact of a monovalent XBB.1.5 variant-adapted Fall 2023 COVID-19 vaccine (modified version: XBB monovalent) for adults aged ≥18 years on these outcomes. METHODS A previously developed Susceptible-Exposed-Infected-Recovered model for the United States (US) was adapted to Japan. The numbers of symptomatic infections, COVID-19-related hospitalizations, and deaths were calculated. Given differences in vaccination coverage, masking practices and social mixing patterns between the US and Japan, all inputs were updated to reflect the Japanese context. Vaccine effectiveness (VE) values are hypothetical, but predicted based on existing VE values of bivalent BA.4/BA.5 boosters against BA.4/BA.5 in Japan, from the VERSUS test-negative case-control study. Sensitivity analyses were performed. RESULTS The base case model predicts overall that there will be approximately 35.2 million symptomatic COVID-19 infections, 690,000 hospitalizations, and 62,000 deaths in Japan between September 2023 and August 2024. If an updated COVID-19 vaccine is offered to all adults aged 18 years and older in Fall 2023, the model predicts that 7.3 million infections, 275,000 hospitalizations and 26,000 deaths will be prevented. If vaccines are only given to those aged 65 years and older, only 2.9 million infections, 180,000 hospitalizations and 19,000 deaths will be prevented. Sensitivity analysis results suggest that hospitalizations and deaths prevented are most sensitive to initial VE against infection and hospitalizations, and the waning rate associated with VE against infection. Symptomatic infections prevented was most sensitive to initial VE against infection and VE waning. CONCLUSIONS Results suggest that a Fall 2023 COVID-19 vaccine would reduce total numbers of COVID-19-related infections, hospitalizations, and deaths.
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Affiliation(s)
- Michele Kohli
- Quadrant Health Economics Inc, 92 Cottonwood Crescent, Cambridge, Ontario, Canada.
| | - Michael Maschio
- Quadrant Health Economics Inc, 92 Cottonwood Crescent, Cambridge, Ontario, Canada
| | - Amy Lee
- Quadrant Health Economics Inc, 92 Cottonwood Crescent, Cambridge, Ontario, Canada
| | - Ataru Igarashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo Ward, Tokyo 113-0033, Japan; Graduate School of Data Sciences, Yokohama City University School of Medicine, 22-2 Seto, Kanazawa Ward, Yokohama, Kanagawa 236-0027, Japan
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Ambalavanan R, Snead RS, Marczika J, Malioukis A. Epidemiological contemplation for a currently pragmatic COVID-19 health passport: a perspective. Front Public Health 2024; 12:1347623. [PMID: 38414904 PMCID: PMC10896918 DOI: 10.3389/fpubh.2024.1347623] [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: 12/01/2023] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) has caused a global pandemic that has wreaked havoc on the lives of millions of people around the world. Confinement measures aim to reduce the epidemic's spread and minimize the burden of morbidity and mortality. In response to the challenges caused by the pandemic, digital health passports have been developed exponentially. We highlight the latent epidemiological barriers to health passports to achieve standardized digital care platforms. This review paper not only highlights the epidemiological barriers but also articulates the possible infrastructure required to make the International Standard for a multi-factor authenticated and validated health passport.
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Affiliation(s)
- Radha Ambalavanan
- Research Department, The Self Research Institute, Broken Arrow, OK, United States
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Yarovaya OI, Filimonov AS, Baev DS, Borisevich SS, Zaykovskaya AV, Chirkova VY, Marenina MK, Meshkova YV, Belenkaya SV, Shcherbakov DN, Gureev MA, Luzina OA, Pyankov OV, Salakhutdinov NF, Khvostov MV. The Potential of Usnic-Acid-Based Thiazolo-Thiophenes as Inhibitors of the Main Protease of SARS-CoV-2 Viruses. Viruses 2024; 16:215. [PMID: 38399993 PMCID: PMC10893357 DOI: 10.3390/v16020215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (-)-usnic acid and studied their ability to inhibit the main protease of SARS-CoV-2. Substances containing unsubstituted thiophene groups or methyl- or bromo-substituted thiophene moieties showed moderate activity. Derivatives containing nitro substituents in the thiophene heterocycle-just as pure (+)- and (-)-usnic acids-showed no anti-3CLpro activity. Kinetic parameters of the most active compound, (+)-3e, were investigated, and molecular modeling of the possible interaction of the new thiazolo-thiophenes with the active site of the main protease was carried out. We evaluated the binding energies of the ligand and protein in a ligand-protein complex. Active compound (+)-3e was found to bind with minimum free energy; the binding of inactive compound (+)-3g is characterized by higher values of minimum free energy; the positioning of pure (+)-usnic acid proved to be unstable and is accompanied by the formation of intermolecular contacts with many amino acids of the catalytic binding site. Thus, the molecular dynamics results were consistent with the experimental data. In an in vitro antiviral assay against six strains (Wuhan, Delta, and four Omicron sublineages) of SARS-CoV-2, (+)-3e demonstrated pronounced antiviral activity against all the strains.
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Affiliation(s)
- Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Aleksandr S. Filimonov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Dmitriy S. Baev
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
| | - Sophia S. Borisevich
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
- Laboratory of Chemical Physics, Ufa Institute of Chemistry, Ufa Federal Research Centre, 450078 Ufa, Russia
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Varvara Yu. Chirkova
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Mariya K. Marenina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Yulia V. Meshkova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Svetlana V. Belenkaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Dmitriy N. Shcherbakov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Maxim A. Gureev
- Laboratory of Bio- and Cheminformatics, St. Petersburg School of Physics, Mathematics and Computer Science, HSE University, 194100 St. Peterburg, Russia;
| | - Olga A. Luzina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Mikhail V. Khvostov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
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Wicaksono IA, Suhandi C, Elamin KM, Wathoni N. Efficacy and safety of casirivimab-imdevimab combination on COVID-19 patients: A systematic review and meta-analysis randomized controlled trial. Heliyon 2023; 9:e22839. [PMID: 38058433 PMCID: PMC10696184 DOI: 10.1016/j.heliyon.2023.e22839] [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: 07/20/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023] Open
Abstract
Background The advantages and disadvantages of casirivimab-imdevimab for coronavirus disease 2019 are not well understood. We conducted a systematic review and meta-analysis of relevant literature to determine the therapeutic effectiveness and potential side effects of casirivimab-imdevimab in COVID-19 patients. Methods Databases were searched from the time of their commencement until February 28th, 2023. The primary results evaluated were the death rate at 28 days, progression of current clinical symptoms within 28 days, viral load, discharge from hospital, and any adverse events. Also, we contrasted the effects of the casirivimab-imdevimab treatment with placebo or standard of care. The protocol registration for this systematic review and meta-analysis was recorded in the PROSPERO database (CRD42023412835). Results A total of eight studies were included, comprising 19,819 patients, and conducted a qualitative assessment of their risk of bias using the Cochrane risk of bias tool. Casirivimab-imdevimab effectively reduced the mortality rate (OR = 0.62; 95 % CI of 0.40-0.98; p = 0.04; I2 = 30 %) and reduced the progression of clinical symptoms (OR = 0.86; 95 % CI of 0.79-0.93; p = 0.0003; I2 = 57 %). Casirivimab-imdevimab also improved viral load clearance and hospital discharge. Additionally, the trials' findings demonstrated a slight decrease in the likelihood of adverse events occurring with the use of casirivimab-imdevimab. Conclusion Our research suggests that casirivimab-imdevimab may be a valuable, safe, and effective anti-SARS-CoV-2 regimen.
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Affiliation(s)
- Imam Adi Wicaksono
- Department of Pharmacology and Clinical Pharmacy, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
| | - Cecep Suhandi
- Department of Pharmaceutics and Pharmaceutical Technology, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
| | - Khaled M. Elamin
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Nasrul Wathoni
- Department of Pharmaceutics and Pharmaceutical Technology, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
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Gurung S, Tewari E, Pradhan P, Bhutia TD, Chhophel TP, Rasaily MM, Gurung M, Rai A, Sarda M, Gurung B, Pradhan PD, Sharma DK. Vaccine Breakthrough Infections Among Healthcare Workers in a COVID-19-Designated Tertiary Care Government Hospital in Sikkim. Cureus 2023; 15:e46752. [PMID: 37946886 PMCID: PMC10631761 DOI: 10.7759/cureus.46752] [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] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
Introduction Since the emergence of the coronavirus disease 2019 (COVID-19) virus at the beginning of 2020, the world has gone through various waves of pandemics. The health care workers (HCWs) or the COVID warriors as they were termed were the first line of defense against the virus. They were armed with personal protective equipment and prophylactic doses of the COVID-19 vaccine. Despite these precautions, some of the HCWs still contracted the disease and a few others succumbed to it. The objective of this study was to estimate the prevalence of COVID-19 infections and vaccine breakthrough infections (BTIs) in HCWs after receiving the COVID-19 vaccine during the second wave of the pandemic. Methods This was a cross-sectional, hospital-based study conducted over a period of four months from September 2021 to December 2021 on HCWs aged 18 years and above working at the COVID-19-designated tertiary care government hospital in Sikkim. A structured coded questionnaire with no patient identifiers was used to gather details on demographics, vaccination history, breakthrough infection, and other social details. HCWs who had received at least one dose of the COVID-19 vaccine at the time of initiation of the study and were >18 years of age were included in this study. Results A total of 678 HCWs were screened, out of which 229 (33%) participants tested positive for COVID-19 and the rest of the participants (455; 67%) tested negative. COVID-19 infections and vaccine BTIs (COVID-19 infection >14 days after the second vaccination) were recorded and 137 (20%) respondents had a post-vaccination COVID-19 infection out of which 115 (18.5%) were BTI. The majority of the participants were females and of the age group of 26-35 years. The correlation of COVID-19 infections with the dose gap between vaccination, gender, age, profession, department, area posted during COVID duty, cycles of duty performed, hospitalization due to infection, influenza vaccination, and comorbidity was analyzed. Conclusion COVID-19 vaccines are disease-modifying and they decrease the severity of BTIs in HCWs. Pandemics and outbreaks cannot be predicted; therefore, it becomes very important to have healthy frontline workers who are constantly exposed to infectious agents. Monitoring of health and surveillance of infectious diseases among the HCWs should be encouraged.
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Affiliation(s)
- Shrijana Gurung
- Virology, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Ekta Tewari
- Virology, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Pooja Pradhan
- Virology, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Tsultem D Bhutia
- Paediatrics, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Tashi P Chhophel
- Virology, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | | | - Mani Gurung
- Obstetrics and Gynaecology, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Ashish Rai
- Radiation Oncology, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Manoj Sarda
- Surgery, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Birendra Gurung
- Paediatrics, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Priya D Pradhan
- Pathology, Sir Thutob Namgyal Memorial Hospital, Government of Sikkim, Gangtok, IND
| | - Dhruva K Sharma
- Pharmacology and Therapeutics, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Gangtok, IND
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Zeng Z, Geng X, Wen X, Chen Y, Zhu Y, Dong Z, Hao L, Wang T, Yang J, Zhang R, Zheng K, Sun Z, Zhang Y. Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future. Front Microbiol 2023; 14:1232453. [PMID: 37645223 PMCID: PMC10461067 DOI: 10.3389/fmicb.2023.1232453] [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: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.
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Affiliation(s)
- Zhaomu Zeng
- Department of Neurosurgery, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- Department of Neurosurgery, Xiangya Hospital Jiangxi Hospital of Central South University, National Regional Medical Center for Nervous System Diseases, Nanchang, China
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiuchao Geng
- Department of Nursing, School of Medicine, Taizhou University, Taizhou, China
| | - Xichao Wen
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yueyue Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yixi Zhu
- Department of Pharmacy, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zishu Dong
- Department of Zoology, Advanced Research Institute, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Liangchao Hao
- Department of Plastic Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Tingting Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Jifeng Yang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ruobing Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Kebin Zheng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yuhao Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
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Bhardwaj P, Mishra SK, Behera SP, Zaman K, Kant R, Singh R. Genomic evolution of the SARS-CoV-2 Variants of Concern: COVID-19 pandemic waves in India. EXCLI JOURNAL 2023; 22:451-465. [PMID: 37534220 PMCID: PMC10390896 DOI: 10.17179/excli2023-6098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 08/04/2023]
Abstract
SARS-CoV-2 has mutated rapidly since its first case report in Wuhan, China, leading to the emergence of an indefinite number of variants. India has witnessed three waves of the COVID-19 pandemic. The country saw its first wave of SARS-CoV-2 illness from late January 2020 to February 2021. With a peak surge of cases in mid-September 2020, India recorded more than 11 million cases and a death toll of more than 0.165 million at this time. India faced a brutal second wave driven by the emergence of highly infectious SARS-CoV-2 variants B.1.617.2 (Delta variant) and the third wave with the leading cause of BA.2 (Omicron variant), which has led to an unprecedented rise in COVID-19 cases in the country. On September 14, 2022, India recorded a cumulative 44.51 million cases of COVID-19 with more than 0.528 million deaths. The discovery of common circulating mutants is facilitated by genome sequencing. The changes in the Spike surface glycoprotein recombinant binding domains served as the critical alterations, resulting in enhanced infectivity and transmissibility, with severe clinical effects. Further, the predominant mutation in the SARS-CoV-2 spike protein; the D614G strains served as a model for vaccine development. The mutation of the Wuhan strain to the Variant of Concern led to a significant increase in SARS-CoV-2 infections. In addition, there was a shift in the age group affected by SARS-CoV-2 variant infection. The current review summarized the COVID-19 pandemic's Variant of Concern and the advent of SARS-CoV-2 in India.
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Affiliation(s)
- Pooja Bhardwaj
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Kamran Zaman
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajni Kant
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajeev Singh
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
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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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Rahman MS, Hoque MN, Chowdhury SR, Siddique MM, Islam OK, Galib SM, Islam MT, Hossain MA. Temporal dynamics and fatality of SARS-CoV-2 variants in Bangladesh. Health Sci Rep 2023; 6:e1209. [PMID: 37077184 PMCID: PMC10108430 DOI: 10.1002/hsr2.1209] [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: 01/11/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
Background and Aims Since the beginning of the SARS-CoV-2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS-CoV-2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes. Methods We retrieved 6610 complete whole genome sequences of the SARS-CoV-2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in-silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS-CoV-2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID-19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID-19 cases. Results SARS-CoV-2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS-CoV-2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS-CoV-2 reference genome of Wuhan/Hu-1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time-dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal-Wallis test) and CFR (p = 0.032, Kruskal-Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in Bangladesh. Remarkably, the highest CFR (1.91%) from SARS-CoV-2 variants was recorded in 2021. Conclusion Our findings highlight the importance of genomic surveillance for careful monitoring of variants of concern emergence to interpret correctly their relative IFR and CFR, and thus, for implementation of strengthened public health and social measures to control the spread of the virus. Furthermore, the results of the present study may provide important context for sequence-based inference in SARS-CoV-2 variant(s) evolution and clinical epidemiology beyond Bangladesh.
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Affiliation(s)
- M. Shaminur Rahman
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive HealthBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Susmita Roy Chowdhury
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Moradul Siddique
- Department of Computer Science and EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Ovinu Kibria Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Syed Md. Galib
- Department of Computer Science and EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Tanvir Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - M. Anwar Hossain
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
- Jashore University of Science and TechnologyJashoreBangladesh
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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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Chakraborty C, Chatterjee S, Bhattacharya M, Chopra H, Bhattacharya P, Islam MA, Dhama K. The D614G mutation helps to increase the transmissibility and reduce the virulence of SARS-CoV-2 variants through natural selection. Int J Surg 2023; 109:171-174. [PMID: 36799841 PMCID: PMC10389482 DOI: 10.1097/js9.0000000000000155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/18/2023]
Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal
| | - Srijan Chatterjee
- Institute for Skeletal Aging and Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, Gangwon-do, Republic of Korea
| | | | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Prosun Bhattacharya
- COVID-19 Research, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, Stockholm, Sweden
| | - Md. Aminul Islam
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
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Szpulak A, Garlak U, Ćwirko H, Witkowska B, Rombel-Bryzek A, Witkowska D. SARS-CoV-2 and its impact on the cardiovascular and digestive systems - The interplay between new virus variants and human cells. Comput Struct Biotechnol J 2023; 21:1022-1029. [PMID: 36694807 PMCID: PMC9850860 DOI: 10.1016/j.csbj.2023.01.024] [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: 11/05/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
Since infection with the novel coronavirus SARS-CoV-2 first emerged in Wuhan, China, in December 2019, the world has been battling the pandemic COVID-19. Patients of all ages and genders are now becoming infected with the new coronavirus variant (Omicron) worldwide, and its subvariants continue to pose a threat to health and life. This article provides a literature review of cardiovascular and gastrointestinal complications resulting from SARS-CoV-2 infection. COVID-19 primarily caused respiratory symptoms, but complications can affect many vital organs. SARS-CoV-2 binds to a human cell receptor (angiotensin-converting enzyme 2 - ACE2) that is predominantly expressed primarily in the heart and gastrointestinal tract, which is why we focused on complications in these organs. Since the high transmissibility of Omicron and its ability to evade the immune system have raised worldwide concern, we have tried to summarise the current knowledge about its development from a structural point of view and to highlight the differences in its binding to human receptors and proteases compared to previous VOC.
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Affiliation(s)
- Angelika Szpulak
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Urszula Garlak
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Hanna Ćwirko
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Bogusława Witkowska
- Institute of Health Sciences, University of Opole, Katowicka 68, 45-060 Opole, Poland
| | | | - Danuta Witkowska
- Institute of Health Sciences, University of Opole, Katowicka 68, 45-060 Opole, Poland
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14
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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: 80] [Impact Index Per Article: 80.0] [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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SV P, Lorenz JM, Ittamalla R, Dhama K, Chakraborty C, Kumar DVS, Mohan T. Twitter-Based Sentiment Analysis and Topic Modeling of Social Media Posts Using Natural Language Processing, to Understand People's Perspectives Regarding COVID-19 Booster Vaccine Shots in India: Crucial to Expanding Vaccination Coverage. Vaccines (Basel) 2022; 10:1929. [PMID: 36423024 PMCID: PMC9692646 DOI: 10.3390/vaccines10111929] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 07/26/2023] Open
Abstract
This study analyzed perceptions of Indians regarding COVID-19 booster dose vaccines using natural language processing techniques, particularly, sentiment analysis and topic modeling. We analyzed tweets generated by Indian citizens for this study. In late July 2022, the Indian government hastened the process of COVID-19 booster dose vaccinations. Understanding the emotions and concerns of the citizens regarding the health policy being implemented will assist the government, health policy officials, and policymakers implement the policy efficiently so that desired results can be achieved. Seventy-six thousand nine hundred seventy-nine tweets were used for this study. The sentiment analysis study revealed that out of those 76,979 tweets, more than half (n = 40,719 tweets (52.8%) had negative sentiments, 24,242 tweets (31.5%) had neutral sentiments, and 12,018 tweets (15.6%) had positive sentiments. Social media posts by Indians on the COVID-19 booster doses have focused on the feelings that younger people do not need vaccines and that vaccinations are unhealthy.
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Affiliation(s)
- Praveen SV
- Department of Management Studies, National Institute of Technology, Tiruchirappalli 20015, Tamil Nadu, India
| | - Jose Manuel Lorenz
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Vinus, 32900 Ourense, Spain
- Facultade de Ciencias de Ourense, Universidade de Vigo, Área de Tecnoloxía dos Alimentos, 32004 Ourense, Spain
| | - Rajesh Ittamalla
- Department of Management Studies, Indian Institute of Technology, Hyderabad 502285, Telangana, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Admas University, Kolkatta 700126, West Bengal, India
| | | | - Thivyaa Mohan
- Department of Management Studies, National Institute of Technology, Tiruchirappalli 20015, Tamil Nadu, India
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