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Ghosh S, Bhattacharya S, Mukherjee S, Chakravarty S. Promote to protect: data-driven computational model of peer influence for vaccine perception. Sci Rep 2024; 14:306. [PMID: 38172556 PMCID: PMC10764860 DOI: 10.1038/s41598-023-50756-3] [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: 01/11/2023] [Accepted: 12/24/2023] [Indexed: 01/05/2024] Open
Abstract
Vaccine hesitancy and acceptance, driven by social influence, is usually explored by most researchers using exhaustive survey-based studies, which investigate public preferences, fundamental values, beliefs, barriers, and drivers through closed or open-ended questionnaires. Commonly used simple statistical tools do not do justice to the richness of this data. Considering the gradual development of vaccine acceptance in a society driven by multiple local/global factors as a compartmental contagion process, we propose a novel methodology where drivers and barriers of these dynamics are detected from survey participants' responses, instead of heuristic arguments. Applying rigorous natural language processing analysis to the survey responses of participants from India, who are from various socio-demographics, education, and perceptions, we identify and categorize the most important factors as well as interactions among people of different perspectives on COVID-19 vaccines. With a goal to achieve improvement in vaccine perception, we also analyze the resultant behavioral transitions through platforms of unsupervised machine learning and natural language processing to derive a compartmental contagion model from the data. Analysis of the model shows that positive peer influence plays a very important role and causes a bifurcation in the system that reflects threshold-sensitive dynamics.
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Affiliation(s)
| | | | - Shagata Mukherjee
- Centre for Social and Behaviour Change, Ashoka University, Delhi, India
- Behavioural Insights Unit of India, NITI Aayog, New Delhi, India
| | - Sujoy Chakravarty
- School of Social Sciences, Jawaharlal Nehru University, New Delhi, India
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2
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Wolszczak-Biedrzycka B, Bieńkowska A, Cieślikiewicz B, Smolińska-Fijołek E, Biedrzycki G, Dorf J. The effect of the third dose of the BNT162b2 vaccine on anti-SARS-CoV-2 spike antibody levels in healthcare workers with and without COVID-19 infection. Ann Med 2023; 55:722-732. [PMID: 36820816 PMCID: PMC9970245 DOI: 10.1080/07853890.2023.2182907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/18/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
AIM A third (booster) dose of the anti-SARS-CoV-2 vaccine became necessary due to the observed decrease in anti-SARS-CoV-2S antibody levels over time, new mutations, and low global vaccination rates. In this study, anti-SARS-CoV-2S antibody levels were measured (ECLIA assay) in 50 healthcare workers with and without a history of COVID-19 infection to determine the humoral immune response to the third dose of the BNT162b2 vaccine. METHODS Antibody levels were determined in the blood serum, and blood was sampled for analysis 20-40 days after the administration of the booster dose. RESULTS A greater increase in anti-SARS-CoV-2S antibody titers was noted in persons without a history of infection, but antibody levels continued to be higher in previously infected individuals when the results were adjusted for age, gender, BMI, type of work, and presence of comorbidities. CONCLUSION The results of this study can be used to improve the vaccination strategy for the general population.KEY MESSAGESThree doses of the vaccine BNT162b2 strongly stimulate the immune system to produce anti-SARS-CoV-2s antibodies, especially in people with a previous infection COVID-19.Age, gender, and BMI may be associated with different humoral immune response to the BNT162b2 vaccine.
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Affiliation(s)
- Blanka Wolszczak-Biedrzycka
- Department of Psychology and Sociology of Health and Public Health, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- The Oncology Center of the Region of Warmia and Mazury in Olsztyn, Hospital of the Ministry of the Interior and Administration, Olsztyn, Poland
| | - Anna Bieńkowska
- Department of Psychology and Sociology of Health and Public Health, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- The Oncology Center of the Region of Warmia and Mazury in Olsztyn, Hospital of the Ministry of the Interior and Administration, Olsztyn, Poland
| | - Beata Cieślikiewicz
- Department of Psychology and Sociology of Health and Public Health, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | | | - Grzegorz Biedrzycki
- Hospital Dispensary, Regional Specialist Hospital in Olsztyn, Olsztyn, Poland
| | - Justyna Dorf
- Department of Clinical Laboratory Diagnostics, Medical University of Białystok, Bialystok, Poland
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3
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Palalay H, Vyas R, Tafuto B. Real-world effectiveness of mRNA COVID-19 vaccines in the elderly during the Delta and Omicron variants: Systematic review. World J Meta-Anal 2023; 11:167-180. [PMID: 37575964 PMCID: PMC10421623 DOI: 10.13105/wjma.v11.i5.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/09/2023] [Accepted: 04/18/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND As of 31 December 2022, there were over 6.6 million coronavirus disease 2019 (COVID-19) deaths and over 651 million cases across 200 countries worldwide. Despite the increase in vaccinations and booster shots, COVID-19 cases and deaths continue to remain high. While the effectiveness of these vaccines has already been established by different manufacturers, the fact remains that these vaccines were created quickly for global emergency use, tested under controlled clinical conditions from voluntary subjects and age groups whose general characteristics may differ from the actual general population. AIM To conduct a systematic review to determine the real-world effectiveness of mRNA COVID-19 vaccines in the elderly during the predominance of Delta and Omicron variants in preventing COVID-19 related infection, hospital, intensive care unit (ICU) admission and intubation, and death. METHODS A combination of Medical Subject Headings and non-Medical Subject Headings was carried out to identify all relevant research articles that meets the inclusion and exclusion criteria from PubMed, Cochrane, CINAHL, Scopus, ProQuest, Embase, Web of Science, and Google Scholar databases, as well as qualified research studies from pre-print servers using medRxiv and Research Square, published from January 1, 2021 - December 31, 2022. RESULTS As per the inclusion and exclusion criteria, the effectiveness of Pfizer-BioNTech and Moderna vaccines were evaluated from an estimated total study population of 26,535,692 using infection, hospital, ICU admission and intubation, and death as outcome measures from studies published between 2021 and 2022, conducted in New York, Finland, Canada, Costa Rica, Qatar, Greece, and Brazil. The risk of bias was evaluated using risk of bias in nonrandomized studies of interventions (ROBINS-I) tool for cohort, case-control, and cross-sectional studies. While clinical trial data on Pfizer-BioNTech and Moderna vaccines demonstrated 94% vaccine effectiveness in the elderly, the results in this study showed that vaccine effectiveness in real-world settings is marginally lower against infection (40%-89%), hospitalization (92%), ICU admission and intubation (98%-85%), and death (77%-87%) with an indication of diminished effectiveness of vaccine over time. Furthermore, 2 doses of mRNA vaccines are inadequate and only provides interim protection. CONCLUSION Because of the natural diminishing effectiveness of the vaccine, the need for booster dose to restore its efficacy is vital. From a research perspective, the use of highly heterogeneous outcome measures inhibits the comparison, contrast, and integration of the results which makes data pooling across different studies problematic. While pharmaceutical intervention like vaccination is important to fight an epidemic, utilizing common outcome measurements or carrying out studies with minimal heterogeneity in outcome measurements, is equally crucial to better understand and respond to an international health crisis.
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Affiliation(s)
- Harvey Palalay
- Department of Health Informatics, Rutgers University, Piscataway, NJ 08854, United States
| | - Riddhi Vyas
- Department of Health Informatics, Rutgers University, Piscataway, NJ 08854, United States
| | - Barbara Tafuto
- Department of Health Informatics, Rutgers University, Piscataway, NJ 08854, United States
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Al-Hatamleh MA, Abusalah MA, Hatmal MM, Alshaer W, Ahmad S, Mohd-Zahid MH, Rahman ENSE, Yean CY, Alias IZ, Uskoković V, Mohamud R. Understanding the challenges to COVID-19 vaccines and treatment options, herd immunity and probability of reinfection. J Taibah Univ Med Sci 2023; 18:600-638. [PMID: 36570799 PMCID: PMC9758618 DOI: 10.1016/j.jtumed.2022.11.007] [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: 08/20/2022] [Revised: 10/29/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Unlike pandemics in the past, the outbreak of coronavirus disease 2019 (COVID-19), which rapidly spread worldwide, was met with a different approach to control and measures implemented across affected countries. The lack of understanding of the fundamental nature of the outbreak continues to make COVID-19 challenging to manage for both healthcare practitioners and the scientific community. Challenges to vaccine development and evaluation, current therapeutic options, convalescent plasma therapy, herd immunity, and the emergence of reinfection and new variants remain the major obstacles to combating COVID-19. This review discusses these challenges in the management of COVID-19 at length and highlights the mechanisms needed to provide better understanding of this pandemic.
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Affiliation(s)
- Mohammad A.I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Mai A. Abusalah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Ma'mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa, Jordan
| | - Walhan Alshaer
- Cell Therapy Center (CTC), The University of Jordan, Amman, Jordan
| | - Suhana Ahmad
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Manali H. Mohd-Zahid
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Engku Nur Syafirah E.A. Rahman
- Department of Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Chan Y. Yean
- Department of Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Iskandar Z. Alias
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | | | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
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Bijukchhe SM, O'Reilly PJ, Theiss-Nyland K, Gurung M, Pokhrel B, Kelly S, Acharya S, Maharjan S, Shrestha A, Pandey B, Lama M, Shrestha I, Voysey M, Eordogh A, Shrestha S, Feng ES, Li G, Shah G, Pollard AJ, Shrestha S. COVID-19 vaccine effectiveness and variants in Nepal: study protocol for a test-negative case-control study with SARS-CoV-2 genetic sequencing. BMJ Open 2023; 13:e068334. [PMID: 37072367 PMCID: PMC10123857 DOI: 10.1136/bmjopen-2022-068334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
INTRODUCTION Inactivated, viral vector and mRNA vaccines have been used in the Nepali COVID-19 vaccination programme but there is little evidence on the effectiveness of these vaccines in this setting. The aim of this study is to describe COVID-19 vaccine effectiveness in Nepal and provide information on infections with SARS-CoV-2 variants. METHODS AND ANALYSIS This is a hospital-based, prospective test-negative case-control study conducted at Patan Hospital, Kathmandu. All patients >18 years of age presenting to Patan Hospital with COVID-19-like symptoms who have received a COVID-19 antigen/PCR test are eligible for inclusion. The primary outcome is vaccine effectiveness of licensed COVID-19 vaccines against laboratory-confirmed COVID-19 disease.After enrolment, information will be collected on vaccine status, date of vaccination, type of vaccine, demographics and other medical comorbidities. The primary outcome of interest is laboratory-confirmed SARS-CoV-2 infection. Cases (positive for SARS-CoV-2) and controls (negative for SARS-CoV-2) will be enrolled in a 1:4 ratio. Vaccine effectiveness against COVID-19 disease will be analysed by comparing vaccination status with SARS-CoV-2 test results.Positive SARS-CoV-2 samples will be sequenced to identify circulating variants and estimate vaccine effectiveness against common variants.Measuring vaccine effectiveness and identifying SARS-CoV-2 variants in Nepal will help to inform public health efforts. Describing disease severity in relation to specific SARS-CoV-2 variants and vaccine status will also inform future prevention and care efforts. ETHICS AND DISSEMINATION Ethical approval was obtained from the University of Oxford Tropical Ethics Committee (OxTREC) (ref: 561-21) and the Patan Academy of Health Sciences Institutional Review Board (ref: drs2111121578). The protocol and supporting study documents were approved for use by the Nepal Health Research Council (NHRC 550-2021). Results will be disseminated in peer-reviewed journals and to the public health authorities in Nepal.
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Affiliation(s)
- Sanjeev M Bijukchhe
- Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | | | | | - Meeru Gurung
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | - Bhishma Pokhrel
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | - Sarah Kelly
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Samita Acharya
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | | | - Ashis Shrestha
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | - Bimal Pandey
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | - Mipsang Lama
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | - Ira Shrestha
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | - Merryn Voysey
- Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Agnes Eordogh
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sonu Shrestha
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Grace Li
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Ganesh Shah
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
| | - Andrew J Pollard
- Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Shrijana Shrestha
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Nepal
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Cheng S, Pain CC, Guo YK, Arcucci R. Real-time updating of dynamic social networks for COVID-19 vaccination strategies. JOURNAL OF AMBIENT INTELLIGENCE AND HUMANIZED COMPUTING 2023:1-14. [PMID: 37360777 PMCID: PMC10062280 DOI: 10.1007/s12652-023-04589-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/05/2023] [Indexed: 06/28/2023]
Abstract
Vaccination strategy is crucial in fighting the COVID-19 pandemic. Since the supply is still limited in many countries, contact network-based interventions can be most powerful to set an efficient strategy by identifying high-risk individuals or communities. However, due to the high dimension, only partial and noisy network information can be available in practice, especially for dynamic systems where contact networks are highly time-variant. Furthermore, the numerous mutations of SARS-CoV-2 have a significant impact on the infectious probability, requiring real-time network updating algorithms. In this study, we propose a sequential network updating approach based on data assimilation techniques to combine different sources of temporal information. We then prioritise the individuals with high-degree or high-centrality, obtained from assimilated networks, for vaccination. The assimilation-based approach is compared with the standard method (based on partially observed networks) and a random selection strategy in terms of vaccination effectiveness in a SIR model. The numerical comparison is first carried out using real-world face-to-face dynamic networks collected in a high school, followed by sequential multi-layer networks generated relying on the Barabasi-Albert model emulating large-scale social networks with several communities.
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Affiliation(s)
- Sibo Cheng
- Data Science Instituite, Department of Computing, Imperial College London, London, UK
| | - Christopher C. Pain
- Department of Earth Science and Engineering, Imperial College London, London, UK
| | - Yi-Ke Guo
- Data Science Instituite, Department of Computing, Imperial College London, London, UK
| | - Rossella Arcucci
- Data Science Instituite, Department of Computing, Imperial College London, London, UK
- Department of Earth Science and Engineering, Imperial College London, London, UK
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Xue Y, Chen D, Smith SR, Ruan X, Tang S. Coupling the Within-Host Process and Between-Host Transmission of COVID-19 Suggests Vaccination and School Closures are Critical. Bull Math Biol 2023; 85:6. [PMID: 36536179 PMCID: PMC9762651 DOI: 10.1007/s11538-022-01104-5] [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: 05/31/2021] [Accepted: 11/02/2022] [Indexed: 12/23/2022]
Abstract
Most models of COVID-19 are implemented at a single micro or macro scale, ignoring the interplay between immune response, viral dynamics, individual infectiousness and epidemiological contact networks. Here we develop a data-driven model linking the within-host viral dynamics to the between-host transmission dynamics on a multilayer contact network to investigate the potential factors driving transmission dynamics and to inform how school closures and antiviral treatment can influence the epidemic. Using multi-source data, we initially determine the viral dynamics and estimate the relationship between viral load and infectiousness. Then, we embed the viral dynamics model into a four-layer contact network and formulate an agent-based model to simulate between-host transmission. The results illustrate that the heterogeneity of immune response between children and adults and between vaccinated and unvaccinated infections can produce different transmission patterns. We find that school closures play a significant effect on mitigating the pandemic as more adults get vaccinated and the virus mutates. If enough infected individuals are diagnosed by testing before symptom onset and then treated quickly, the transmission can be effectively curbed. Our multiscale model reveals the critical role played by younger individuals and antiviral treatment with testing in controlling the epidemic.
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Affiliation(s)
- Yuyi Xue
- grid.43169.390000 0001 0599 1243School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an, 710049 People’s Republic of China
| | - Daipeng Chen
- grid.43169.390000 0001 0599 1243School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an, 710049 People’s Republic of China ,grid.5132.50000 0001 2312 1970Mathematical Institute, Leiden University, Leiden, The Netherlands
| | - Stacey R. Smith
- grid.28046.380000 0001 2182 2255The Department of Mathematics and Faculty of Medicine, The University of Ottawa, Ottawa, Canada
| | - Xiaoe Ruan
- grid.43169.390000 0001 0599 1243School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an, 710049 People’s Republic of China
| | - Sanyi Tang
- School of Mathematics and Statistics, Shaanxi Normal university, Xi'an, 710062, People's Republic of China.
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Karimi S, Nazarian S, Sotoodehnejadnematalahi F, Dorostkar R, Amani J. Designing and Expression of Recombinant Chimeric Spike Protein from SARS-CoV-2 in Escherichia coli and Its Immunogenicity Assessment. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2023; 22:e137751. [PMID: 38116554 PMCID: PMC10728857 DOI: 10.5812/ijpr-137751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/17/2023] [Accepted: 08/09/2023] [Indexed: 12/21/2023]
Abstract
Since December 2019, the world has been grappling with an ongoing global COVID-19 pandemic. Various virus variants have emerged over the past two years, each posing a greater threat than its predecessors. The recent appearance of the omicron variant (B.1.1.529) has raised significant alarm within the field of epidemiology due to its highly contagious nature and rapid transmission rate. The omicron variant possessed mutations in the key receptor-binding domain (RBD) region, the S region, and these modifications have shown a notable impact on the strain's susceptibility to neutralizing antibodies. Developing safe and efficient vaccines to prevent a future severe acute respiratory outbreak of coronavirus syndrome 2 (SARS-CoV-2) is significant. Viral surface spike proteins are ideal targets for vaccines. This study aimed to find a multi-subunit chimeric vaccine. After conducting bioinformatics analysis, the recombinant spike (RS) protein of SARS-CoV-2 was deliberately designed and subsequently produced using E. coli expression systems. The immunogenicity of RS and neutralizing antibody responses were evaluated on immunized BALB/c mice. There was a significant difference in antibody titers between RS-immunized mice and control groups. The endpoint of the serum antibody titer of mice immunized with our chimeric protein was 2.5 times higher than that of the negative control. The chimeric construct could present multiple antigens simultaneously, influentially affecting immunization. Sera from mice vaccinated by RS could recognize the SARS-CoV-2 virus and neutralize antibodies. Our chimeric peptide could bind to antibodies in the serum of patients infected with different serotypes of the SARS-CoV-2 virus, such as alpha, delta, and omicron variants. The results indicated that the RS protein would be a potential novel antigenic candidate for subunit vaccine development and could be used as a useful alternative to generate diagnostic serological tests for SARS-CoV-2 infection.
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Affiliation(s)
- Sahar Karimi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | | | - Roohollah Dorostkar
- Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Chen BL, Yuan B, Jiang WX, Yu YT, Ji M. Research on epidemic spread model based on cold chain input. Soft comput 2023; 27:2251-2268. [PMID: 36694866 PMCID: PMC9851120 DOI: 10.1007/s00500-023-07823-8] [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: 01/05/2023] [Indexed: 01/20/2023]
Abstract
In recent years, the new type of coronary pneumonia (COVID-19) has become a highly contagious disease worldwide, posing a serious threat to the public health. This paper is based on the SEIR model of the new coronavirus pneumonia, considering the impact of cold chain input and re-positive on the spread of the virus in the COVID-19. In the process of model design, the food cold chain and re-positive are used as parameters, and its stability is analyzed and simulated. The experimental results show that taking into account the cold chain input and re-positive can effectively simulate the spread of the epidemic. The research results have important research value and practical significance for the prevention and control of the COVID-19 and the prediction of important time nodes.
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Affiliation(s)
- Bo-Lun Chen
- Department of Computer Science, Huaiyin Institute of Technology, Huaiyin, 223003 Jiangsu China ,Institute of Informatics, University of Zurich, 8050 Zurich, Switzerland
| | - Ben Yuan
- Department of Computer Science, Huaiyin Institute of Technology, Huaiyin, 223003 Jiangsu China
| | - Win-Xin Jiang
- Department of Computer Science, Huaiyin Institute of Technology, Huaiyin, 223003 Jiangsu China
| | - Yong-Tao Yu
- Department of Computer Science, Huaiyin Institute of Technology, Huaiyin, 223003 Jiangsu China
| | - Min Ji
- Department of Computer Science, Huaiyin Institute of Technology, Huaiyin, 223003 Jiangsu China
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Singh M, Katre R, Aggarwal P, Bahurupi Y, Saxena G, Singh P, Saxena V. COVID-19 Vaccination status among Health care workers diagnosed with COVID-19 in a tertiary care institute of Uttarakhand: A Cross-sectional Study. INDIAN JOURNAL OF COMMUNITY HEALTH 2022. [DOI: 10.47203/ijch.2022.v34i04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Background: Vaccines are considered as the one of the main pillars in halting and ending the presently on-going coronavirus disease (COVID-19 disease) pandemic which has spread globally since it was first detected in Wuhan, China in December 2019. In the absence of specific therapy, infection prevention practices and mass vaccination remains the mainstay in controlling the disease. Objectives: Objective of the study was to assess COVID-19 vaccination status, socio-demographic and clinical profile among healthcare workers diagnosed with COVID-19. Methodology: A cross-sectional survey from 1st March 2021 to 30th June 2021 among healthcare workers who were diagnosed with COVID-19 in a tertiary care institute of Uttarakhand, India was conducted, and universal sampling was used. Institutional Ethics Committee approved this study. Results: Total 662 healthcare workers were diagnosed with COVID-19. 429 (64.8%) of these COVID-19 diagnosed healthcare workers had received either single (129,30%) or both dose (300,70%) of COVID-19 vaccine while remaining 233 (35.2%) belonged to non-vaccinated group. History of exposure to COVID-19 positive patients was higher in vaccinated (66.4%) than in non-vaccinated group (55%) (p = 0.004). Hospitalisation was found to be higher among non-vaccinated (5.6%) than vaccinated group (2.3%) (p = 0.029). Conclusions: This study concludes that being vaccinated against COVID-19 disease provides protection against severe infection and reduces the need for hospitalization.
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11
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Nowroozi A, Rezaei N. Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) delta variant of concern breakthrough infections: Are vaccines failing us? Infect Control Hosp Epidemiol 2022; 43:1754-1755. [PMID: 34353385 PMCID: PMC8387681 DOI: 10.1017/ice.2021.363] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Ali Nowroozi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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12
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Dimeglio C, Herin F, Da-Silva I, Gernigon C, Porcheron M, Chapuy-Regaud S, Izopet J. Decreased Efficiency of Neutralizing Antibodies from Previously Infected or Vaccinated Individuals against the B.1.617.2 (Delta) SARS-CoV-2 Variant. Microbiol Spectr 2022; 10:e0270621. [PMID: 35867411 PMCID: PMC9430143 DOI: 10.1128/spectrum.02706-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/16/2022] [Indexed: 12/13/2022] Open
Abstract
The neutralizing antibody response is a key component of adaptive immunity and a primary protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The increased transmissibility of the SARS-CoV-2 Delta variant and its capacity to cause more severe disease could be linked to a significant reduction in neutralizing antibodies generated during a previous infection or vaccination. We analyzed blood samples from 162 unvaccinated health care workers (HCWs) collected 1 to 3 months postinfection and from 263 vaccinated health care workers 1 month after the last injection. We have compared the neutralizing antibody titers obtained using two virus strains, B.1.160 and B.1.617.2 (Delta variant). Binding antibody concentrations were measured by an immunoassay. The median neutralizing antibody titer against the B.1.160 strain was 128 (interquartile range [IQR], 16 to 256) and 32 (IQR, 8 to 128) against the Delta variant. To obtain a neutralizing antibody titer of 32 or 64, a binding antibody concentration of 182 binding antibody units (BAU)/mL (IQR, 81 to 974) was required with the strain B.1.160, while a concentration of 2,595 BAU/mL (IQR, 1,176 to 5,353) was required with the Delta variant. Our data indicate that antibodies neutralize the SARS-CoV-2 Delta variant 4 times less efficiently than they neutralize an earlier strain. Half of the HCWs had decreased protection from 94% to 76.8% or less for the same total antibody concentration. But neutralization might be correlated with other immune responses. The contributions of other responses, such as those of the T cell and B cell systems, to protection require further investigation. IMPORTANCE Recent studies showed that the neutralizing antibody titer is an important contributor to protection against SARS-CoV-2. With the emergence of new variants, the question arises of maintaining the neutralizing capacities of vaccines and/or of a past infection. We had protective data associated with total antibody concentrations and neutralizing antibody titers for a B.1.160 strain. We showed that to maintain the same levels of protection and, therefore, the same levels of neutralizing antibodies, a total antibody concentration 8.5 times greater is required with the Delta strain. (This study has been registered at ClinicalTrials.gov under registration no. NCT04385108.).
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Affiliation(s)
- Chloé Dimeglio
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, Toulouse, France
- INSERM UMR1291 – CNRS UMR5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Fabrice Herin
- Occupational Diseases Department, Toulouse University Hospital, Toulouse, France
- UMR1295, unité mixte INSERM - Université Toulouse III Paul Sabatier, Centre for Epidemiology and Research in Population Health Unit (CERPOP), Toulouse, France
| | | | - Caroline Gernigon
- Occupational Diseases Department, Toulouse University Hospital, Toulouse, France
- UMR1295, unité mixte INSERM - Université Toulouse III Paul Sabatier, Centre for Epidemiology and Research in Population Health Unit (CERPOP), Toulouse, France
| | - Marion Porcheron
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, Toulouse, France
| | - Sabine Chapuy-Regaud
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, Toulouse, France
- INSERM UMR1291 – CNRS UMR5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, Toulouse, France
- INSERM UMR1291 – CNRS UMR5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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13
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Eales O, Page AJ, de Oliveira Martins L, Wang H, Bodinier B, Haw D, Jonnerby J, Atchison C, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Chadeau-Hyam M, Donnelly CA, Elliott P. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infect Dis 2022; 22:647. [PMID: 35896970 PMCID: PMC9326417 DOI: 10.1186/s12879-022-07628-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/04/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. METHODS We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September-27 September 2021) and 15 (19 October-5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. RESULTS We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8-23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. CONCLUSIONS As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.
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Affiliation(s)
- Oliver Eales
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | | | | | - Haowei Wang
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Barbara Bodinier
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - David Haw
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Jakob Jonnerby
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Christina Atchison
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Deborah Ashby
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Taylor
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Helen Ward
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Ara Darzi
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Institute of Global Health Innovation, Imperial College London, London, UK
| | - Steven Riley
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Marc Chadeau-Hyam
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Christl A Donnelly
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK.
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK.
- Department of Statistics, University of Oxford, Oxford, UK.
| | - Paul Elliott
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK.
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK.
- Imperial College Healthcare NHS Trust, London, UK.
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK.
- Health Data Research (HDR) UK, Imperial College London, London, UK.
- UK Dementia Research Institute Centre at Imperial, Imperial College London, London, UK.
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14
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Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview. J Diabetes Metab Disord 2022; 21:1763-1783. [PMID: 35891981 PMCID: PMC9305048 DOI: 10.1007/s40200-022-01002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 12/02/2022]
Abstract
With the unexpected emergence of the novel 2019 Wuhan coronavirus, the world was faced with a sudden uproar that quickly shifted into a serious life-threatening pandemic. Affecting the lives of the global population and leaving drastic damage in various sections and systems, several measures have been constantly taken to tackle down this crisis. For instance, numerous vaccines have been developed in the past two years, some of which have been granted emergency use, thus providing sufficient immunity to the vaccinated individuals. However, the appearance of newly emerged SARS-CoV-2 variants with accelerated transmission and fatality has led the world towards another pandemic. Having undergone various mutations in genomic and/or amino acid profiles, some of the emerged variants of concern (VOCs) including Alpha, Beta, Gamma, and Delta have displayed immune evasion and pathogenicity even in the vaccinated population, hence raising concerns regarding the efficacy of current vaccines against new VOCs of COVID-19. Therefore, genomic investigations of SARS-CoV-2 mutations are expected to provide valuable insight into the evolution of SARS-CoV-2, while also determining the impact of different mutations on infection severity. This study was constructed with the aim of shining light on recent advances regarding mutations in major COVID-19 VOCs, as well as vaccination efficacy against those VOCs.
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15
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Williams A, Zhan CG. Fast Prediction of Binding Affinities of SARS-CoV-2 Spike Protein and Its Mutants with Antibodies through Intermolecular Interaction Modeling-Based Machine Learning. J Phys Chem B 2022; 126:5194-5206. [PMID: 35817617 PMCID: PMC9301770 DOI: 10.1021/acs.jpcb.2c02123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Indexed: 11/30/2022]
Abstract
Since the introduction of the novel SARS-CoV-2 virus (COVID-19) in late 2019, various new variants have appeared with mutations that confer resistance to the vaccines and monoclonal antibodies that were developed in response to the wild-type virus. As we continue through the pandemic, an accurate and efficient methodology is needed to help predict the effects certain mutations will have on both our currently produced therapeutics and those that are in development. Using published cryo-electron microscopy and X-ray crystallography structures of the spike receptor binding domain region with currently known antibodies, in the present study, we created and cross-validated an intermolecular interaction modeling-based multi-layer perceptron machine learning approach that can accurately predict the mutation-caused shifts in the binding affinity between the spike protein (wild-type or mutant) and various antibodies. This validated artificial intelligence (AI) model was used to predict the binding affinity (Kd) of reported SARS-CoV-2 antibodies with various variants of concern, including the most recently identified "Deltamicron" (or "Deltacron") variant. This AI model may be employed in the future to predict the Kd of developed novel antibody therapeutics to overcome the challenging antibody resistance issue and develop structural bases for the effects of both current and new mutants of the spike protein. In addition, the similar AI strategy and approach based on modeling of the intermolecular interactions may be useful in development of machine learning models predicting binding affinities for other protein-protein binding systems, including other antibodies binding with their antigens.
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Affiliation(s)
- Alexander
H. Williams
- Molecular
Modeling and Biopharmaceutical Center, University
of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Chang-Guo Zhan
- Molecular
Modeling and Biopharmaceutical Center, University
of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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16
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Upreti S, Samant M. A Review on Immunological Responses to SARS-CoV-2 and Various COVID-19 Vaccine Regimens. Pharm Res 2022; 39:2119-2134. [PMID: 35773445 PMCID: PMC9247891 DOI: 10.1007/s11095-022-03323-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/24/2022] [Indexed: 12/19/2022]
Abstract
The transmission of SARS-CoV-2 has caused serious health crises globally. So far, 7 vaccines that are already being assessed in Phase IV clinical trials are, Comirnaty/ Pfizer; Spikevax/Moderna (m RNA vaccine); Vaxzevria or Covishield; Ad26.COV2.S; Ad5-nCoV (adenoviral vector-based vaccine); CoronaVac and BBIBP-CorV (inactivated virus vaccine). Besides, there are about 280 vaccines that are undergoing preclinical and clinical trials including Sputnik-V, Covaxin or BBV152, and NVX-CoV2373. These vaccines are being studied for their immunological responses and efficiency against COVID-19, and have been reported to demonstrate effective T and B cell responses. However, the long-lasting immunity of these vaccine regimens still needs to be investigated. An in-depth understanding of the vaccine efficacy and immune control mechanism is imperative for the rational purposing and implementation of the vaccines. Hence, in this review, we have comprehensively discussed the immune response induced in COVID-19 patients, as well as in the convalescent individuals to avoid reinfection. Moreover, we have also summarized the immunological responses and prophylactic efficacy of various COVID-19 vaccine regimens. In this context, this review can give insights into the development of effective vaccines against SARS-CoV-2 and its variants in the future.
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Affiliation(s)
- Shobha Upreti
- Cell and Molecular Biology Laboratory, Department Of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India.,Department Of Zoology, Kumaun University, Nainital, Uttarakhand, India
| | - Mukesh Samant
- Cell and Molecular Biology Laboratory, Department Of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India.
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17
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Guo Y, Gao J, Sims OT. Associations between Bonus and Lottery COVID-19 Vaccine Incentive Policies and Increases in COVID-19 Vaccination Rates: A Social Epidemiologic Analysis. Trop Med Infect Dis 2022; 7:118. [PMID: 35878130 PMCID: PMC9320144 DOI: 10.3390/tropicalmed7070118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 01/25/2023] Open
Abstract
The objectives of this longitudinal study were to analyze the impact of COVID-19 vaccine incentive policies (e.g., bonuses and lottery entries) on county-level COVID-19 vaccination rates, and to examine the interactive effects between COVID-19 vaccine incentive policies and socioeconomic factors on COVID-19 vaccination rates. Using publicly available data, county-level COVID-19 vaccination rates and socioeconomic data between January 2021 and July 2021 were extracted and analyzed across counties in the United States (US)-an analysis of 19,992 observations over time. Pooled ordinary least squares (OLS) analysis was employed to longitudinally examine associations with COVID-19 vaccination rates, and four random-effects models were developed to analyze interaction effects. Bonus incentive policies were effective in counties with a high per capita income, high levels of education, and a high percentage of racial minorities, but not in counties with high unemployment. Lottery incentive policies were effective in counties with a high percentage of racial minorities, but not in counties with high per capita income, high levels of education, and high unemployment. County-level socioeconomic factors should be considered ahead of implementing incentive policies, versus a blanket approach, to avoid the unintentional misuse of economic resources for futile COVID-19 vaccination outcomes.
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Affiliation(s)
- Yuqi Guo
- School of Social Work, College of Health and Human Services, University of North Carolina at Charlotte, Charlotte, NC 28262, USA;
- School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28262, USA
| | - Jingjing Gao
- Public Policy Program, University of North Carolina at Charlotte, Charlotte, NC 28262, USA;
| | - Omar T. Sims
- Department of Health Behavior, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35222, USA
- Department of Social Work, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL 35222, USA
- Center for AIDS Research, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35222, USA
- Integrative Center for Aging Research, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35222, USA
- African American Studies, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL 35222, USA
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18
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Hoteit R, Yassine HM. Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences. Vaccines (Basel) 2022; 10:919. [PMID: 35746526 PMCID: PMC9230982 DOI: 10.3390/vaccines10060919] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.
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Affiliation(s)
- Reem Hoteit
- Clinical Research Institute, Faculty of Medicine, American University of Beirut, Beirut 110236, Lebanon;
| | - Hadi M. Yassine
- Biomedical Research Center and College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar
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19
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Brinkac L, Diepold S, Mitchell S, Sarnese S, Kolakowski LF, Nelson WM, Jennings K. SARS-CoV-2 Delta variant isolates from vaccinated individuals. BMC Genomics 2022; 23:417. [PMID: 35658876 PMCID: PMC9166184 DOI: 10.1186/s12864-022-08652-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/18/2022] [Indexed: 12/29/2022] Open
Abstract
Background The SARS-CoV-2 Delta variant was first identified in the U.S. in March 2021 and has rapidly become the predominant lineage across the U.S. due to increased transmissibility, immune evasion and vaccine breakthrough. The aim of this study was to better understand the genetic diversity and the potential impact of mutations observed in SARS-CoV-2 viruses circulating in the U.S. in vaccinated individuals. Results Whole genome sequencing was performed on thirty-four SARS-CoV-2 positive samples using the Oxford Nanopore MinION. Evolutionary genomic analysis revealed two novel mutations, ORF1b:V2354F and a premature stop codon, ORF7a:Q94*, identified in a cluster of SARS-CoV-2 Delta isolates collected from vaccinated individuals in Colorado. The ORF1b:V2354F mutation, corresponding to NSP15:V303F, may induce a conformational change and result in a disruption to a flanking beta-sheet structure. The premature stop codon, ORF7a:Q94*, truncates the transmembrane protein and cytosolic tail used to mediate protein transport. This may affect protein localization to the ER-Golgi. In addition to these novel mutations, the cluster of vaccinated isolates contain an additional mutation in the spike protein, at position 112, compared to the Delta variant defining mutations. This mutation, S112L, exists in isolates previously obtained in the U.S. The S112L mutation substitutes a bulky hydrophobic side chain for a polar side chain, which results in a non-conservative substitution within the protein that may affect antibody-binding affinity. Additionally, the vaccinated cluster of isolates contains non-synonymous mutations within ORF8 and NSPs which further distinguish this cluster from the respective ancestral Delta variant. Conclusions These results show there is an emerging sub-lineage of the ancestral Delta variant circulating in the U.S. As mutations emerge in constellations, those with a potentially beneficial advantage to the virus may continue to circulate while others will cease. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08652-z.
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20
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Chadha J, Khullar L, Mittal N. Facing the wrath of enigmatic mutations: a review on the emergence of severe acute respiratory syndrome coronavirus 2 variants amid coronavirus disease-19 pandemic. Environ Microbiol 2022; 24:2615-2629. [PMID: 34320263 PMCID: PMC8441773 DOI: 10.1111/1462-2920.15687] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging respiratory virus responsible for the ongoing coronavirus disease 19 (COVID-19) pandemic. More than a year into this pandemic, the COVID-19 fatigue is still escalating and takes hold of the entire world population. Driven by the ongoing geographical expansion and upcoming mutations, the COVID-19 pandemic has taken a new shape in the form of emerging SARS-CoV-2 variants. These mutations in the viral spike (S) protein enhance the virulence of SARS-CoV-2 variants by improving viral infectivity, transmissibility and immune evasion abilities. Such variants have resulted in cluster outbreaks and fresh infection waves in various parts of the world with increased disease severity and poor clinical outcomes. Hence, the variants of SARS-CoV-2 pose a threat to human health and public safety. This review enlists the most recent updates regarding the presently characterized variants of SARS-CoV-2 recognized by the global regulatory health authorities (WHO, CDC). Based on the slender literature on SARS-CoV-2 variants, we collate information on the biological implications of these mutations on virus pathology. We also shed light on the efficacy of therapeutics and COVID-19 vaccines against the emerging SARS-CoV-2 variants.
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Affiliation(s)
- Jatin Chadha
- Department of MicrobiologyPanjab UniversityChandigarhIndia
| | | | - Nidhi Mittal
- Molecular Biophysics UnitIndian Institute of Science (IISc)BengaluruIndia
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21
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Williams SV, Whitaker HJ, Mumford L, Callaghan C, Curtis RMK, Stowe J, Kirsebom F, Thomas J, Ushiro-Lumb I, Ravanan R, Lopez-Bernal J. Effectiveness of COVID-19 Vaccines Against Hospitalization and Death With the SARS-CoV-2 Delta Variant in Solid Organ and Islet Transplant Recipients. Transplantation 2022; 106:e310-e311. [PMID: 35283455 PMCID: PMC9128400 DOI: 10.1097/tp.0000000000004104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/25/2022]
Affiliation(s)
| | | | - Lisa Mumford
- National Health Service Blood and Transplant, Stoke Gifford, Bristol, United Kingdom
| | - Chris Callaghan
- National Health Service Blood and Transplant, Stoke Gifford, Bristol, United Kingdom
| | - Rebecca M. K. Curtis
- National Health Service Blood and Transplant, Stoke Gifford, Bristol, United Kingdom
| | - Julia Stowe
- UK Health Security Agency, London, United Kingdom
| | | | - James Thomas
- UK Health Security Agency, London, United Kingdom
| | - Ines Ushiro-Lumb
- National Health Service Blood and Transplant, Stoke Gifford, Bristol, United Kingdom
| | - Rommel Ravanan
- National Health Service Blood and Transplant, Stoke Gifford, Bristol, United Kingdom
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22
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Al-Tawfiq JA, Koritala T, Alhumaid S, Barry M, Alshukairi AN, Temsah MH, Al Mutair A, Rabaan A, Tirupathi R, Gautret P. Implication of the emergence of the delta (B.1.617.2) variants on vaccine effectiveness. Infection 2022; 50:583-596. [PMID: 35113351 PMCID: PMC8811010 DOI: 10.1007/s15010-022-01759-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/15/2022] [Indexed: 12/14/2022]
Abstract
INTRODUCTION COVID-19 vaccines have been developed to compact the current SARS-CoV-2 pandemic and have been administered to people all over the world. These vaccines have been quite effective in reducing the possibility of severe illness, hospitalization and death. However, the recent emergence of Variants of Concern specifically the delta variant, B.1.617.2, had resulted in additional waves of the pandemic. METHODS We aim to review the literature to understand the transmission and disease severity, and determine the efficacy of the current COVID-19 vaccines. We searched Pubmed, Scopus, and Embase till August 4th 2021, and used the search terms "delta variant", "vaccinations"," breakthrough infections", and "neutralizing antibody". For the meta-analysis, 21 studies were screened in particular and five articles (148,071 cases) were included in the study, and only four were analyzed in the meta-analysis. RESULTS In this review, both in vitro and in vivo studies showed significant reductions in neutralization rates against delta variants for vaccinated individuals and convalescent patients with prior history of COVID-19. However, There was a lower incidence of infection with SARS-CoV-2 due to Delta variant was found after the second dose of Pfizer-BioNTech, Oxford-AstraZeneca and Moderna vaccines. CONCLUSION In fully vaccinated individuals, symptomatic infection with the delta variant was significantly reduced, and therefore, vaccinations play an important role to assist the fight against delta variant.
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Affiliation(s)
- Jaffar A Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Dhahran Health Center, Johns Hopkins Aramco Healthcare, Rm A-420, Building 61, P.O. Box 76, Dhahran, 31311, Saudi Arabia.
- Infectious Diseases Unit, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
- Infectious Diseases Unit, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Thoyaja Koritala
- Department of Internal Medicine, Mayo Clinic Health System, Mankato, MN, USA
| | - Saad Alhumaid
- Aministration of Pharmaceutical Care, Alahsa Health Cluster, Ministry of Health, Alahsa, Saudi Arabia
| | - Mazin Barry
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, King Saud University and King Saud University Medical City, Riyadh, Saudi Arabia
- Division of Infectious Diseases, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Abeer N Alshukairi
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Mohamad-Hani Temsah
- Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Alahsa, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, Australia
- College of Nursing, Princess Norah Bint Abdul Rahman University, Riyadh, Saudi Arabia
| | - Ali Rabaan
- Molecular Diagnostics Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Raghavendra Tirupathi
- Department of Medicine Keystone Health, Penn State University School of Medicine, Hershey, PA, USA
- Department of Medicine Wellspan Chambersburg and Waynesboro Hospitals, Penn State, Chambersburg, PA, USA
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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23
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Berning P, Huang L, Razavi AC, Boakye E, Osuji N, Stokes AC, Martin SS, Ayers JW, Blaha MJ, Dzaye O. Association of Online Search Trends With Vaccination in the United States: June 2020 Through May 2021. Front Immunol 2022; 13:884211. [PMID: 35514956 PMCID: PMC9066639 DOI: 10.3389/fimmu.2022.884211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
Abstract
Stagnating COVID-19 vaccination rates and vaccine hesitancy remain a threat to public health. Improved strategies for real-time tracking and estimation of population-level behavior regarding vaccinations are needed. The aim of this study was to evaluate whether online search trends for COIVD-19 and influenza mirror vaccination rates. State-level weekly fraction of online searches for top vaccination-related search terms and CDC vaccination data were obtained from June 1, 2020, to May 31, 2021. Next, trends in online search and vaccination data for COVID-19 and influenza were analyzed for visual and quantitative correlation patterns using Spearman’s rank correlation analysis. Online searches in the US for COVID-19 vaccinations increased 2.71-fold (95% CI: 1.98-3.45) in the 4 weeks after the FDA emergency authorization compared to the precedent 4 weeks. In March-April 2021, US online searches reached a plateau that was followed by a decline of 83.3% (95% CI: 31.2%-135.3%) until May 31, 2021. The timing of peaks in online searches varied across US states. Online searches were strongly correlated with vaccination rates (r=0.71, 95% CI: 0.45 - 0.87), preceding actual reported vaccination rates in 44 of 51 states. Online search trends preceded vaccination trends by a median of 3.0 weeks (95% CI: 2.0-4.0 weeks) across all states. For influenza vaccination searches, seasonal peaks in September-October between 2016-2020 were noted. Influenza search trends highly correlated with the timing of actual vaccinations for the 2019-2020 (r=0.82, 95% CI: 0.64 – 0.93) and 2020-2021 season (r=0.91, 95% CI: 0.78 – 0.97). Search trends and real-world vaccination rates are highly correlated. Temporal alignment and correlation levels were higher for influenza vaccinations; however, only online searches for COVID-19 vaccination preceded vaccination trends. These findings indicate that US online search data can potentially guide public health efforts, including policy changes and identifying geographical areas to expand vaccination campaigns.
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Affiliation(s)
- Philipp Berning
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Hematology and Oncology, University Hospital Muenster, Muenster, Germany
| | - Leu Huang
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Radiology and Neuroradiology, Charité, Berlin, Germany
| | - Alexander C Razavi
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Emory Center for Heart Disease Prevention, Emory University School of Medicine, Atlanta, GA, United States
| | - Ellen Boakye
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ngozi Osuji
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrew C Stokes
- Department of Global Health, Boston University School of Public Health, Boston, MA, United States
| | - Seth S Martin
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - John W Ayers
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, CA, United States
| | - Michael J Blaha
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Omar Dzaye
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Radiology and Neuroradiology, Charité, Berlin, Germany
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24
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Biswas S, Mahmud S, Mita MA, Afrose S, Hasan MR, Paul GK, Shimu MSS, Uddin MS, Zaman S, Park MN, Siyadatpanah A, Obaidullah AJ, Saleh MA, Simal-Gandara J, Kim B. The Emergence of SARS-CoV-2 Variants With a Lower Antibody Response: A Genomic and Clinical Perspective. Front Med (Lausanne) 2022; 9:825245. [PMID: 35602477 PMCID: PMC9121733 DOI: 10.3389/fmed.2022.825245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/21/2022] [Indexed: 12/19/2022] Open
Abstract
The emergence of several novel SARS-CoV-2 variants regarded as variants of concern (VOCs) has exacerbated pathogenic and immunologic prominences, as well as reduced diagnostic sensitivity due to phenotype modification-capable mutations. Furthermore, latent and more virulent strains that have arisen as a result of unique mutations with increased evolutionary potential represent a threat to vaccine effectiveness in terms of incoming and existing variants. As a result, resisting natural immunity, which leads to higher reinfection rates, and avoiding vaccination-induced immunization, which leads to a lack of vaccine effectiveness, has become a crucial problem for public health around the world. This study attempts to review the genomic variation and pandemic impact of emerging variations of concern based on clinical characteristics management and immunization effectiveness. The goal of this study is to gain a better understanding of the link between genome level polymorphism, clinical symptom manifestation, and current vaccination in the instance of VOCs.
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Affiliation(s)
- Suvro Biswas
- Miocrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shafi Mahmud
- Miocrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Gobindo Kumar Paul
- Miocrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Md. Salah Uddin
- Miocrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shahriar Zaman
- Miocrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Moon Nyeo Park
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md. Abu Saleh
- Miocrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, University of Vigo, Ourense, Spain
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
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25
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McLean G, Kamil J, Lee B, Moore P, Schulz TF, Muik A, Sahin U, Türeci Ö, Pather S. The Impact of Evolving SARS-CoV-2 Mutations and Variants on COVID-19 Vaccines. mBio 2022; 13:e0297921. [PMID: 35352979 PMCID: PMC9040821 DOI: 10.1128/mbio.02979-21] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/26/2022] Open
Abstract
The emergence of several new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in recent months has raised concerns around the potential impact on ongoing vaccination programs. Data from clinical trials and real-world evidence suggest that current vaccines remain highly effective against the alpha variant (B.1.1.7), while some vaccines have reduced efficacy and effectiveness against symptomatic disease caused by the beta variant (B.1.351) and the delta variant (B.1.617.2); however, effectiveness against severe disease and hospitalization caused by delta remains high. Although data on the effectiveness of the primary regimen against omicron (B.1.1.529) are limited, booster programs using mRNA vaccines have been shown to restore protection against infection and symptomatic disease (regardless of the vaccine used for the primary regimen) and maintain high effectiveness against hospitalization. However, effectiveness against infection and symptomatic disease wanes with time after the booster dose. Studies have demonstrated reductions of varying magnitude in neutralizing activity of vaccine-elicited antibodies against a range of SARS-CoV-2 variants, with the omicron variant in particular exhibiting partial immune escape. However, evidence suggests that T-cell responses are preserved across vaccine platforms, regardless of variant of concern. Nevertheless, various mitigation strategies are under investigation to address the potential for reduced efficacy or effectiveness against current and future SARS-CoV-2 variants, including modification of vaccines for certain variants (including omicron), multivalent vaccine formulations, and different delivery mechanisms.
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Affiliation(s)
- Gary McLean
- School of Human Sciences, London Metropolitan University and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jeremy Kamil
- Louisiana State University Health, Shreveport, Louisiana, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Penny Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, The University of the Witwatersrand, Johannesburg, South Africa
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
- German Centre for Infection Research, Hannover-Braunschweig Site, Germany
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26
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Jaiswal V, Lee HJ. Conservation and Evolution of Antigenic Determinants of SARS-CoV-2: An Insight for Immune Escape and Vaccine Design. Front Immunol 2022; 13:832106. [PMID: 35444664 PMCID: PMC9014086 DOI: 10.3389/fimmu.2022.832106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 11/20/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is the most devastating pandemic of the century, which is still far from over. The remarkable success of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines is the working hope, but the evolving variants are the huge concern that can turn the tide. Potential immune escape mutations (PIEMs) in the past and circulating variants were not studied at large scale (all available data). Hence, the conservation of antigenic determinants (epitopes) was analyzed in all available sequences of SARS-CoV-2 according to time (months), proteins, hosts, and variants. Numerous highly conserved B- and T-cell epitopes were identified in 24 proteins of SARS-CoV-2. A decrease in the conservation of epitopes with time was observed in almost all proteins, which was more rapid in neutralizing epitopes. Delta variant still has the highest PIEM in the circulating strains, which pose threat to the effectiveness of current vaccines. The inclusion of identified, highly conserved, and important epitopes in subunit vaccines can increase vaccine effectiveness against evolving variants. Trends in the conservation of epitopes in different proteins, hosts, and variants with time may also help to inspire the counter measure against the current pandemic.
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Affiliation(s)
- Varun Jaiswal
- Department of Food and Nutrition, College of BioNano Technology, Gachon University, Seongnam-si, South Korea
| | - Hae-Jeung Lee
- Department of Food and Nutrition, College of BioNano Technology, Gachon University, Seongnam-si, South Korea.,Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam-si, South Korea.,Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, South Korea
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27
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de Souza AS, de Freitas Amorim VM, Guardia GDA, dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses 2022; 14:827. [PMID: 35458557 PMCID: PMC9029021 DOI: 10.3390/v14040827] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Vitor Martins de Freitas Amorim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Filipe F. dos Santos
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
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28
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Chia PY, Ong SWX, Chiew CJ, Ang LW, Chavatte JM, Mak TM, Cui L, Kalimuddin S, Chia WN, Tan CW, Chai LYA, Tan SY, Zheng S, Lin RTP, Wang L, Leo YS, Lee VJ, Lye DC, Young BE. Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine breakthrough infections: a multicentre cohort study. Clin Microbiol Infect 2022; 28:612.e1-612.e7. [PMID: 34826623 DOI: 10.1101/2021.1107.1128.21261295v21261291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/16/2021] [Accepted: 11/06/2021] [Indexed: 05/23/2023]
Abstract
OBJECTIVES Highly effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed but variants of concerns are worrisome, especially B.1.617.2 (Delta) which has rapidly spread across the world. We aim to study if vaccination alters virological and serological kinetics in breakthrough infections. METHODS We conducted a multicentre retrospective cohort study of patients in Singapore who had received a licensed mRNA vaccine and been admitted to hospital with B.1.617.2 SARS-CoV-2 infection. We compared clinical features, virological and serological kinetics (anti-nucleocapsid, anti-spike and surrogate virus neutralization titres) between fully vaccinated and unvaccinated individuals. RESULTS Out of 218 individuals with B.1.617.2 infection, 84 received an mRNA vaccine of which 71 were fully vaccinated, 130 were unvaccinated and four received a non-mRNA vaccine. Despite significantly older age in the vaccine breakthrough group, only 2.8% (2/71) developed severe COVID-19 requiring oxygen supplementation compared with 53.1% (69/130) in the unvaccinated group (p < 0.001). Odds of severe COVID-19 following vaccination were significantly lower (adjusted odds ratio 0.07 95% CI 0.015-0.335, p 0.001). PCR cycle threshold values were similar between vaccinated and unvaccinated groups at diagnosis, but viral loads decreased faster in vaccinated individuals. Early, robust boosting of anti-spike protein antibodies was observed in vaccinated patients; however, these titres were significantly lower against B.1.617.2 than the wildtype vaccine strain. DISCUSSION The mRNA vaccines are highly effective at preventing symptomatic and severe COVID-19 associated with B.1.617.2 infection. Vaccination is associated with faster decline in viral RNA load and a robust serological response. Vaccination remains a key strategy for control of the COVID-19 pandemic.
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Affiliation(s)
- Po Ying Chia
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore; Ministry of Health, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore
| | | | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore
| | - Shirin Kalimuddin
- Singapore General Hospital, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore
| | - Wan Ni Chia
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Chee Wah Tan
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Louis Yi Ann Chai
- National University Health System, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | - Linfa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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29
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Chia PY, Ong SWX, Chiew CJ, Ang LW, Chavatte JM, Mak TM, Cui L, Kalimuddin S, Chia WN, Tan CW, Chai LYA, Tan SY, Zheng S, Lin RTP, Wang L, Leo YS, Lee VJ, Lye DC, Young BE. Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine breakthrough infections: a multicentre cohort study. Clin Microbiol Infect 2022. [PMID: 34826623 DOI: 10.1101/2021.07.28.21261295] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
OBJECTIVES Highly effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed but variants of concerns are worrisome, especially B.1.617.2 (Delta) which has rapidly spread across the world. We aim to study if vaccination alters virological and serological kinetics in breakthrough infections. METHODS We conducted a multicentre retrospective cohort study of patients in Singapore who had received a licensed mRNA vaccine and been admitted to hospital with B.1.617.2 SARS-CoV-2 infection. We compared clinical features, virological and serological kinetics (anti-nucleocapsid, anti-spike and surrogate virus neutralization titres) between fully vaccinated and unvaccinated individuals. RESULTS Out of 218 individuals with B.1.617.2 infection, 84 received an mRNA vaccine of which 71 were fully vaccinated, 130 were unvaccinated and four received a non-mRNA vaccine. Despite significantly older age in the vaccine breakthrough group, only 2.8% (2/71) developed severe COVID-19 requiring oxygen supplementation compared with 53.1% (69/130) in the unvaccinated group (p < 0.001). Odds of severe COVID-19 following vaccination were significantly lower (adjusted odds ratio 0.07 95% CI 0.015-0.335, p 0.001). PCR cycle threshold values were similar between vaccinated and unvaccinated groups at diagnosis, but viral loads decreased faster in vaccinated individuals. Early, robust boosting of anti-spike protein antibodies was observed in vaccinated patients; however, these titres were significantly lower against B.1.617.2 than the wildtype vaccine strain. DISCUSSION The mRNA vaccines are highly effective at preventing symptomatic and severe COVID-19 associated with B.1.617.2 infection. Vaccination is associated with faster decline in viral RNA load and a robust serological response. Vaccination remains a key strategy for control of the COVID-19 pandemic.
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Affiliation(s)
- Po Ying Chia
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore; Ministry of Health, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore
| | | | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore
| | - Shirin Kalimuddin
- Singapore General Hospital, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore
| | - Wan Ni Chia
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Chee Wah Tan
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Louis Yi Ann Chai
- National University Health System, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | - Linfa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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30
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Bracis C, Moore M, Swan DA, Matrajt L, Anderson L, Reeves DB, Burns E, Schiffer JT, Dimitrov D. Improving vaccination coverage and offering vaccine to all school-age children allowed uninterrupted in-person schooling in King County, WA: Modeling analysis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:5699-5716. [PMID: 35603374 PMCID: PMC9553324 DOI: 10.3934/mbe.2022266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rapid spread of highly transmissible SARS-CoV-2 variants combined with slowing pace of vaccination in Fall 2021 created uncertainty around the future trajectory of the epidemic in King County, Washington, USA. We analyzed the benefits of offering vaccination to children ages 5-11 and expanding the overall vaccination coverage using mathematical modeling. We adapted a mathematical model of SARS-CoV-2 transmission, calibrated to data from King County, Washington, to simulate scenarios of vaccinating children aged 5-11 with different starting dates and different proportions of physical interactions (PPI) in schools being restored. Dynamic social distancing was implemented in response to changes in weekly hospitalizations. Reduction of hospitalizations and estimated time under additional social distancing measures are reported over the 2021-2022 school year. In the scenario with 85% vaccination coverage of 12+ year-olds, offering early vaccination to children aged 5-11 with 75% PPI was predicted to prevent 756 (median, IQR 301-1434) hospitalizations cutting youth hospitalizations in half compared to no vaccination and largely reducing the need for additional social distancing measures over the school year. If, in addition, 90% overall vaccination coverage was reached, 60% of remaining hospitalizations would be averted and the need for increased social distancing would almost certainly be avoided. Our work suggests that uninterrupted in-person schooling in King County was partly possible because reasonable precaution measures were taken at schools to reduce infectious contacts. Rapid vaccination of all school-aged children provides meaningful reduction of the COVID-19 health burden over this school year but only if implemented early. It remains critical to vaccinate as many people as possible to limit the morbidity and mortality associated with future epidemic waves.
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Affiliation(s)
- Chloe Bracis
- Université Grenoble Alpes, TIMC-IMAG/MAGE, Grenoble 38000, France
| | - Mia Moore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David A. Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Larissa Anderson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dobromir Dimitrov
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
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31
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Cantoni D, Mayora-Neto M, Nadesalingam A, Wells DA, Carnell GW, Ohlendorf L, Ferrari M, Palmer P, Chan ACY, Smith P, Bentley EM, Einhauser S, Wagner R, Page M, Raddi G, Baxendale H, Castillo-Olivares J, Heeney J, Temperton N. Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Front Immunol 2022; 13:773982. [PMID: 35330908 PMCID: PMC8940306 DOI: 10.3389/fimmu.2022.773982] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/07/2022] [Indexed: 01/16/2023] Open
Abstract
The rise of SARS-CoV-2 variants has made the pursuit to define correlates of protection more troublesome, despite the availability of the World Health Organisation (WHO) International Standard for anti-SARS-CoV-2 Immunoglobulin sera, a key reagent used to standardise laboratory findings into an international unitage. Using pseudotyped virus, we examine the capacity of convalescent sera, from a well-defined cohort of healthcare workers (HCW) and Patients infected during the first wave from a national critical care centre in the UK to neutralise B.1.1.298, variants of interest (VOI) B.1.617.1 (Kappa), and four VOCs, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta), including the B.1.617.2 K417N, informally known as Delta Plus. We utilised the WHO International Standard for anti-SARS-CoV-2 Immunoglobulin to report neutralisation antibody levels in International Units per mL. Our data demonstrate a significant reduction in the ability of first wave convalescent sera to neutralise the VOCs. Patients and HCWs with more severe COVID-19 were found to have higher antibody titres and to neutralise the VOCs more effectively than individuals with milder symptoms. Using an estimated threshold for 50% protection, 54 IU/mL, we found most asymptomatic and mild cases did not produce titres above this threshold.
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Affiliation(s)
- Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, United Kingdom
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, United Kingdom
| | - Angalee Nadesalingam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David A Wells
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - George W Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Luis Ohlendorf
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Matteo Ferrari
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Phil Palmer
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew C Y Chan
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Peter Smith
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Emma M Bentley
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Mark Page
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Gianmarco Raddi
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Helen Baxendale
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Javier Castillo-Olivares
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, United Kingdom
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Comparative effectiveness of the BNT162b2 and ChAdOx1 vaccines against Covid-19 in people over 50. Nat Commun 2022; 13:1519. [PMID: 35314696 PMCID: PMC8938429 DOI: 10.1038/s41467-022-29159-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/24/2022] [Indexed: 11/16/2022] Open
Abstract
Although pivotal trials with varying populations and study methods suggest higher efficacy for mRNA than adenoviral Covid-19 vaccines, not many studies have directly compared vaccine effectiveness in the population. Here, we conduct a head-to-head comparison of BNT162b2 versus ChAdOx1 against Covid-19. We analyse 235,181 UK Biobank participants aged 50 years or older and vaccinated with one or two doses of BNT162b2 or ChAdOx1. People are followed from the vaccination date until 18/10/2021. Inverse probability weighting is used to minimise confounding and the Cox models to derive hazard ratio. We find that, compared with one dose of ChAdOx1, vaccination with BNT162b2 is associated with a 28% (95% CI, 12-42) decreased risk of SARS-CoV-2 infection. Also, two doses of BNT162b2 vs ChAdOx1 confers 30% (95% CI, 25-35) and 29% (95% CI, 10-45) lower risks of both infection and hospitalisation during the study period when the Delta variant is dominant. Furthermore, the comparative protection against the infection persists for at least six months among the fully vaccinated, suggesting no differential waning between the two vaccines. These findings can inform evidence-based Covid-19 vaccination campaigns and booster strategies.
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Wu X, Wang Y, Cheng L, Ni F, Zhu L, Ma S, Huang B, Ji M, Hu H, Li Y, Xu S, Shi H, Zhang D, Liu L, Nawaz W, Hu Q, Ye S, Liu Y, Wu Z. Short-Term Instantaneous Prophylaxis and Efficient Treatment Against SARS-CoV-2 in hACE2 Mice Conferred by an Intranasal Nanobody (Nb22). Front Immunol 2022; 13:865401. [PMID: 35371009 PMCID: PMC8967979 DOI: 10.3389/fimmu.2022.865401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 12/30/2022] Open
Abstract
Current COVID-19 vaccines need to take at least one month to complete inoculation and then become effective. Around 51% of the global population is still not fully vaccinated. Instantaneous protection is an unmet need among those who are not fully vaccinated. In addition, breakthrough infections caused by SARS-CoV-2 are widely reported. All these highlight the unmet needing for short-term instantaneous prophylaxis (STIP) in the communities where SARS-CoV-2 is circulating. Previously, we reported nanobodies isolated from an alpaca immunized with the spike protein, exhibiting ultrahigh potency against SARS-CoV-2 and its variants. Herein, we found that Nb22, among our previously reported nanobodies, exhibited ultrapotent neutralization against Delta variant with an IC50 value of 0.41 ng/ml (5.13 pM). Furthermore, the crystal structural analysis revealed that the binding of Nb22 to WH01 and Delta RBDs both effectively blocked the binding of RBD to hACE2. Additionally, intranasal Nb22 exhibited protection against SARS-CoV-2 Delta variant in the post-exposure prophylaxis (PEP) and pre-exposure prophylaxis (PrEP). Of note, intranasal Nb22 also demonstrated high efficacy against SARS-CoV-2 Delta variant in STIP for seven days administered by single dose and exhibited long-lasting retention in the respiratory system for at least one month administered by four doses, providing a strategy of instantaneous short-term prophylaxis against SARS-CoV-2. Thus, ultrahigh potency, long-lasting retention in the respiratory system and stability at room-temperature make the intranasal or inhaled Nb22 to be a potential therapeutic or STIP agent against SARS-CoV-2.
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Affiliation(s)
- Xilin Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
- Department of Antibody, Abrev Biotechnology Co., Ltd., Nanjing, China
| | - Yaxing Wang
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Fengfeng Ni
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Linjing Zhu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
- Department of Antibody, Abrev Biotechnology Co., Ltd., Nanjing, China
| | - Sen Ma
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Bilian Huang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Mengmeng Ji
- School of Life Sciences, Ningxia University, Yinchuan, China
| | - Huimin Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yuncheng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Shijie Xu
- Department of Antibody, Y-clone Medical Science Co. Ltd., Suzhou, China
| | - Haixia Shi
- Department of Antibody, Y-clone Medical Science Co. Ltd., Suzhou, China
| | - Doudou Zhang
- Department of Antibody, Y-clone Medical Science Co. Ltd., Suzhou, China
| | - Linshuo Liu
- Department of Antibody, Y-clone Medical Science Co. Ltd., Suzhou, China
| | - Waqas Nawaz
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Qinxue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
- Life Sciences Institute, Zhejiang University, Zhejiang, China
- *Correspondence: Zhiwei Wu, ; Sheng Ye, ; Yalan Liu,
| | - Yalan Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Zhiwei Wu, ; Sheng Ye, ; Yalan Liu,
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
- School of Life Sciences, Ningxia University, Yinchuan, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China
- *Correspondence: Zhiwei Wu, ; Sheng Ye, ; Yalan Liu,
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Exploring the attitudes, concerns, and knowledge regarding COVID-19 vaccine by the parents of children with rheumatic disease: Cross-sectional online survey. Vaccine 2022; 40:1829-1836. [PMID: 35151508 PMCID: PMC8813553 DOI: 10.1016/j.vaccine.2022.01.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 02/08/2023]
Abstract
Background Vaccination programs are effective strategies in preventing infectious diseases and controlling epidemics. Vaccination against SARS-CoV-2 in children has not yet been approved globally, and it is unclear what attitude families will take when it is approved in children. We aimed to investigate the underlying causes of vaccine acceptance, hesitation, and refusal, as well as concerns about the acceptability of the COVID-19 vaccine by parents of children with rheumatic diseases. Methods Parents of children followed up with a diagnosis of rheumatic disease in the pediatric rheumatology outpatient clinic of a university hospital were included in the study. We applied a closed web-based online survey conducted cross-sectionally and sent to the participants via mobile smartphones. Results For fathers, mothers, and their children, acceptance rates for a COVID-19 vaccine were 64.2%, 57.7%, and 41.8%, respectively. In the multivariate analysis, factors affecting parents' acceptance of vaccines for their children were as follows: “Receiving antirheumatic medications regularly (AOR 5.40, 95% CI 1.10–26.33, p = 0.03), the previous history of getting special recommended vaccines (AOR 4.12, 95% CI 1.12–27.85, p = 0.03), relying on vaccines for ending pandemic (AOR 8.84, 95% CI 2.80–27.85, p = 0.001), complying with the pandemic measures entirely (AOR 5.24, 95% CI 1.46–18.74, p = 0.01)“. The two most common reasons for vaccine rejection were fear of the side effects of the vaccine and its possible interaction with rheumatic drugs used by children. Conclusion According to our survey, parents were more likely to accept a COVID-19 vaccine for themselves than their children. The success of COVID-19 vaccination programs sources highly on people's willingness to accept the vaccine. It is crucial to vaccinate children for achieving herd immunity and in terms of avoiding vaccine hesitancy. Larger data examining the causes of concerns in parents of both healthy children and children with chronic diseases should be delineated.
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35
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Krueger T, Gogolewski K, Bodych M, Gambin A, Giordano G, Cuschieri S, Czypionka T, Perc M, Petelos E, Rosińska M, Szczurek E. Risk assessment of COVID-19 epidemic resurgence in relation to SARS-CoV-2 variants and vaccination passes. COMMUNICATIONS MEDICINE 2022; 2:23. [PMID: 35603303 PMCID: PMC9053266 DOI: 10.1038/s43856-022-00084-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/03/2022] [Indexed: 12/18/2022] Open
Abstract
The introduction of COVID-19 vaccination passes (VPs) by many countries coincided with the Delta variant fast becoming dominant across Europe. A thorough assessment of their impact on epidemic dynamics is still lacking. Here, we propose the VAP-SIRS model that considers possibly lower restrictions for the VP holders than for the rest of the population, imperfect vaccination effectiveness against infection, rates of (re-)vaccination and waning immunity, fraction of never-vaccinated, and the increased transmissibility of the Delta variant. Some predicted epidemic scenarios for realistic parameter values yield new COVID-19 infection waves within two years, and high daily case numbers in the endemic state, even without introducing VPs and granting more freedom to their holders. Still, suitable adaptive policies can avoid unfavorable outcomes. While VP holders could initially be allowed more freedom, the lack of full vaccine effectiveness and increased transmissibility will require accelerated (re-)vaccination, wide-spread immunity surveillance, and/or minimal long-term common restrictions. Assessing the impact of vaccines, other public health measures, and declining immunity on SARS-CoV-2 control is challenging. This is particularly true in the context of vaccination passes, whereby vaccinated individuals have more freedom of making contacts than unvaccinated ones. Here, we use a mathematical model to simulate various scenarios and investigate the likelihood of containing COVID-19 outbreaks in example European countries. We demonstrate that both Alpha and Delta SARS-CoV-2 variants inevitably lead to recurring outbreaks when measures are lifted for vaccination pass holders. High re-vaccination rates and a lowered fraction of the unvaccinated population increase the benefit of vaccination passes. These observations are important for policy making, highlighting the need for continued vigilance, even where the epidemic is under control, especially when new variants of concern emerge. Krueger, Gogolewski, and Bodych et al. assess the risk of COVID-19 epidemic resurgence in relation to SARS-CoV-2 variants and vaccination passes. Their model predicts that new COVID-19 infection waves within two years from the onset of the vaccination program are possible but that suitable adaptive policies can help to avoid unfavorable outcomes.
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36
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Abusalah MAH, Khalifa M, Al-Hatamleh MAI, Jarrar M, Mohamud R, Chan YY. Nucleic Acid-Based COVID-19 Therapy Targeting Cytokine Storms: Strategies to Quell the Storm. J Pers Med 2022; 12:386. [PMID: 35330388 PMCID: PMC8948998 DOI: 10.3390/jpm12030386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has shaken the world and triggered drastic changes in our lifestyle to control it. Despite the non-typical efforts, COVID-19 still thrives and plagues humanity worldwide. The unparalleled degree of infection has been met with an exceptional degree of research to counteract it. Many drugs and therapeutic technologies have been repurposed and discovered, but no groundbreaking antiviral agent has been introduced yet to eradicate COVID-19 and restore normalcy. As lethality is directly correlated with the severity of disease, hospitalized severe cases are of the greatest importance to reduce, especially the cytokine storm phenomenon. This severe inflammatory phenomenon characterized by elevated levels of inflammatory mediators can be targeted to relieve symptoms and save the infected patients. One of the promising therapeutic strategies to combat COVID-19 is nucleic acid-based therapeutic approaches, including microRNAs (miRNAs). This work is an up-to-date review aimed to comprehensively discuss the current nucleic acid-based therapeutics against COVID-19 and their mechanisms of action, taking into consideration the emerging SARS-CoV-2 variants of concern, as well as providing potential future directions. miRNAs can be used to run interference with the expression of viral proteins, while endogenous miRNAs can be targeted as well, offering a versatile platform to control SARS-CoV-2 infection. By targeting these miRNAs, the COVID-19-induced cytokine storm can be suppressed. Therefore, nucleic acid-based therapeutics (miRNAs included) have a latent ability to break the COVID-19 infection in general and quell the cytokine storm in particular.
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Affiliation(s)
- Mai Abdel Haleem Abusalah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia;
| | - Moad Khalifa
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Kelantan, Malaysia;
| | - Mohammad A. I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia; (M.A.I.A.-H.); (R.M.)
| | - Mu’taman Jarrar
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
- Medical Education Department, King Fahd Hospital of the University, Al-Khobar 34445, Saudi Arabia
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia; (M.A.I.A.-H.); (R.M.)
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia;
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Wang Z, Galea ER, Grandison A, Ewer J, Jia F. A coupled Computational Fluid Dynamics and Wells-Riley model to predict COVID-19 infection probability for passengers on long-distance trains. SAFETY SCIENCE 2022; 147:105572. [PMID: 34803226 PMCID: PMC8590932 DOI: 10.1016/j.ssci.2021.105572] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/02/2021] [Accepted: 11/01/2021] [Indexed: 05/15/2023]
Abstract
Coupled Wells-Riley (WR) and Computational Fluid Dynamics (CFD) modelling (WR-CFD) facilitates a detailed analysis of COVID-19 infection probability (IP). This approach overcomes issues associated with the WR 'well-mixed' assumption. The WR-CFD model, which makes uses of a scalar approach to simulate quanta dispersal, is applied to Chinese long-distance trains (G-train). Predicted IPs, at multiple locations, are validated using statistically derived (SD) IPs from reported infections on G-trains. This is the first known attempt to validate a coupled WR-CFD approach using reported COVID-19 infections derived from the rail environment. There is reasonable agreement between trends in predicted and SD IPs, with the maximum SD IP being 10.3% while maximum predicted IP was 14.8%. Additionally, predicted locations of highest and lowest IP, agree with those identified in the statistical analysis. Furthermore, the study demonstrates that the distribution of infectious aerosols is non-uniform and dependent on the nature of the ventilation. This suggests that modelling techniques neglecting these differences are inappropriate for assessing mitigation measures such as physical distancing. A range of mitigation strategies were analysed; the most effective being the majority (90%) of passengers correctly wearing high efficiency masks (e.g. N95). Compared to the base case (40% of passengers wearing low efficiency masks) there was a 95% reduction in average IP. Surprisingly, HEPA filtration was only effective for passengers distant from an index patient, having almost no effect for those in close proximity. Finally, as the approach is based on CFD it can be applied to a range of other indoor environments.
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Affiliation(s)
- Zhaozhi Wang
- Fire Safety Engineering Group, University of Greenwich, Old Royal Naval College, 30 Park Row, Greenwich, London SE10 9LS, UK
| | - Edwin R Galea
- Fire Safety Engineering Group, University of Greenwich, Old Royal Naval College, 30 Park Row, Greenwich, London SE10 9LS, UK
| | - Angus Grandison
- Fire Safety Engineering Group, University of Greenwich, Old Royal Naval College, 30 Park Row, Greenwich, London SE10 9LS, UK
| | - John Ewer
- Fire Safety Engineering Group, University of Greenwich, Old Royal Naval College, 30 Park Row, Greenwich, London SE10 9LS, UK
| | - Fuchen Jia
- Fire Safety Engineering Group, University of Greenwich, Old Royal Naval College, 30 Park Row, Greenwich, London SE10 9LS, UK
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Huang Z, Su Y, Zhang T, Xia N. A review of the safety and efficacy of current COVID-19 vaccines. Front Med 2022; 16:39-55. [PMID: 35122210 PMCID: PMC8815389 DOI: 10.1007/s11684-021-0893-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/24/2021] [Indexed: 01/06/2023]
Abstract
Vaccination is the most effective and feasible way to contain the Coronavirus disease 2019 (COVID-19) pandemic. The rapid development of effective COVID-19 vaccines is an extraordinary achievement. This study reviewed the efficacy/effectiveness, immunogenicity, and safety profile of the 12 most progressed COVID-19 vaccines and discussed the challenges and prospects of the vaccine-based approaches in a global crisis. Overall, most of the current vaccines have shown safety and efficacy/effectiveness during actual clinical trials or in the real-world studies, indicating a development of pandemic control. However, many challenges are faced by pandemic control in terms of maximizing the effect of vaccines, such as rapid vaccine coverage, strategies to address variants with immune escape capability, and surveillance of vaccine safety in the medium- and long-terms.
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Affiliation(s)
- Zehong Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Yingying Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Tianying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, 361102, China.
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Hamady A, Lee J, Loboda ZA. Waning antibody responses in COVID-19: what can we learn from the analysis of other coronaviruses? Infection 2022; 50:11-25. [PMID: 34324165 PMCID: PMC8319587 DOI: 10.1007/s15010-021-01664-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The coronavirus disease 2019 (COVID-19), caused by the novel betacoronavirus severe acute respiratory syndrome 2 (SARS-CoV-2), was declared a pandemic in March 2020. Due to the continuing surge in incidence and mortality globally, determining whether protective, long-term immunity develops after initial infection or vaccination has become critical. METHODS/RESULTS In this narrative review, we evaluate the latest understanding of antibody-mediated immunity to SARS-CoV-2 and to other coronaviruses (SARS-CoV, Middle East respiratory syndrome coronavirus and the four endemic human coronaviruses) in order to predict the consequences of antibody waning on long-term immunity against SARS-CoV-2. We summarise their antibody dynamics, including the potential effects of cross-reactivity and antibody waning on vaccination and other public health strategies. At present, based on our comparison with other coronaviruses we estimate that natural antibody-mediated protection for SARS-CoV-2 is likely to last for 1-2 years and therefore, if vaccine-induced antibodies follow a similar course, booster doses may be required. However, other factors such as memory B- and T-cells and new viral strains will also affect the duration of both natural and vaccine-mediated immunity. CONCLUSION Overall, antibody titres required for protection are yet to be established and inaccuracies of serological methods may be affecting this. We expect that with standardisation of serological testing and studies with longer follow-up, the implications of antibody waning will become clearer.
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Affiliation(s)
- Ali Hamady
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - JinJu Lee
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Zuzanna A Loboda
- Department of Immunology and Inflammation, Imperial College London, London, UK.
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40
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A Continuous Markov-Chain Model for the Simulation of COVID-19 Epidemic Dynamics. BIOLOGY 2022; 11:biology11020190. [PMID: 35205057 PMCID: PMC8869237 DOI: 10.3390/biology11020190] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/23/2022]
Abstract
Simple Summary Predicting the spreading trend of the COVID-19 epidemic is one of the hot topics in the modeling field. In this study, we applied a continuous Markov-chain model to simulate the spread of the COVID-19 epidemic. The results of this study indicate that the herd immunity threshold should be significantly higher than 1 − 1/R0. Taking the immunity waning effect into consideration, the model could predict an epidemic resurgence after the herd immunity threshold. Meanwhile, this Markov-chain approach could also forecast the epidemic distribution and predict the epidemic hotspots at different times. It is implied from our model that it is significantly challenging to eradicate SARS-CoV-2 in the short term. The actual epidemic development is consistent with our prediction. In the end, this method displayed great potential as an alternative approach to traditional compartment models. Abstract To address the urgent need to accurately predict the spreading trend of the COVID-19 epidemic, a continuous Markov-chain model was, for the first time, developed in this work to predict the spread of COVID-19 infection. A probability matrix of infection was first developed in this model based upon the contact frequency of individuals within the population, the individual’s characteristics, and other factors that can effectively reflect the epidemic’s temporal and spatial variation characteristics. The Markov-chain model was then extended to incorporate both the mutation effect of COVID-19 and the decaying effect of antibodies. The developed comprehensive Markov-chain model that integrates the aforementioned factors was finally tested by real data to predict the trend of the COVID-19 epidemic. The result shows that our model can effectively avoid the prediction dilemma that may exist with traditional ordinary differential equations model, such as the susceptible–infectious–recovered (SIR) model. Meanwhile, it can forecast the epidemic distribution and predict the epidemic hotspots geographically at different times. It is also demonstrated in our result that the influence of the population’s spatial and geographic distribution in a herd infection event is needed in the model for a better prediction of the epidemic trend. At the same time, our result indicates that no simple derivative relationship exists between the threshold of herd immunity and the virus basic reproduction number R0. The threshold of herd immunity achieved through natural immunity is significantly higher than 1 − 1/R0. These not only explain the theoretical misconceptions of herd immunity thresholds in herd immunity theory but also provide a guidance for predicting the optimal vaccination coverage. In addition, our model can predict the temporal and spatial distribution of infections in different epidemic waves. It is implied from our model that it is challenging to eradicate COVID-19 in the short term for a large population size and a wide spatial distribution. It is predicted that COVID-19 is likely to coexist with humans for a long time and that it will exhibit multipoint epidemic effects at a later stage. The statistical evidence is consistent with our prediction and strongly supports our modeling results.
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Rahman S, Rahman MM, Miah M, Begum MN, Sarmin M, Mahfuz M, Hossain ME, Rahman MZ, Chisti MJ, Ahmed T, Arifeen SE, Rahman M. COVID-19 reinfections among naturally infected and vaccinated individuals. Sci Rep 2022; 12:1438. [PMID: 35082344 PMCID: PMC8792012 DOI: 10.1038/s41598-022-05325-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/03/2022] [Indexed: 12/17/2022] Open
Abstract
The protection against emerging SARS-CoV-2 variants by pre-existing antibodies elicited due to the current vaccination or natural infection is a global concern. We aimed to investigate the rate of SARS-CoV-2 infection and its clinical features among infection-naïve, infected, vaccinated, and post-infection-vaccinated individuals. A cohort was designed among icddr,b staff registered for COVID-19 testing by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). Reinfection cases were confirmed by whole-genome sequencing. From 19 March 2020 to 31 March 2021, 1644 (mean age, 38.4 years and 57% male) participants were enrolled; where 1080 (65.7%) were tested negative and added to the negative cohort. The positive cohort included 750 positive patients (564 from baseline and 186 from negative cohort follow-up), of whom 27.6% were hospitalized and 2.5% died. Among hospitalized patients, 45.9% had severe to critical disease and 42.5% required oxygen support. Hypertension and diabetes mellitus were found significantly higher among the hospitalised patients compared to out-patients; risk ratio 1.3 and 1.6 respectively. The risk of infection among positive cohort was 80.2% lower than negative cohort (95% CI 72.6-85.7%; p < 0.001). Genome sequences showed that genetically distinct SARS-CoV-2 strains were responsible for reinfections. Naturally infected populations were less likely to be reinfected by SARS-CoV-2 than the infection-naïve and vaccinated individuals. Although, reinfected individuals did not suffer severe disease, a remarkable proportion of naturally infected or vaccinated individuals were (re)-infected by the emerging variants.
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Affiliation(s)
- Sezanur Rahman
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - M Mahfuzur Rahman
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mojnu Miah
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mst Noorjahan Begum
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Monira Sarmin
- Nutrition and Clinical Services Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mustafa Mahfuz
- Nutrition and Clinical Services Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohammad Enayet Hossain
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohammed Ziaur Rahman
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohammod Jobayer Chisti
- Nutrition and Clinical Services Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Shams El Arifeen
- Maternal and Child Health Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh.
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González Viacava MB, Varese A, Mazzitelli I, Lanari L, Ávila L, García Vampa MJ, Geffner J, Cascone O, Dokmetjian JC, de Roodt AR, Fingermann M. Immune Maturation Effects on Viral Neutralization and Avidity of Hyperimmunized Equine Anti-SARS-CoV-2 Sera. Antibodies (Basel) 2022; 11:3. [PMID: 35076465 PMCID: PMC8788445 DOI: 10.3390/antib11010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/19/2021] [Accepted: 09/09/2021] [Indexed: 01/19/2023] Open
Abstract
Mass-vaccination against COVID-19 is still a distant goal for most low-to-middle income countries. The experience gained through decades producing polyclonal immunotherapeutics (such as antivenoms) in many of those countries is being redirected to develop similar products able to neutralize SARS-CoV-2 infection. In this study we analyzed the biological activity (viral neutralization or NtAb) and immunochemical properties of hyperimmune horses' sera (HHS) obtained during initial immunization (I) and posterior re-immunization (R) cycles using the RBD domain of the SARS-CoV-2 spike protein as antigen. HHS at the end of the R cycle showed higher NtAb titers when compared to those after the I cycle (35,585 vs. 7000 mean NtAb, respectively). Moreover, this increase paralleled an increase in avidity (95.2% to 65.2% mean avidity units, respectively). The results presented herein are relevant for manufacturers of these therapeutic tools against COVID-19.
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Affiliation(s)
- Myriam Belén González Viacava
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, Vélez Sársfield 563, Buenos Aires 1282, Argentina; (M.B.G.V.); (L.L.); (L.Á.); (M.J.G.V.); (O.C.); (J.C.D.); (A.R.d.R.)
| | - Augusto Varese
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires (UBA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, 11th Floor, Buenos Aires 1113, Argentina; (A.V.); (I.M.); (J.G.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires 1425, Argentina
| | - Ignacio Mazzitelli
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires (UBA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, 11th Floor, Buenos Aires 1113, Argentina; (A.V.); (I.M.); (J.G.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires 1425, Argentina
| | - Laura Lanari
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, Vélez Sársfield 563, Buenos Aires 1282, Argentina; (M.B.G.V.); (L.L.); (L.Á.); (M.J.G.V.); (O.C.); (J.C.D.); (A.R.d.R.)
| | - Lucía Ávila
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, Vélez Sársfield 563, Buenos Aires 1282, Argentina; (M.B.G.V.); (L.L.); (L.Á.); (M.J.G.V.); (O.C.); (J.C.D.); (A.R.d.R.)
| | - María Julia García Vampa
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, Vélez Sársfield 563, Buenos Aires 1282, Argentina; (M.B.G.V.); (L.L.); (L.Á.); (M.J.G.V.); (O.C.); (J.C.D.); (A.R.d.R.)
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires (UBA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, 11th Floor, Buenos Aires 1113, Argentina; (A.V.); (I.M.); (J.G.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires 1425, Argentina
| | - Osvaldo Cascone
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, Vélez Sársfield 563, Buenos Aires 1282, Argentina; (M.B.G.V.); (L.L.); (L.Á.); (M.J.G.V.); (O.C.); (J.C.D.); (A.R.d.R.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires 1425, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires (UBA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Junín 956, Buenos Aires 1113, Argentina
| | - José Christian Dokmetjian
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, Vélez Sársfield 563, Buenos Aires 1282, Argentina; (M.B.G.V.); (L.L.); (L.Á.); (M.J.G.V.); (O.C.); (J.C.D.); (A.R.d.R.)
| | - Adolfo Rafael de Roodt
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, Vélez Sársfield 563, Buenos Aires 1282, Argentina; (M.B.G.V.); (L.L.); (L.Á.); (M.J.G.V.); (O.C.); (J.C.D.); (A.R.d.R.)
- Cátedra de Toxicología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, Buenos Aires 1113, Argentina
| | - Matías Fingermann
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, Vélez Sársfield 563, Buenos Aires 1282, Argentina; (M.B.G.V.); (L.L.); (L.Á.); (M.J.G.V.); (O.C.); (J.C.D.); (A.R.d.R.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires 1425, Argentina
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Angeli M, Neofotistos G, Mattheakis M, Kaxiras E. Modeling the effect of the vaccination campaign on the COVID-19 pandemic. CHAOS, SOLITONS, AND FRACTALS 2022; 154:111621. [PMID: 34815624 PMCID: PMC8603113 DOI: 10.1016/j.chaos.2021.111621] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 05/31/2023]
Abstract
Population-wide vaccination is critical for containing the SARS-CoV-2 (COVID-19) pandemic when combined with restrictive and prevention measures. In this study we introduce SAIVR, a mathematical model able to forecast the COVID-19 epidemic evolution during the vaccination campaign. SAIVR extends the widely used Susceptible-Infectious-Removed (SIR) model by considering the Asymptomatic (A) and Vaccinated (V) compartments. The model contains several parameters and initial conditions that are estimated by employing a semi-supervised machine learning procedure. After training an unsupervised neural network to solve the SAIVR differential equations, a supervised framework then estimates the optimal conditions and parameters that best fit recent infectious curves of 27 countries. Instructed by these results, we performed an extensive study on the temporal evolution of the pandemic under varying values of roll-out daily rates, vaccine efficacy, and a broad range of societal vaccine hesitancy/denial levels. The concept of herd immunity is questioned by studying future scenarios which involve different vaccination efforts and more infectious COVID-19 variants.
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Affiliation(s)
- Mattia Angeli
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Georgios Neofotistos
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Marios Mattheakis
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Efthimios Kaxiras
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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Heron P, Spanakis P, Crosland S, Johnston G, Newbronner E, Wadman R, Walker L, Gilbody S, Peckham E. Loneliness among people with severe mental illness during the COVID-19 pandemic: Results from a linked UK population cohort study. PLoS One 2022. [PMID: 35025915 DOI: 10.1101/2021.07.14.21260307] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
AIM/GOAL/PURPOSE Population surveys underrepresent people with severe mental ill health. This paper aims to use multiple regression analyses to explore perceived social support, loneliness and factor associations from self-report survey data collected during the Covid-19 pandemic in a sample of individuals with severe mental ill health. DESIGN/METHODOLOGY/APPROACH We sampled an already existing cohort of people with severe mental ill health. Researchers contacted participants by phone or by post to invite them to take part in a survey about how the pandemic restrictions had impacted health, Covid-19 experiences, perceived social support, employment and loneliness. Loneliness was measured by the three item UCLA loneliness scale. FINDINGS In the pandemic sub-cohort, 367 adults with a severe mental ill health diagnosis completed a remote survey. 29-34% of participants reported being lonely. Loneliness was associated with being younger in age (adjusted OR = -.98, p = .02), living alone (adjusted OR = 2.04, p = .01), high levels of social and economic deprivation (adjusted OR = 2.49, p = .04), and lower perceived social support (B = -5.86, p < .001). Living alone was associated with lower perceived social support. Being lonely was associated with a self-reported deterioration in mental health during the pandemic (adjusted OR = 3.46, 95%CI 2.03-5.91). PRACTICAL IMPLICATIONS Intervention strategies to tackle loneliness in the severe mental ill health population are needed. Further research is needed to follow-up the severe mental ill health population after pandemic restrictions are lifted to understand perceived social support and loneliness trends. ORIGINALITY Loneliness was a substantial problem for the severe mental ill health population before the Covid-19 pandemic but there is limited evidence to understand perceived social support and loneliness trends during the pandemic.
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Affiliation(s)
- Paul Heron
- Mental Health and Addiction Research Group, University of York, York, United Kingdom
| | - Panagiotis Spanakis
- Mental Health and Addiction Research Group, University of York, York, United Kingdom
| | - Suzanne Crosland
- Mental Health and Addiction Research Group, University of York, York, United Kingdom
| | | | - Elizabeth Newbronner
- Mental Health and Addiction Research Group, University of York, York, United Kingdom
| | - Ruth Wadman
- Mental Health and Addiction Research Group, University of York, York, United Kingdom
| | - Lauren Walker
- Mental Health and Addiction Research Group, University of York, York, United Kingdom
| | - Simon Gilbody
- Mental Health and Addiction Research Group, University of York, York, United Kingdom
- Hull York Medical School, York, United Kingdom
| | - Emily Peckham
- Mental Health and Addiction Research Group, University of York, York, United Kingdom
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Qi X, Shen L, Chen J, Shi M, Shen B. Predicting the Disease Severity of Virus Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1368:111-139. [DOI: 10.1007/978-981-16-8969-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Hawman DW, Meade-White K, Archer J, Leventhal S, Wilson D, Shaia C, Randall S, Khandhar AP, Hsiang TY, Gale M, Berglund P, Fuller DH, Feldmann H, Erasmus JH. SARS-CoV2 variant-specific replicating RNA vaccines protect from disease and pathology and reduce viral shedding following challenge with heterologous SARS-CoV2 variants of concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.10.472134. [PMID: 34931189 PMCID: PMC8687464 DOI: 10.1101/2021.12.10.472134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite mass public health efforts, the SARS-CoV2 pandemic continues as of late-2021 with resurgent case numbers in many parts of the world. The emergence of SARS-CoV2 variants of concern (VoC) and evidence that existing vaccines that were designed to protect from the original strains of SARS-CoV-2 may have reduced potency for protection from infection against these VoC is driving continued development of second generation vaccines that can protect against multiple VoC. In this report, we evaluated an alphavirus-based replicating RNA vaccine expressing Spike proteins from the original SARS-CoV-2 Alpha strain and recent VoCs delivered in vivo via a lipid inorganic nanoparticle. Vaccination of both mice and Syrian Golden hamsters showed that vaccination induced potent neutralizing titers against each homologous VoC but reduced neutralization against heterologous challenges. Vaccinated hamsters challenged with homologous SARS-CoV2 variants exhibited complete protection from infection. In addition, vaccinated hamsters challenged with heterologous SARS-CoV-2 variants exhibited significantly reduced shedding of infectious virus. Our data demonstrate that this vaccine platform elicits significant protective immunity against SARS-CoV2 variants and supports continued development of this platform.
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Affiliation(s)
- David W Hawman
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | | | - Shanna Leventhal
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Drew Wilson
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Samantha Randall
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | | | - Tien-Ying Hsiang
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | | | | | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Jesse H Erasmus
- HDT Bio, Seattle, WA 98102, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98109, USA
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Heijnen L, Elsinga G, de Graaf M, Molenkamp R, Koopmans MPG, Medema G. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149456. [PMID: 34371414 PMCID: PMC8332926 DOI: 10.1016/j.scitotenv.2021.149456] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/15/2021] [Accepted: 07/31/2021] [Indexed: 04/15/2023]
Abstract
Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.
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Affiliation(s)
- Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands.
| | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands
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Heijnen L, Elsinga G, de Graaf M, Molenkamp R, Koopmans MPG, Medema G. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149456. [PMID: 34371414 DOI: 10.1101/2021.03.25.21254324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/15/2021] [Accepted: 07/31/2021] [Indexed: 05/20/2023]
Abstract
Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.
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Affiliation(s)
- Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands.
| | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands
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Evans JP, Zeng C, Carlin C, Lozanski G, Saif LJ, Oltz EM, Gumina RJ, Liu SL. Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.06.471455. [PMID: 34909777 PMCID: PMC8669844 DOI: 10.1101/2021.12.06.471455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The waning efficacy of SARS-CoV-2 vaccines combined with the continued emergence of variants resistant to vaccine-induced immunity has reignited debate over the need for booster vaccines. To address this, we examined the neutralizing antibody (nAb) response against four major SARS-CoV-2 variants-D614G, Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2)-in health care workers (HCWs) at pre-vaccination, post-first and post-second mRNA vaccine dose, and six months post-second mRNA vaccine dose. Neutralizing antibody titers against all variants, especially the Delta variant, declined dramatically from four weeks to six months post-second mRNA vaccine dose. Notably, SARS-CoV-2 infection enhanced vaccine durability, and mRNA-1273 vaccinated HCWs also exhibited ~2-fold higher nAb titers than BNT162b2 vaccinated HCWs. Together these results demonstrate possible waning of protection from infection against SARS-CoV-2 Delta variant based on decreased nAb titers, dependent on COVID-19 status and the mRNA vaccine received.
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Affiliation(s)
- John P. Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Cong Zeng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Linda J. Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J. Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
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Klugar M, Riad A, Mohanan L, Pokorná A. COVID-19 Vaccine Booster Hesitancy (VBH) of Healthcare Workers in Czechia: National Cross-Sectional Study. Vaccines (Basel) 2021; 9:1437. [PMID: 34960183 PMCID: PMC8705445 DOI: 10.3390/vaccines9121437] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
The emerging SARS-CoV-2 variants and waning vaccine-elicited immunity are two public health challenges that occurred simultaneously and synergistically during the summer of 2021 and led to a surging demand for COVID-19 vaccine booster dose (BD) rollout. This study aimed to evaluate the COVID-19 vaccine booster hesitancy (VBH) among Czech healthcare workers to explore the potential determinants of VBH. A national cross-sectional survey-based study was carried out between 3 and 11 November 2021, using an online self-administered questionnaire (SAQ) that explored the participants' demographic characteristics, COVID-19 infection and vaccine anamneses, willingness to receive COVID-19 vaccine BD, and the psychosocial drivers of VBH. A total of 3454 HCW properly responded to the online SAQ, of which 80.9% were females, 30.3% were medical professionals, and 50.5% were ≤47 years old. Most of the participants were already inoculated against SARS-CoV-2 (95.2%), and BTN162b2 was the most commonly administered vaccine (90.7%). As the study sample was planned to represent the target population, it revealed a high level of BD acceptance (71.3%) among Czech HCW, while 12.2% were still hesitant and 16.6% were against the currently available BD. These results are consistent with other recent results from central Europe. Medical professional, male, and older participants were more likely to accept BD rather than allied health professional, female, and younger participants. The BDs' perceived effectiveness against severe illness, symptomatic infection, and community transmission was a significant and strong predictor for BD acceptance, while the effectiveness against the circulating variants was not that important for our target population. The BDs' perceived safety and ethical dilemmas of vaccine justice should be addressed sufficiently while communicating with HCW and other population groups. The altruistic reasons for BD acceptance, i.e., family protection, patient protection, and community health protection, underpin the recommendation of postponing the COVID-19 vaccine mandating in favour of stressing these altruistic concerns amid public health messaging.
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Affiliation(s)
- Miloslav Klugar
- Czech National Centre for Evidence-Based Healthcare and Knowledge Translation (Cochrane Czech Republic, Czech EBHC: JBI Centre of Excellence, Masaryk University GRADE Centre), Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, 625 00 Brno, Czech Republic; (M.K.); (L.M.); (A.P.)
- Department of Health Sciences, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Health Information and Statistics of the Czech Republic, 128 01 Prague, Czech Republic
| | - Abanoub Riad
- Czech National Centre for Evidence-Based Healthcare and Knowledge Translation (Cochrane Czech Republic, Czech EBHC: JBI Centre of Excellence, Masaryk University GRADE Centre), Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, 625 00 Brno, Czech Republic; (M.K.); (L.M.); (A.P.)
- Department of Public Health, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Lekshmi Mohanan
- Czech National Centre for Evidence-Based Healthcare and Knowledge Translation (Cochrane Czech Republic, Czech EBHC: JBI Centre of Excellence, Masaryk University GRADE Centre), Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, 625 00 Brno, Czech Republic; (M.K.); (L.M.); (A.P.)
| | - Andrea Pokorná
- Czech National Centre for Evidence-Based Healthcare and Knowledge Translation (Cochrane Czech Republic, Czech EBHC: JBI Centre of Excellence, Masaryk University GRADE Centre), Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, 625 00 Brno, Czech Republic; (M.K.); (L.M.); (A.P.)
- Department of Health Sciences, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Health Information and Statistics of the Czech Republic, 128 01 Prague, Czech Republic
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