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Zaborska M, Chruszcz M, Sadowski J, Klaudel T, Pelczarski M, Sztangreciak-Lehun A, Bułdak RJ. The most common skin symptoms in young adults and adults related to SARS-CoV-2 virus infection. Arch Dermatol Res 2024; 316:292. [PMID: 38819524 PMCID: PMC11142985 DOI: 10.1007/s00403-024-02991-5] [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: 04/11/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 06/01/2024]
Abstract
Scientists from various areas of the world indicate in their studies that skin lesions occur in the course of infection with the SARS-CoV-2 virus. This article is a review of the most frequently described cutaneous manifestations of SARS-CoV-2 virus infection and the potential pathophysiology of their development, as well as information on abnormalities in histopathological tests. The article describes the impact of some factors related to the COVID-19 pandemic on the exacerbation of chronic dermatological diseases. This work was constructed on the basis of 142 research studies, reviews, and meta-analyses, focusing on the methods and materials used in individual works as well as the results and conclusions resulting from them. Some skin lesions may be a potential prognostic marker of the course of the disease and may also be a prodromal symptom or the only symptom of SARS-CoV-2 virus infection. Stress related to the COVID-19 pandemic may exacerbate some chronic dermatological diseases. A correlation was observed between the type of skin lesions and the patient's age. The occurrence of skin diseases may also be influenced by drugs used to treat infections caused by SARS-CoV-2. A relationship was observed between the patient's ethnic origin and skin lesions occurring in the course of COVID-19. There is a need to further diagnose the cutaneous manifestations of SARS-CoV-2 infection and to learn the detailed pathomechanism of their occurrence in order to better understand the essence of the disease and find an appropriate treatment method.
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Affiliation(s)
- Monika Zaborska
- Student Scientific Society of Clinical Biochemistry and Regenerative Medicine, Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, 45-052, Opole, Poland.
| | - Maksymilan Chruszcz
- Student Scientific Society of Clinical Biochemistry and Regenerative Medicine, Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Jakub Sadowski
- Student Scientific Society of Clinical Biochemistry and Regenerative Medicine, Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Tomasz Klaudel
- Student Scientific Society of Clinical Biochemistry and Regenerative Medicine, Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Michał Pelczarski
- Student Scientific Society of Clinical Biochemistry and Regenerative Medicine, Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Anna Sztangreciak-Lehun
- Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Rafał Jakub Bułdak
- Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, 45-052, Opole, Poland
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Zhang Y, Li Q, Xiang JL, Li XH, Li J. Comparison of Computed Tomography and Clinical Features Between Patients Infected with the SARS-CoV-2 Omicron Variant and the Original Strain. Infect Drug Resist 2024; 17:807-818. [PMID: 38476766 PMCID: PMC10929164 DOI: 10.2147/idr.s448713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Purpose To investigate potential differences in clinical and computed tomography (CT) features between patients with the SARS-CoV-2 Omicron variant and the original strain. Patients and Methods This retrospective study included 69 hospitalized patients infected with Omicron variant from November to December 2022, and 96 hospitalized patients infected with the original strain from February to March 2020 in Chongqing, China. The clinical features, CT manifestations, degrees of lung involvement in different stages on CT, and imaging changes after the reverse-transcription polymerase chain reaction (RT-PCR) results turned negative were compared between the two groups. Results For clinical features, patients with Omicron were predominantly old people and females, without manifestation of any clinical symptoms, who had low serum levels of C-reactive protein and procalcitonin. Shorter interval from symptoms onset to initial CT scan was observed in Omicron patients compared to patients with the original strain (all P < 0.05). For CT features, patients with Omicron were more likely to present with round-like opacities and tree-in-bud pattern (all P < 0.05), but less likely to exhibit a diffuse distribution, patchy and linear opacities, as well as vascular enlargement pattern (all P < 0.05). The Omicron group was more susceptible to exhibiting lower CT involvement scores in each stage (all P < 0.05) and imaging progression after the RT-PCR results turned negative (P < 0.001). Conclusion Patients infected with the Omicron variant exhibited less severe changes on chest CT compared to those infected with the original strain. Furthermore, imaging progression under low viral load conditions was more common in patients with Omicron than in those with the original strain.
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Affiliation(s)
- Yue Zhang
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Qi Li
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Jiang-Lin Xiang
- Department of Infectious Disease, Chongqing University Three Gorges Hospital, Chongqing, 404000, People’s Republic of China
| | - Xing-Hua Li
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Jing Li
- Medical Department, Liangjiang New Area Renhe Community Health Service Center, Chongqing, 401147, People’s Republic of China
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Ahmed R, Samanta S, Banerjee J, Dash SK. XBB and BQ.1, the two Omicron cousins dominating globally: Is it the time we should think again? Presse Med 2024; 53:104220. [PMID: 38103589 DOI: 10.1016/j.lpm.2023.104220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 11/27/2023] [Indexed: 12/19/2023] Open
Affiliation(s)
- Rubai Ahmed
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Sovan Samanta
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Jhimli Banerjee
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Sandeep Kumar Dash
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India.
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Gao L, Tang S, Zheng W. Strategic Deployment of ICU Nurses in Response to the Omicron Variant Epidemic in Shanghai. Risk Manag Healthc Policy 2023; 16:2907-2913. [PMID: 38155846 PMCID: PMC10752819 DOI: 10.2147/rmhp.s438496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/02/2023] [Indexed: 12/30/2023] Open
Abstract
Objective In the first half of 2022, Shanghai faced the challenge of an emerging wave of epidemics caused by the Omicron variant. In response, 48 hospitals, spanning municipal and district levels, were rapidly converted into designated hospitals. This case study focuses on the South Branch of Renji Hospital, School of Medicine, Shanghai Jiaotong University, as one such designated hospital. Methods Facing unprecedented challenges without prior experience, we devised a strategic approach to deploy ICU nurses effectively. This approach involved crisis event gradation, establishing a human resources pool, and classifying nursing staff based on qualifications and proficiencies. Results By May 11, 2022, all 48 designated hospitals were operational. The South Branch of Renji Hospital treated 3310 Omicron-infected patients between April 7 and June 21, 2022, including 115 critically ill patients in a 38-bed ICU. We meticulously assigned 136 nurses, distributed as follows: Grade A 12.5%, Grade B 12.5%, Grade C 40%, and Grade D 35%, with three specialized nursing managers. Nurses worked tirelessly in 4-hour shifts, wearing full protective gear. Remarkably, the hospital maintained a flawless record, with no nursing-related adverse events and zero patient mortality in the ICU. Conclusion Effective management of ICU nursing personnel is associated with patient safety. Strategic rostering and placement of ICU nurses in designated hospitals optimize resource utilization, enhancing service effectiveness and working conditions. This technique is a crucial resource for hospitals facing unforeseen public health crises requiring rapid ICU nurse resource allocation and management.
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Affiliation(s)
- Leiqing Gao
- Department of Nursing, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Department of Nursing, Pu Jiang Hospital, Minhang District, Shanghai, People’s Republic of China
| | - Shi Tang
- Department of Nursing, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Weiyan Zheng
- Department of Nursing, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
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Zhu P, Wang W, Qian M, Shi G, Zhang Q, Xu T, Xu H, Zhang H, Gu X, Ding Y, Lee A, Hayter M. Severe Loneliness and Isolation in Nursing Students during COVID-19 Lockdown: A Phenomenological Study. Healthcare (Basel) 2023; 12:19. [PMID: 38200925 PMCID: PMC10778901 DOI: 10.3390/healthcare12010019] [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: 10/18/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
In 2022, COVID-19 continued to spread across the globe, and to stop the spread of the virus and protect people's health, universities across China continued to remain in a lockdown state. Loneliness is an important topic among college students, and the coronavirus pandemic has exacerbated loneliness. This prolonged school lockdown was unprecedented and it caused severe social isolation and emotional loneliness for students. Few people know how nursing students experience loneliness and find a way through their experience. This qualitative phenomenological study was conducted to reveal the lived experiences of nursing students who indicated COVID-19 lockdown-related loneliness in a previous quantitative survey. We performed 20 semi-structured interviews with nursing students aged 19-23 yrs during their lockdown (April 2022 to June 2022). Our research applied Colaizzi's seven-step data analysis processes to reveal shared patterns in terms of how nursing students experienced lockdown and found the following four themes: emotional challenges associated with loneliness; causes of loneliness; positive and negative motivation to learn; and accepting solitude and reconstructing real life.
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Affiliation(s)
- Pingting Zhu
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou 225009, China
| | - Wen Wang
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Meiyan Qian
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Guanghui Shi
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Qianqian Zhang
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Ting Xu
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Huiwen Xu
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Hui Zhang
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Xinyue Gu
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Yinwen Ding
- School of Nursing, School of Public Health, Yangzhou University, Yangzhou 225009, China; (W.W.); (M.Q.); (G.S.); (Q.Z.); (T.X.); (H.X.); (H.Z.); (X.G.); (Y.D.)
| | - Amanda Lee
- Faculty of Health & Education, Manchester Metropolitan University, Manchester M15 6GX, UK; (A.L.); (M.H.)
| | - Mark Hayter
- Faculty of Health & Education, Manchester Metropolitan University, Manchester M15 6GX, UK; (A.L.); (M.H.)
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Pinhata JMW, Brandao AP, Leite D, Oliveira RSD, Fukasawa LO, Gonçalves MG, Guerra JM, Araujo LJTD, Mansueli GP, Santos LB, Borghesan TC, Kimura LM, Takahashi JPF, Garcia JA, Piza ARDT, Ferreira CSDS, Polatto R, Guerra MLLES, Fazioli RDA, Zanella RC, Blanco RM, Ial-Working Group. Rapid response of a public health reference laboratory to the COVID-19 pandemic. J Med Microbiol 2023; 72. [PMID: 37801010 DOI: 10.1099/jmm.0.001757] [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] [Indexed: 10/07/2023] Open
Abstract
Introduction. Brazil was one of the most affected countries by the COVID-19 pandemic. Instituto Adolfo Lutz (IAL) is the reference laboratory for COVID-19 in São Paulo, the most populous state in Brazil. In April 2020, a secondary diagnostic pole named IAL-2 was created to enhance IAL's capacity for COVID-19 diagnosis.Hypothesis/Gap Statement. Public health laboratories must be prepared to rapidly respond to emerging epidemics or pandemics.Aim. To describe the design of IAL-2 and correlate the results of RT-qPCR tests for COVID-19 with secondary data on suspected cases of SARS-CoV-2 infection in the São Paulo state.Methodology. This is a retrospective study based on the analysis of secondary data from patients suspected of infection by SARS-CoV-2 whose clinical samples were submitted to real-time PCR after reverse transcription (RT-qPCR) at IAL-2, between 1 April 2020 and 8 March 2022. RT-qPCR Ct results of the different kits used were also analysed.Results. IAL-2 was implemented in April 2020, just over a month after the detection of the first COVID-19 case in Brazil. The laboratory performed 304,250 RT-qPCR tests during the study period, of which 98 319 (32.3 %) were positive, 205827 (67.7 %) negative, and 104 (0.03 %) inconclusive for SARS-CoV-2. RT-qPCR Ct values≤30 for E/N genes of SARS-CoV-2 were presented by 79.7 % of all the samples included in the study.Conclusion. IAL was able to rapidly implement a new laboratory structure to support the processing of an enormous number of samples for diagnosis of COVID-19, outlining strategies to carry out work with quality, using different RT-qPCR protocols.
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Affiliation(s)
| | - Angela Pires Brandao
- Instituto Adolfo Lutz, Centro de Bacteriologia, Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
- Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil, 4365, 21040-360, Rio de Janeiro, RJ, Brazil
| | - Daniela Leite
- Instituto Adolfo Lutz, Centro de Bacteriologia, Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | | | - Lucila Okuyama Fukasawa
- Instituto Adolfo Lutz, Centro de Imunologia, Av. Dr. Arnaldo, 351, 11º andar, 01246-000, São Paulo, SP, Brazil
| | - Maria Gisele Gonçalves
- Instituto Adolfo Lutz, Centro de Imunologia, Av. Dr. Arnaldo, 351, 11º andar, 01246-000, São Paulo, SP, Brazil
| | - Juliana Mariotti Guerra
- Instituto Adolfo Lutz, Centro de Patologia, Av. Dr. Arnaldo, 351, 7º andar, 01246-000, São Paulo, SP, Brazil
| | | | - Gina Ploeger Mansueli
- Instituto Adolfo Lutz, Centro de Bacteriologia, Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Lilian Beserra Santos
- Instituto Adolfo Lutz, Centro de Bacteriologia, Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Tarcilla Corrente Borghesan
- Instituto Adolfo Lutz, Centro de Bacteriologia, Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Lidia Midori Kimura
- Instituto Adolfo Lutz, Centro de Patologia, Av. Dr. Arnaldo, 351, 7º andar, 01246-000, São Paulo, SP, Brazil
| | - Juliana Possatto Fernandes Takahashi
- Instituto Adolfo Lutz, Centro de Patologia, Av. Dr. Arnaldo, 351, 7º andar, 01246-000, São Paulo, SP, Brazil
- Universidade Federal do Mato Grosso do Sul, Faculdade de Medicina, Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Cidade Universitária, Caixa Postal 549, 79070-900, Campo Grande, MS, Brazil
| | - Juliana Alves Garcia
- Instituto Adolfo Lutz, Centro de Patologia, Av. Dr. Arnaldo, 351, 7º andar, 01246-000, São Paulo, SP, Brazil
| | - Ana Rita de Toledo Piza
- Instituto Adolfo Lutz, Centro de Patologia, Av. Dr. Arnaldo, 351, 7º andar, 01246-000, São Paulo, SP, Brazil
| | | | - Ricardo Polatto
- Instituto Adolfo Lutz, Centro de Bacteriologia, Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | | | | | - Rosemeire Cobo Zanella
- Instituto Adolfo Lutz, Centro de Bacteriologia, Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Roberta Morozetti Blanco
- Instituto Adolfo Lutz, Centro de Bacteriologia, Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
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Daziano R, Budziński W. Evolution of preferences for COVID-19 vaccine throughout the pandemic - The choice experiment approach. Soc Sci Med 2023; 332:116093. [PMID: 37515953 DOI: 10.1016/j.socscimed.2023.116093] [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: 12/30/2022] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023]
Abstract
In this study, we employ a choice experiment to study individual preferences for COVID-19 vaccines in the US. A unique characteristic of the microdata (N = 5671) is that the survey was conducted in five distinct waves from October 2020 to October 2021. Because of this dynamic feature, it is possible to control for evolving pandemic conditions such as the number of COVID-19 active cases, vaccination uptake, and the frequency of Google searches related to the vaccines. Furthermore, we employ a hybrid choice model to incorporate respondents' attitudes related to their perceived vulnerability to diseases, as well as their perceived health status. The hybrid choice model was extended to incorporate latent classes as well as random effects. We find that the rate of vaccinated individuals in the population actually increases the probability of vaccine hesitancy, and therefore may discourage people to get vaccinated. This may be evidence of free-riding behavior. On the other hand, the number of COVID-19 cases has a positive effect on the probability of getting vaccinated, suggesting that individuals react to the pandemic conditions by taking some protective measures. Google trend data do not seem to have a straightforward effect on the vaccination demand, but it increases consumers' willingness to pay for several vaccine characteristics. With respect to the analyzed attitudes, we find that perceived uninfectability is a significant driver of vaccine hesitancy, probably related to the frequent "natural immunity" argument. In turn, germ aversion has a positive effect on the probability of getting vaccinated as well as on the marginal willingness to pay. Finally, health status has a limited effect on whether the individual will decide to vaccinate or not.
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Affiliation(s)
- Ricardo Daziano
- School of Civil and Environmental Engineering, Cornell University, USA.
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de Moura Junior CF, Ochi D, Freitas ED, Kerwald J, d'Ávila MA, Beppu MM. Synthesis and characterization of n-phosphonium chitosan and its virucidal activity evaluation against coronavirus. Int J Biol Macromol 2023; 246:125665. [PMID: 37406900 DOI: 10.1016/j.ijbiomac.2023.125665] [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: 05/30/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Despite the worldwide vaccination effort against COVID-19, the demand for biocidal materials has increased. One promising solution is the chemical modification of polysaccharides, such as chitosan, which can provide antiviral activity through the insertion of cationic terminals. In this study, chitosan was modified with (4-carboxybutyl) triphenylphosphonium bromide to create N-phosphonium chitosan (NPCS), a quaternized derivative. The resulting NPCS samples with three degrees of substitution (15.6 %, 19.8 % and 24.2 %) were characterized and found to have improved solubility in water and alkaline solutions but reduced thermal stability. The particles zeta potential exhibits positive charges and is directly correlated with the degree of substitution of the derivative. In virucidal assays, all NPCS samples were able to inhibit 99.999 % of the MHV-3 coronavirus within 5 min at low concentrations of 0.1 mg/mL, while maintaining low cytotoxicity to L929 cells. In addition to its potential application against current coronavirus strains, NPCS could also be valuable in combating future pandemics caused by other viral pathogens. The antiviral properties of NPCS make it a promising material for use in coating surface and personal protective equipment to limit the spread of disease-causing viruses.
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Affiliation(s)
- Celso Fidelis de Moura Junior
- School of Chemical Engineering, Department of Materials and Bioprocess Engineering, University of Campinas, Av. Albert Einstein, Campinas 13083-852, Brazil
| | - Deise Ochi
- School of Chemical Engineering, Department of Materials and Bioprocess Engineering, University of Campinas, Av. Albert Einstein, Campinas 13083-852, Brazil
| | - Emanuelle Dantas Freitas
- School of Chemical Engineering, Department of Materials and Bioprocess Engineering, University of Campinas, Av. Albert Einstein, Campinas 13083-852, Brazil
| | - Jonas Kerwald
- School of Chemical Engineering, Department of Materials and Bioprocess Engineering, University of Campinas, Av. Albert Einstein, Campinas 13083-852, Brazil
| | - Marcos Akira d'Ávila
- School of Mechanical Engineering, Department of Manufacturing and Materials Engineering, University of Campinas, Campinas 13083-860, Brazil
| | - Marisa Masumi Beppu
- School of Chemical Engineering, Department of Materials and Bioprocess Engineering, University of Campinas, Av. Albert Einstein, Campinas 13083-852, Brazil.
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Wang H, Lan Y. The global dynamic transmissibility of COVID-19 and its influencing factors: an analysis of control measures from 176 countries. BMC Public Health 2023; 23:404. [PMID: 36855085 PMCID: PMC9971674 DOI: 10.1186/s12889-023-15174-0] [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: 10/24/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023] Open
Abstract
OBJECTIVE To summarise the dynamic characteristics of COVID-19 transmissibility; To analyse and quantify the effect of control measures on controlling the transmissibility of COVID-19; To predict and compare the effectiveness of different control measures. METHODS We used the basic reproduction number ([Formula: see text]) to measure the transmissibility of COVID-19, the transmissibility of COVID-19 and control measures of 176 countries and regions from January 1, 2020 to May 14, 2022 were included in the study. The dynamic characteristics of COVID-19 transmissibility were summarised through descriptive research and a Dynamic Bayesian Network (DBN) model was constructed to quantify the effect of control measures on controlling the transmissibility of COVID-19. RESULTS The results show that the spatial transmissibility of COVID-19 is high in Asia, Europe and Africa, the temporal transmissibility of COVID-19 increases with the epidemic of Beta and Omicron strains. Dynamic Bayesian Network (DBN) model shows that the transmissibility of COVID-19 is negatively correlated with control measures. Restricting population mobility has the strongest effect, nucleic acid testing (NAT) has a strong effect, and vaccination has the weakest effect. CONCLUSION Strict control measures are essential for controlling the COVID-19 outbreak; Restricting population mobility and nucleic acid testing (NAT) have significant impacts on controlling the COVID-19 transmissibility, while vaccination has no significant impact. In light of these findings, future control measures may include the widespread use of new NAT technology and the promotion of booster immunization.
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Affiliation(s)
- Hongjian Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yajia Lan
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
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Davies MA, Morden E, Rousseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Roux SL, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NA, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A. Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa. Int J Infect Dis 2023; 127:63-68. [PMID: 36436752 PMCID: PMC9686046 DOI: 10.1016/j.ijid.2022.11.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/28/2022] [Accepted: 11/19/2022] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection. METHODS We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection. RESULTS Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective. CONCLUSION Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.
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Affiliation(s)
- Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa,Corresponding author: Mary-Ann Davies University of Cape Town, Faculty of Health Sciences, Anzio Road, Observatory, 7925, Cape Town, South Africa
| | - Erna Morden
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jamy-Lee Bam
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
| | - Linda Boloko
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Keith Cloete
- Western Cape Government: Health, Cape Town, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Chetty
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Pierre Dane
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, South Africa
| | - Mehreen Hunter
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Hannah Hussey
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa,Metro Health Services, Western Cape Government: Health, Cape Town, South Africa
| | - Theuns Jacobs
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Saadiq Kariem
- Western Cape Government: Health, Cape Town, South Africa
| | - Reshma Kassanjee
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Inneke Laenen
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Sue Le Roux
- Western Cape Government: Health, Cape Town, South Africa,Karl Bremer Hospital, Western Cape Government: Health, Cape Town, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Hassan Mahomed
- Metro Health Services, Western Cape Government: Health, Cape Town, South Africa,Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Deborah Maughan
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Graeme Meintjes
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Marc Mendelson
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Ayanda Mnguni
- Khayelitsha District Hospital, Western Cape Government: Health, Cape Town, South Africa
| | - Melvin Moodley
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
| | - Katy Murie
- Western Cape Government: Health, Cape Town, South Africa,Metro Health Services, Western Cape Government: Health, Cape Town, South Africa
| | - Jonathan Naude
- Mitchells Plain Hospital, Western Cape Government: Health, Cape Town, South Africa
| | - Ntobeko A.B. Ntusi
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa,South African Medical Research Council Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, Cape Town, South Africa
| | - Masudah Paleker
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Arifa Parker
- Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa,Division of General Medicine, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - David Pienaar
- Rural Health Services, Western Cape Government: Health, Cape Town, South Africa
| | - Wolfgang Preiser
- National Health Laboratory Service, South Africa,Division of Medical Virology, University of Stellenbosch, Stellenbosch, South Africa
| | - Hans Prozesky
- Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Peter Raubenheimer
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Liezel Rossouw
- Western Cape Government: Health, Cape Town, South Africa
| | - Neshaad Schrueder
- Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of General Medicine, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Barry Smith
- Western Cape Government: Health, Cape Town, South Africa,Karl Bremer Hospital, Western Cape Government: Health, Cape Town, South Africa
| | - Mariette Smith
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Greg Symons
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Jantjie Taljaard
- Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Sean Wasserman
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa,Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Robert J. Wilkinson
- The Francis Crick Institute, London, UK,Department of Infectious Diseases, Imperial College London, London, UK,Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Nicole Wolter
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
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11
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Kumar A, Asghar A, Singh HN, Faiq MA, Kumar S, Narayan RK, Kumar G, Dwivedi P, Sahni C, Jha RK, Kulandhasamy M, Prasoon P, Sesham K, Kant K, Pandey SN. SARS-CoV-2 Omicron Variant Genomic Sequences and Their Epidemiological Correlates Regarding the End of the Pandemic: In Silico Analysis. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2023; 4:e42700. [PMID: 36688013 PMCID: PMC9843602 DOI: 10.2196/42700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Background Emergence of the new SARS-CoV-2 variant B.1.1.529 worried health policy makers worldwide due to a large number of mutations in its genomic sequence, especially in the spike protein region. The World Health Organization (WHO) designated this variant as a global variant of concern (VOC), which was named "Omicron." Following Omicron's emergence, a surge of new COVID-19 cases was reported globally, primarily in South Africa. Objective The aim of this study was to understand whether Omicron had an epidemiological advantage over existing variants. Methods We performed an in silico analysis of the complete genomic sequences of Omicron available on the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyze the functional impact of the mutations present in this variant on virus-host interactions in terms of viral transmissibility, virulence/lethality, and immune escape. In addition, we performed a correlation analysis of the relative proportion of the genomic sequences of specific SARS-CoV-2 variants (in the period from October 1 to November 29, 2021) with matched epidemiological data (new COVID-19 cases and deaths) from South Africa. Results Compared with the current list of global VOCs/variants of interest (VOIs), as per the WHO, Omicron bears more sequence variation, specifically in the spike protein and host receptor-binding motif (RBM). Omicron showed the closest nucleotide and protein sequence homology with the Alpha variant for the complete sequence and the RBM. The mutations were found to be primarily condensed in the spike region (n=28-48) of the virus. Further mutational analysis showed enrichment for the mutations decreasing binding affinity to angiotensin-converting enzyme 2 receptor and receptor-binding domain protein expression, and for increasing the propensity of immune escape. An inverse correlation of Omicron with the Delta variant was noted (r=-0.99, P<.001; 95% CI -0.99 to -0.97) in the sequences reported from South Africa postemergence of the new variant, subsequently showing a decrease. There was a steep rise in new COVID-19 cases in parallel with the increase in the proportion of Omicron isolates since the report of the first case (74%-100%). By contrast, the incidence of new deaths did not increase (r=-0.04, P>.05; 95% CI -0.52 to 0.58). Conclusions In silico analysis of viral genomic sequences suggests that the Omicron variant has more remarkable immune-escape ability than existing VOCs/VOIs, including Delta, but reduced virulence/lethality than other reported variants. The higher power for immune escape for Omicron was a likely reason for the resurgence in COVID-19 cases and its rapid rise as the globally dominant strain. Being more infectious but less lethal than the existing variants, Omicron could have plausibly led to widespread unnoticed new, repeated, and vaccine breakthrough infections, raising the population-level immunity barrier against the emergence of new lethal variants. The Omicron variant could have thus paved the way for the end of the pandemic.
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Affiliation(s)
- Ashutosh Kumar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Adil Asghar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Himanshu N Singh
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Systems Biology Columbia University Irving Medical Center New York, NY United States
| | - Muneeb A Faiq
- Etiologically Elusive Disorders Research Network New Delhi India
- New York University Langone Health Center Robert I Grossman School of Medicine New York University New York, NY United States
| | - Sujeet Kumar
- Etiologically Elusive Disorders Research Network New Delhi India
- Center for Proteomics and Drug Discovery Amity Institute of Biotechnology Amity University, Maharashtra Mumbai India
| | - Ravi K Narayan
- Etiologically Elusive Disorders Research Network New Delhi India
- Dr BC Roy Multi-speciality Medical Research Centre Indian Institute of Technology Kharagpur India
| | - Gopichand Kumar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Prakhar Dwivedi
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Chetan Sahni
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Anatomy Institute of Medical Sciences Banaras Hindu University Varanasi India
| | - Rakesh K Jha
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Maheswari Kulandhasamy
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Biochemistry Maulana Azad Medical College New Delhi India
| | - Pranav Prasoon
- Etiologically Elusive Disorders Research Network New Delhi India
- School of Medicine University of Pittsburgh Pittsburgh, PA United States
| | - Kishore Sesham
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Anatomy All India Institute of Medical Sciences-Mangalagiri Mangalagiri India
| | - Kamla Kant
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Microbiology All India Institute of Medical Sciences-Bathinda Bathinda India
| | - Sada N Pandey
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Zoology Banaras Hindu University Varanasi India
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12
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Chakraborti S, Gill J, Goswami R, Kumar S, Chandele A, Sharma A. Structural Profiles of SARS-CoV-2 Variants in India. Curr Microbiol 2023; 80:1. [PMID: 36414797 PMCID: PMC9684916 DOI: 10.1007/s00284-022-03094-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022]
Abstract
India was severely affected by several waves of SARS-CoV-2 infection that occurred during April-June 2021 (second wave) and December 2021-January 2022 (third wave) and thereafter, resulting in >10 million new infections and a significant number of deaths. Global Initiative on Sharing Avian Influenza Data database was used to collect the sequence information of ~10,000 SARS-CoV-2 patients from India and our sequence analysis identified three variants B.1.1.7 (alpha, α), B1.617.2 (delta, Δ), B.1.1.529 (Omicron, Oo) and one Omicron sub-variant BA.2.75 as the primary drivers for SARS-CoV-2 waves in India. Structural visualization and analysis of important mutations of alpha, delta, Omicron and its sub-variants of SARS-CoV-2 Receptor-Binding Domain (RBD) was performed and our analysis clearly shows that mutations occur throughout the RBD, including the RBD surface responsible for human angiotensin-converting enzyme 2 (hACE-2) receptor-binding. A comparison between alpha, delta and omicron variants/sub-variants reveals many omicron mutations in the hACE-2 binding site and several other mutations within 5 Å of this binding region. Further, computational analysis highlights the importance of electrostatic interactions in stabilizing RBD-hACE-2-binding, especially in the omicron variant. Our analysis explores the likely role of key alpha, delta and omicron mutations on binding with hACE-2. Taken together, our study provides novel structural insights into the implications of RBD mutations in alpha, delta and omicron and its sub-variants that were responsible for India's SARS-CoV-2 surge.
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Affiliation(s)
- Soumyananda Chakraborti
- National Institute of Malaria Research, New Delhi, 110077, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India.
| | - Jasmita Gill
- National Institute of Malaria Research, New Delhi, 110077, India.
| | - Ritu Goswami
- National Institute of Malaria Research, New Delhi, 110077, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Amit Sharma
- National Institute of Malaria Research, New Delhi, 110077, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
- Structural Parasitology, Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
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13
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Li M, Ge H, Sun Z, Fu J, Cao L, Feng X, Meng G, Peng Y, Liu Y, Zhao C. A loop-mediated isothermal amplification-enabled analytical assay for the detection of SARS-CoV-2: A review. Front Cell Infect Microbiol 2022; 12:1068015. [PMID: 36619749 PMCID: PMC9816412 DOI: 10.3389/fcimb.2022.1068015] [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: 10/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The number of words: 4645, the number of figures: 4, the number of tables: 1The outbreak of COVID-19 in December 2019 caused a global pandemic of acute respiratory disease, and with the increasing virulence of mutant strains and the number of confirmed cases, this has resulted in a tremendous threat to global public health. Therefore, an accurate diagnosis of COVID-19 is urgently needed for rapid control of SARS-CoV-2 transmission. As a new molecular biology technology, loop-mediated isothermal amplification (LAMP) has the advantages of convenient operation, speed, low cost and high sensitivity and specificity. In the past two years, rampant COVID-19 and the continuous variation in the virus strains have demanded higher requirements for the rapid detection of pathogens. Compared with conventional RT-PCR and real-time RT-PCR methods, genotyping RT-LAMP method and LAMP plus peptide nucleic acid (PNA) probe detection methods have been developed to correctly identified SARS-CoV-2 variants, which is also why LAMP technology has attracted much attention. LAMP detection technology combined with lateral flow assay, microfluidic technology and other sensing technologies can effectively enhance signals by nucleic acid amplification and help to give the resulting output in a faster, more convenient and user-friendly way. At present, LAMP plays an important role in the detection of SARS-CoV-2.
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Affiliation(s)
- Mingna Li
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Hongjuan Ge
- College of public health, Jilin Medical University, Jilin, China
| | - Zhe Sun
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Jangshan Fu
- College of public health, Jilin Medical University, Jilin, China
| | - Lele Cao
- College of public health, Jilin Medical University, Jilin, China
| | - Xinrui Feng
- College of public health, Jilin Medical University, Jilin, China,Medical college, Yanbian University, Jilin, China
| | - Guixian Meng
- College of medical laboratory, Jilin Medical University, Jilin, China
| | - Yubo Peng
- Business School, The University of Adelaide, Adelaide, SA, Australia
| | - Yan Liu
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
| | - Chen Zhao
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
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14
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Farahat RA, Abdelaal A, Umar TP, El-Sakka AA, Benmelouka AY, Albakri K, Ali I, Al-Ahdal T, Abdelazeem B, Sah R, Rodriguez-Morales AJ. The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends. LE INFEZIONI IN MEDICINA 2022; 30:480-494. [PMID: 36482957 PMCID: PMC9714996 DOI: 10.53854/liim-3004-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) has been the most recent variant of concern (VOC) established by the World Health Organization (WHO). Because of its greater infectivity and immune evasion, this variant quickly became the dominant type of circulating SARS-CoV-2 worldwide. Our literature review thoroughly explains the current state of Omicron emergence, particularly by comparing different omicron subvariants, including BA.2, BA.1, and BA.3. Such elaboration would be based on structural variations, mutations, clinical manifestation, transmissibility, pathogenicity, and vaccination effectiveness. The most notable difference between the three subvariants is the insufficiency of deletion (Δ69-70) in the spike protein, which results in a lower detection rate of the spike (S) gene target known as (S) gene target failure (SGTF). Furthermore, BA.2 had a stronger affinity to the human Angiotensin-converting Enzyme (hACE2) receptor than other Omicron sub-lineages. Regarding the number of mutations, BA.1.1 has the most (40), followed by BA.1, BA.3, and BA.3 with 39, 34, and 31 mutations, respectively. In addition, BA.2 and BA.3 have greater transmissibility than other sub-lineages (BA.1 and BA.1.1). These characteristics are primarily responsible for Omicron's vast geographical spread and high contagiousness rates, particularly BA.2 sub-lineages.
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Affiliation(s)
| | - Abdelaziz Abdelaal
- Harvard Medical School, Boston, MA,
USA,Boston University, MA,
USA,General Practitioner, Tanta University Hospitals,
Egypt
| | | | | | | | - Khaled Albakri
- Faculty of Medicine, The Hashemite University, Zarqa,
Jordan
| | - Iftikhar Ali
- Department of Pharmacy, Paraplegic Center, Peshawar,
Pakistan
| | - Tareq Al-Ahdal
- Institute of Global Health (HIGH), Heidelberg University, Heidelberg,
Germany
| | - Basel Abdelazeem
- Department of Internal Medicine, McLaren Health Care, Flint, Michigan,
USA,Department of Internal Medicine, Michigan State University, East Lansing, Michigan,
USA
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu,
Nepal,Dr. D.Y Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra,
India
| | - Alfonso J. Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de Las Américas, Pereira, Risaralda,
Colombia,Faculty of Medicine, Institución Universitaria Vision de Las Americas, Pereira, Risaralda,
Colombia,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36,
Lebanon,Master of Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima,
Perú
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15
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Wu Y, Long Y, Wang F, Liu W, Wang Y. Emergence of SARS-CoV-2 Omicron variant and strategies for tackling the infection. Immun Inflamm Dis 2022; 10:e733. [PMID: 36444634 PMCID: PMC9639460 DOI: 10.1002/iid3.733] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION Nowadays, emerging SARS-CoV-2 Omicron, the novel highly mutated VOC, has quickly spread as the dominant variant in over 190 countries worldwide through the first part of 2022, which is influencing the infectivity, transmissibility, pathogenicity, and severity of COVID-19 pandemic. Additionally, clinical cases and experimental studies have reported that Omicron variant likely leads to weakened immune protection elicited by infection, antibody therapies, and vaccines. The new wave, from late February, 2022, was escalated abruptly by higher levels of transmission of Omicron BA.2 sublineage in China. METHODS AND RESULTS Following a systematic database search, this review summarizes the salient features of Omicron sublineages, and their impact on transmissibility, disease severity as well as the efficacy of the available vaccines and treatment against the Omicron. CONCLUSION We hope this study will provide a scientific reference for alleviating the burden of COVID-19.
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Affiliation(s)
- Yan Wu
- Department of Clinical Laboratory MedicineTianjin TEDA HospitalTianjinChina
| | - Yiyin Long
- Tianjin Institute of UrologyThe Second Hospital of Tianjin Medical UniversityTianjinChina
| | - Feng Wang
- Department of Genetics, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Wei Liu
- Tianjin Children's HospitalChildren's Hospital of Tianjin UniversityTianjinChina
| | - Yuliang Wang
- Tianjin Institute of UrologyThe Second Hospital of Tianjin Medical UniversityTianjinChina
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16
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Dhawan M, Saied AA, Mitra S, Alhumaydhi FA, Emran TB, Wilairatana P. Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2? Biomed Pharmacother 2022; 154:113522. [PMID: 36030585 PMCID: PMC9376347 DOI: 10.1016/j.biopha.2022.113522] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/19/2022] Open
Abstract
Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid the serious containment efforts against COVID-19 that include physical measures, pharmacological repurposing, immunization, and genomic/community surveillance. Omicron variant (B.1.1.529) has been identified as a highly modified, contagious, and crucial variant among the five VOCs of SARS-CoV-2. The increased affinity of the spike protein (S-protein), and host receptor, angiotensin converting enzyme-2 (ACE-2), due to a higher number of mutations in the receptor-binding domain (RBD) of the S-protein has been proposed as the primary reason for the decreased efficacy of majorly available vaccines against the Omicron variant and the increased transmissible nature of the Omicron variant. Because of its significant competitive advantage, the Omicron variant and its sublineages swiftly surpassed other variants to become the dominant circulating lineages in a number of nations. The Omicron variant has been identified as a prevalent strain in the United Kingdom and South Africa. Furthermore, the emergence of recombinant variants through the conjunction of the Omicron variant with other variants or by the mixing of the Omicron variant's sublineages/subvariants poses a major threat to humanity. This raises various issues and hazards regarding the Omicron variant and its sublineages, such as an Omicron variant breakout in susceptible populations among fully vaccinated persons. As a result, understanding the features and genetic implications of this variant is crucial. Hence, we explained in depth the evolution and features of the Omicron variant and analyzed the repercussions of spike mutations on infectiousness, dissemination ability, viral entry mechanism, and immune evasion. We also presented a viewpoint on feasible strategies for precluding and counteracting any future catastrophic emergence and spread of the omicron variant and its sublineages that could result in a detrimental wave of COVID-19 cases.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, Punjab, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
| | - AbdulRahman A Saied
- National Food Safety Authority (NFSA), Aswan Branch, Aswan 81511, Egypt; Ministry of Tourism and Antiquities, Aswan Office, Aswan 81511, Egypt
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh.
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
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SARS-CoV-2 infection: Pathogenesis, Immune Responses, Diagnosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
COVID-19 has emerged as the most alarming infection of the present time instigated by the virus SARS-CoV-2. In spite of advanced research technologies, the exact pathophysiology and treatment of the condition still need to be explored. However, SARS-CoV-2 has several structural and functional similarities that resemble SARS-CoV and MERS-CoV which may be beneficial in exploring the possible treatment and diagnostic strategies for SARS-CoV-2. This review discusses the pathogen phenotype, genotype, replication, pathophysiology, elicited immune response and emerging variants of SARS-CoV-2 and their similarities with other similar viruses. SARS-CoV-2 infection is detected by a number of diagnostics techniques, their advantages and limitations are also discussed in detail. The review also focuses on nanotechnology-based easy and fast detection of SARS-CoV-2 infection. Various pathways which might play a vital role during SARS-CoV-2 infection have been elaborately discussed since immune response plays a major role during viral infections.
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Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach. 3 Biotech 2022; 12:198. [PMID: 35923684 PMCID: PMC9342843 DOI: 10.1007/s13205-022-03258-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/08/2022] [Indexed: 11/01/2022] Open
Abstract
Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03258-4.
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Chen M, Li R, Ding G, Jin C. Needs of cancer patients during the SARS-CoV-2 Omicron lockdown: A population-based survey in Shanghai, China. Biosci Trends 2022; 16:230-237. [PMID: 35718468 DOI: 10.5582/bst.2022.01251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The aim of this study was to investigate the medical and healthcare needs of cancer patients during the Shanghai lockdown due to the SARS-CoV-2 Omicron pandemic. From April 15 to April 21, 2022, 4,195 cancer patients from every district in Shanghai were surveyed using quota sampling via an online platform. The questionnaire consisted of three main parts: demographic and sociological data, disease diagnosis, and different dimensions of patients' needs. Correlation analysis was used to examine the relationship between participants' need scores in each dimension, and generalized linear regression models were used to analyze the factors influencing patients' need scores. The mean age of participants was 63.23 years (SD: 7.43 years), with more female than male participants (80.38% vs. 19.62%). Among participants, the three leading groups of patients were those with breast cancer (39.02%), colorectal cancer (12.82%), or tracheal and bronchial lung cancer (10.23%). Social support, dietary/nutritional support, and psychological counselling ranked as the top three needs of cancer patients. In addition, vaccination against SARS-CoV-2 may reduce psychological anxiety in cancer patients. Compared to participants who had never received the SARS-CoV-2 vaccine, participants who had received one, two, or three doses of the vaccine were respectively 36% (odds ratio (OR): 0.64, 95% confidence interval (CI): 0.56-0.73), 38% (OR: 0.62, 95% CI: 0.59-0.54), and 37% (OR: 0.63, 95% CI: 0.60-0.66) less likely to have an increased need for psychological counseling. In light of constraints on offline medical resources for cancer patients during the lockdown, the current authors have begun to re-examine the universal accessibility and spread of telemedicine in the future. In addition, immune barriers can be established for cancer patients and vaccination guidelines for different disease stages, tumor types, and treatment regimens can be explored in detail.
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Affiliation(s)
- Minxing Chen
- Shanghai Health Development Research Center, Shanghai Medical Information Center, Shanghai, China
| | - Ruijia Li
- Shanghai Health Development Research Center, Shanghai Medical Information Center, Shanghai, China
| | - Gang Ding
- Oncology Department, Shanghai International Medical Center, Shanghai, China
| | - Chunlin Jin
- Shanghai Health Development Research Center, Shanghai Medical Information Center, Shanghai, China
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