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Wu Y, Namilae S, Srinivasan A, Mubayi A, Scotch M. Parametric analysis of SARS-CoV-2 dose-response models in transportation scenarios. PLoS One 2024; 19:e0301996. [PMID: 38865326 PMCID: PMC11168674 DOI: 10.1371/journal.pone.0301996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/26/2024] [Indexed: 06/14/2024] Open
Abstract
Transportation systems involve high-density crowds of geographically diverse people with variations in susceptibility; therefore, they play a large role in the spread of infectious diseases like SARS-CoV-2. Dose-response models are widely used to model the relationship between the trigger of a disease and the level of exposure in transmission scenarios. In this study, we quantified and bounded viral exposure-related parameters using empirical data from five transportation-related events of SARS-CoV-2 transmission. Dose-response models were then applied to parametrically analyze the infection spread in generic transportation systems, including a single-aisle airplane, bus, and railway coach, and then examined the mitigating efficiency of masks by performing a sensitivity analysis of the related factors. We found that dose level significantly affected the number of secondary infections. In general, we observed that mask usage reduced infection rates at all dose levels and that high-quality masks equivalent to FFP2/N95 masks are effective for all dose levels. In comparison, we found that lower-quality masks exhibit limited mitigation efficiency, especially in the presence of high dosage. The sensitivity analysis indicated that a reduction in the infection distance threshold is a critical factor in mask usage.
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Affiliation(s)
- Yuxuan Wu
- Embry-Riddle Aeronautical University, Daytona Beach, Florida, United States of America
| | - Sirish Namilae
- Embry-Riddle Aeronautical University, Daytona Beach, Florida, United States of America
| | - Ashok Srinivasan
- University of West Florida, Pensacola, Florida, United States of America
| | - Anuj Mubayi
- QVIA, Durham, North Carolina, United States of America
| | - Mathew Scotch
- Arizona State University, Tempe, Arizona, United States of America
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Anderson TL, Nande A, Merenstein C, Raynor B, Oommen A, Kelly BJ, Levy MZ, Hill AL. Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies. Epidemics 2023; 44:100710. [PMID: 37556994 PMCID: PMC10594662 DOI: 10.1016/j.epidem.2023.100710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/17/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023] Open
Abstract
The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. "Superspreading," or "over-dispersion," is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities given data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.
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Affiliation(s)
- Thayer L Anderson
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Anjalika Nande
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Brinkley Raynor
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Anisha Oommen
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Brendan J Kelly
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America; Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America; Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Michael Z Levy
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States of America.
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Nasergivehchi S, Togha M, Jafari E, Sheikhvatan M, Shahamati D. Headache following vaccination against COVID-19 among healthcare workers with a history of COVID-19 infection: a cross-sectional study in Iran with a meta-analytic review of the literature. Head Face Med 2023; 19:19. [PMID: 37202794 DOI: 10.1186/s13005-023-00363-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND There is evidence of the occurrence of headache after vaccination against COVID-19. However, only a few studies have examined the headache characteristics and related determinants, especially among healthcare workers with a history of COVID-19 infection. METHODS We evaluated the incidence of headaches after injection of different types of COVID-19 vaccine to determine factors relating to the incidence of headache after vaccination among the Iranian healthcare workers who had previously contracted COVID-19. A group of 334 healthcare workers with a history of COVID-19 infection were included and vaccinated (at least one month after recovery without any COVID-19 related symptoms) with different COVID-19 vaccines. The baseline information, headache characteristics and vaccine specifications were recorded. RESULTS Overall, 39.2% reported experiencing a post-vaccination headache. Of those with a previous history of headache, 51.1% reported migraine-type, 27.4% tension-type and 21.5% other types. The mean time between vaccination and headache appearance was 26.78 ± 6.93 h, with the headache appearing less than 24 h after vaccination in most patients (83.2%). The headaches reached its peak within 8.62 ± 2.41 h. Most patients reported a compression-type headache. The prevalence of post-vaccination headaches was significantly different according to the type of vaccine used. The highest rates were reported for AstraZeneca, followed by Sputnik V. In regression analysis, the vaccine brand, female gender and initial COVID-19 severity were the main determinants for predicting post-vaccination headache. CONCLUSION Participants commonly experienced a headache following vaccination against COVID-19. Our study results indicated that this was slightly more common in females and in those with a history of severe COVID-19 infection.
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Affiliation(s)
- Somayeh Nasergivehchi
- Department of Headache, Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Neurology, Baharloo University Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mansoureh Togha
- Department of Headache, Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Headache, Neurology Ward, School of Medicine, Sina University Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Elham Jafari
- Department of Headache, Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Sheikhvatan
- Tehran University of Medical Sciences, Tehran, Iran
- Heidelberg University Hospital, Heidelberg, Germany
| | - Donya Shahamati
- Faculty of Nutrition Sciences and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Behehshti University of Medical Sciences Tehran, Tehran, Iran
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Loo BPY, Tsoi KH, Axhausen KW, Cao M, Lee Y, Koh KP. Spatial risk for a superspreading environment: Insights from six urban facilities in six global cities across four continents. Front Public Health 2023; 11:1128889. [PMID: 37089495 PMCID: PMC10113652 DOI: 10.3389/fpubh.2023.1128889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
IntroductionThis study sets out to provide scientific evidence on the spatial risk for the formation of a superspreading environment.MethodsFocusing on six common types of urban facilities (bars, cinemas, gyms and fitness centers, places of worship, public libraries and shopping malls), it first tests whether visitors' mobility characteristics differ systematically for different types of facility and at different locations. The study collects detailed human mobility and other locational data in Chicago, Hong Kong, London, São Paulo, Seoul and Zurich. Then, considering facility agglomeration, visitors' profile and the density of the population, facilities are classified into four potential spatial risk (PSR) classes. Finally, a kernel density function is employed to derive the risk surface in each city based on the spatial risk class and nature of activities.ResultsResults of the human mobility analysis reflect the geographical and cultural context of various facilities, transport characteristics and people's lifestyle across cities. Consistent across the six global cities, geographical agglomeration is a risk factor for bars. For other urban facilities, the lack of agglomeration is a risk factor. Based on the spatial risk maps, some high-risk areas of superspreading are identified and discussed in each city.DiscussionIntegrating activity-travel patterns in risk models can help identify areas that attract highly mobile visitors and are conducive to superspreading. Based on the findings, this study proposes a place-based strategy of non-pharmaceutical interventions that balance the control of the pandemic and the daily life of the urban population.
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Affiliation(s)
- Becky P. Y. Loo
- Department of Geography, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China
| | - Ka Ho Tsoi
- Department of Geography, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Ka Ho Tsoi
| | - Kay W. Axhausen
- Department of Civil, Environment and Geomatic Engineering, ETH Zürich, Zürich, Switzerland
| | - Mengqiu Cao
- School of Architecture and Cities, University of Westminster, London, United Kingdom
| | - Yongsung Lee
- Department of Geography, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Keumseok Peter Koh
- Department of Geography, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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Ngonghala CN, Taboe HB, Safdar S, Gumel AB. Unraveling the dynamics of the Omicron and Delta variants of the 2019 coronavirus in the presence of vaccination, mask usage, and antiviral treatment. APPLIED MATHEMATICAL MODELLING 2023; 114:447-465. [PMID: 36281307 PMCID: PMC9581714 DOI: 10.1016/j.apm.2022.09.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/31/2022] [Accepted: 09/12/2022] [Indexed: 06/13/2023]
Abstract
The effectiveness of control interventions against COVID-19 is threatened by the emergence of SARS-CoV-2 variants of concern. We present a mathematical model for studying the transmission dynamics of two of these variants (Delta and Omicron) in the United States, in the presence of vaccination, treatment of individuals with clinical symptoms of the disease and the use of face masks. The model is parameterized and cross-validated using observed daily case data for COVID-19 in the United States for the period from November 2021 (when Omicron first emerged) to March 2022. Rigorous qualitative analysis of the model shows that the disease-free equilibrium of the model is locally-asymptotically stable when the control reproduction number of the model (denoted by R c ) is less than one. This equilibrium is shown to be globally-asymptotically stable for a special case of the model, where disease-induced mortality is negligible and both vaccine-derived immunity in fully-vaccinated individuals and natural immunity do not wane, when the associated reproduction number is less than one. The epidemiological implication of the latter result is that the combined vaccination-boosting strategy can lead to the elimination of the pandemic if its implementation can bring (and maintain) the associated reproduction number to a value less than one. An analytical expression for the vaccine-derived herd immunity threshold is derived. Using this expression, together with the baseline values of the parameters of the parameterized model, we showed that the vaccine-derived herd immunity can be achieved in the United States (so that the pandemic will be eliminated) if at least 68 % of the population is fully-vaccinated with two of the three vaccines approved for use in the United States (Pfizer or Moderna vaccine). Furthermore, this study showed (as of the time of writing in March 2022) that the control reproduction number of the Omicron variant was approximately 3.5 times that of the Delta variant (the reproduction of the latter is computed to be ≈ 0.2782 ), indicating that Delta had practically died out and that Omicron has competitively-excluded Delta (to become the predominant variant in the United States). Based on our analysis and parameterization at the time of writing of this paper (March 2022), our study suggests that SARS-CoV-2 elimination is feasible by June 2022 if the current baseline level of the coverage of fully-vaccinated individuals is increased by about 20 % . The prospect of pandemic elimination is significantly improved if vaccination is combined with a face mask strategy that prioritizes moderately effective and high-quality masks. Having a high percentage of the populace wearing the moderately-effective surgical mask is more beneficial to the community than having low percentage of the populace wearing the highly-effective N95 masks. We showed that waning natural and vaccine-derived immunity (if considered individually) offer marginal impact on disease burden, except for the case when they wane at a much faster rate (e.g., within three months), in comparison to the baseline (estimated to be within 9 months to a year). Treatment of symptomatic individuals has marginal effect in reducing daily cases of SARS-CoV-2, in comparison to the baseline, but it has significant impact in reducing daily hospitalizations. Furthermore, while treatment significantly reduces daily hospitalizations (and, consequently, deaths), the prospects of COVID-19 elimination in the United States are significantly enhanced if investments in control resources are focused on mask usage and vaccination rather than on treatment.
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Affiliation(s)
- Calistus N Ngonghala
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Hemaho B Taboe
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
- Laboratoire de Biomathématiques et d'Estimations Forestières, University of Abomey-Calavi, Cotonou, Bénin
| | - Salman Safdar
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Abba B Gumel
- Department of Mathematics, University of Maryland, College Park, MD 20742, USA
- Department of Biology & Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
- Department of Mathematics and Applied Mathematics, University of Pretoria, Pretoria 0002, South Africa
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Faizuloev E, Gracheva A, Korchevaya E, Smirnova D, Samoilikov R, Pankratov A, Trunova G, Khokhlova V, Ammour Y, Petrusha O, Poromov A, Leneva I, Svitich O, Zverev V. Cold-adapted SARS-CoV-2 variants with different temperature sensitivity exhibit an attenuated phenotype and confer protective immunity. Vaccine 2023; 41:892-902. [PMID: 36528447 PMCID: PMC9744683 DOI: 10.1016/j.vaccine.2022.12.019] [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: 08/11/2022] [Revised: 11/28/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
As novel SARS-CoV-2 Variants of Concern emerge, the efficacy of existing vaccines against COVID-19 is declining. A possible solution to this problem lies in the development of a live attenuated vaccine potentially able of providing cross-protective activity against a wide range of SARS-CoV-2 antigenic variants. Cold-adapted (ca) SARS-CoV-2 variants, Dubrovka-ca-B4 (D-B4) and Dubrovka-ca-D2 (D-D2), were obtained after long-term passaging of the Dubrovka (D) strain in Vero cells at reduced temperatures. Virulence, immunogenicity, and protective activity of SARS-CoV-2 variants were evaluated in experiments on intranasal infection of Syrian golden hamsters (Mesocricetus auratus). In animal model infecting with ca variants, the absence of body weight loss, the significantly lower viral titer and viral RNA concentration in animal tissues, the less pronounced inflammatory lesions in animal lungs as compared with the D strain indicated the reduced virulence of the virus variant. Single intranasal immunization with D-B4 and D-D2 variants induced the production of neutralizing antibodies in hamsters and protected them from infection with the D strain and the development of severe pneumonia. It was shown that for ca SARS-CoV-2 variants, the temperature-sensitive (ts) phenotype was not obligate for virulence reduction. Indeed, the D-B4 variant, which did not possess the ts phenotype but had lost the ability to infect human lung cells Calu-3, exhibited reduced virulence in hamsters. Consequently, the potential phenotypic markers of attenuation of ca SARS-CoV-2 variants are the ca phenotype, the ts phenotype, and the change in species specificity of the virus. This study demonstrates the great potential of SARS-CoV-2 cold adaptation as a strategy to develop a live attenuated COVID-19 vaccine.
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Affiliation(s)
- Evgeny Faizuloev
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia; Russian Medical Academy of Continuous Professional Education, Moscow, Russia.
| | | | | | - Daria Smirnova
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Roman Samoilikov
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Andrey Pankratov
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Galina Trunova
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Varvara Khokhlova
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Yulia Ammour
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Olga Petrusha
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Artem Poromov
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,Peoples' Friendship University of Russia, Department of Biochemistry, Moscow, Russia
| | - Irina Leneva
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Oxana Svitich
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,I.M. Sechenov First Moscow State Medical University (Sechenov University), F.F. Erisman Institute of Public Health, Moscow, Russia
| | - Vitaly Zverev
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,I.M. Sechenov First Moscow State Medical University (Sechenov University), F.F. Erisman Institute of Public Health, Moscow, Russia
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Safdar S, Ngonghala CN, Gumel AB. Mathematical assessment of the role of waning and boosting immunity against the BA.1 Omicron variant in the United States. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:179-212. [PMID: 36650762 DOI: 10.3934/mbe.2023009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Three safe and effective vaccines against SARS-CoV-2 have played a major role in combating COVID-19 in the United States. However, the effectiveness of these vaccines and vaccination programs has been challenged by the emergence of new SARS-CoV-2 variants of concern. A new mathematical model is formulated to assess the impact of waning and boosting of immunity against the Omicron variant in the United States. To account for gradual waning of vaccine-derived immunity, we considered three vaccination classes that represent high, moderate and low levels of immunity. We showed that the disease-free equilibrium of the model is globally-asymptotically, for two special cases, if the associated reproduction number is less than unity. Simulations of the model showed that vaccine-derived herd immunity can be achieved in the United States via a vaccination-boosting strategy which entails fully vaccinating at least 59% of the susceptible populace followed by the boosting of about 72% of the fully-vaccinated individuals whose vaccine-derived immunity has waned to moderate or low level. In the absence of boosting, waning of immunity only causes a marginal increase in the average number of new cases at the peak of the pandemic, while boosting at baseline could result in a dramatic reduction in the average number of new daily cases at the peak. Specifically, for the fast immunity waning scenario (where both vaccine-derived and natural immunity are assumed to wane within three months), boosting vaccine-derived immunity at baseline reduces the average number of daily cases at the peak by about 90% (in comparison to the corresponding scenario without boosting of the vaccine-derived immunity), whereas boosting of natural immunity (at baseline) only reduced the corresponding peak daily cases (in comparison to the corresponding scenario without boosting of natural immunity) by approximately 62%. Furthermore, boosting of vaccine-derived immunity is more beneficial (in reducing the burden of the pandemic) than boosting of natural immunity. Finally, boosting vaccine-derived immunity increased the prospects of altering the trajectory of COVID-19 from persistence to possible elimination.
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Affiliation(s)
- Salman Safdar
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Calistus N Ngonghala
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Abba B Gumel
- Department of Mathematics, University of Maryland College Park, MD 20742, USA
- Department of Mathematics and Applied Mathematics, University of Pretoria, Pretoria 0002, South Africa
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Anderson TL, Nande A, Merenstein C, Raynor B, Oommen A, Kelly BJ, Levy MZ, Hill AL. Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.12.02.22281853. [PMID: 36523404 PMCID: PMC9753792 DOI: 10.1101/2022.12.02.22281853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. "Superspreading," or "over-dispersion," is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities with data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.
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Affiliation(s)
- Thayer L Anderson
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
| | - Anjalika Nande
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Brinkley Raynor
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Anisha Oommen
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Brendan J Kelly
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael Z Levy
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
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Bispo ECI, Silva-Carvalho AÉ, Sousa MRR, Neves FDAR, Carvalho JL, Arganaraz ER, Saldanha-Araujo F. Differential peripheral blood mononuclear cell reactivity against SARS-CoV-2 proteins in naïve and previously infected subjects following COVID-19 vaccination. CLINICAL IMMUNOLOGY COMMUNICATIONS 2022; 2:172-176. [PMID: 38013967 PMCID: PMC9714124 DOI: 10.1016/j.clicom.2022.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022]
Abstract
The decline in vaccine efficacy and the risk of reinfection by SARS-CoV-2 make new studies important to better characterize the immune response against the virus and its components. Here, we investigated the pattern of activation of T-cells and the expression of inflammatory factors by PBMCs obtained from naïve and previously infected subjects following COVID-19 vaccination, after PBMCs stimulation with S1, RBD, and N-RBD SARS-CoV-2 proteins. PBMCs showed low levels of ACE2 and TMPRSS2 transcripts, which were not modulated by the exposure of these cells to SARS-CoV-2 proteins. Compared to S1 and RBD, N-RBD stimulation showed a greater ability to stimulate T-cell reactivity, according to CD25 and CD69 markers. Interestingly, T-cell reactivity was more pronounced in vaccinated subjects with prior SARS-CoV-2 infection than in vaccinated donors who never had been diagnosed with COVID-19. Finally, N-RBD stimulation promoted greater expression of IL-6 and IFN-γ in PBMCs, which reinforces the greater immunogenic potential of this protein in the vaccinated subjects. These data suggest that PBMCs from previously infected and vaccinated subjects are more reactive than those derived from just vaccinated donors. Moreover, the N-RBD together viral proteins showed a greater stimulatory capacity than S1 and RBD viral proteins.
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Affiliation(s)
- Elizabete Cristina Iseke Bispo
- Laboratório de Hematologia e Células-Tronco, Faculdade de Ciências da Saúde, Universidade de Brasília, Campus Darcy Ribeiro, Av. L2 Norte, Brasília, DF 70.910-900, Brasil
| | - Amandda Évelin Silva-Carvalho
- Laboratório de Hematologia e Células-Tronco, Faculdade de Ciências da Saúde, Universidade de Brasília, Campus Darcy Ribeiro, Av. L2 Norte, Brasília, DF 70.910-900, Brasil
| | - Marielly Reis Resende Sousa
- Laboratório de Hematologia e Células-Tronco, Faculdade de Ciências da Saúde, Universidade de Brasília, Campus Darcy Ribeiro, Av. L2 Norte, Brasília, DF 70.910-900, Brasil
| | - Francisco de Assis Rocha Neves
- Laboratório de Farmacologia Molecular, Faculdade de Ciências da Saúde, Universidade de Brasília, Av. L2 Norte, Brasília, DF 70.910-900, Brasil
| | - Juliana Lott Carvalho
- Laboratório Interdisciplinar de Biociências, Faculdade de Medicina, Universidade de Brasília, Av. L2 Norte, Brasília, DF 70.910-900, Brasil
| | - Enrique Roberto Arganaraz
- Laboratório de Virologia Molecular, Faculdade de Ciências da Saúde, Universidade de Brasília, Av. L2 Norte, Brasília, DF 70.910-900, Brasil
| | - Felipe Saldanha-Araujo
- Laboratório de Hematologia e Células-Tronco, Faculdade de Ciências da Saúde, Universidade de Brasília, Campus Darcy Ribeiro, Av. L2 Norte, Brasília, DF 70.910-900, Brasil
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10
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Pardo-Seco J, Bello X, Gómez-Carballa A, Martinón-Torres F, Muñoz-Barús JI, Salas A. A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations. Int J Mol Sci 2022; 23:12899. [PMID: 36361690 PMCID: PMC9656715 DOI: 10.3390/ijms232112899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/02/2022] [Accepted: 10/18/2022] [Indexed: 08/30/2023] Open
Abstract
Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an unknown SARS-CoV-2 genome in a population (hereafter, estimated time of a queried genome [QG]; tE-QG) can be easily predicted using a phylogenetic model based on a robust reference genome database of the virus, and information on their sampling dates. We evaluate several phylogeny-based approaches, including modeling evolutionary (substitution) rates of the SARS-CoV-2 genome (~10-3 substitutions/nucleotide/year) and the mutational (substitutions) differences separating the QGs from the reference genomes (RGs) in the database. Owing to the mutational characteristics of the virus, the present Viral Molecular Clock Dating (VMCD) method covers timeframes going backwards from about a month in the past. The method has very low errors associated to the tE-QG estimates and narrow intervals of tE-QG, both ranging from a few days to a few weeks regardless of the mathematical model used. The SARS-CoV-2 model represents a proof of concept that can be extrapolated to any other microorganism, provided that a robust genome sequence database is available. Besides obvious applications in epidemiology and microbiology investigations, there are several contexts in forensic casework where estimating tE-QG could be useful, including estimation of the postmortem intervals (PMI) and the dating of samples stored in hospital settings.
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Affiliation(s)
- Jacobo Pardo-Seco
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
| | - Xabier Bello
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
| | - Alberto Gómez-Carballa
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
| | - Federico Martinón-Torres
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
| | - José Ignacio Muñoz-Barús
- Department of Forensic Sciences, Pathology, Gynaecology and Obstetrics and Paediatrics, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Institute of Forensic Sciences (INCIFOR), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
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11
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Gavotte L, Frutos R. The stochastic world of emerging viruses. PNAS NEXUS 2022; 1:pgac185. [PMID: 36714875 PMCID: PMC9802394 DOI: 10.1093/pnasnexus/pgac185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/02/2022] [Indexed: 02/01/2023]
Abstract
The acquisition of new hosts is a fundamental mechanism by which parasitic organisms expand their host range and perpetuate themselves on an evolutionary scale. Among pathogens, viruses, due to their speed of evolution, are particularly efficient in producing new emergence events. However, even though these phenomena are particularly important to the human species and therefore specifically studied, the processes of virus emergence in a new host species are very complex and difficult to comprehend in their entirety. In order to provide a structured framework for understanding emergence in a species (including humans), a comprehensive qualitative model is an indispensable cornerstone. This model explicitly describes all the stages necessary for a virus circulating in the wild to come to the crossing of the epidemic threshold. We have therefore developed a complete descriptive model explaining all the steps necessary for a virus circulating in host populations to emerge in a new species. This description of the parameters presiding over the emergence of a new virus allows us to understand their nature and importance in the emergence process.
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12
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Steiner MC, Novembre J. Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution. PLoS Genet 2022; 18:e1010391. [PMID: 36137003 PMCID: PMC9498967 DOI: 10.1371/journal.pgen.1010391] [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] [Indexed: 11/18/2022] Open
Abstract
Theoretical population genetics has long studied the arrival and geographic spread of adaptive variants through the analysis of mathematical models of dispersal and natural selection. These models take on a renewed interest in the context of the COVID-19 pandemic, especially given the consequences that novel adaptive variants have had on the course of the pandemic as they have spread through global populations. Here, we review theoretical models for the spatial spread of adaptive variants and identify areas to be improved in future work, toward a better understanding of variants of concern in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) evolution and other contemporary applications. As we describe, characteristics of pandemics such as COVID-19-such as the impact of long-distance travel patterns and the overdispersion of lineages due to superspreading events-suggest new directions for improving upon existing population genetic models.
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Affiliation(s)
- Margaret C. Steiner
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
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13
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Gracheva AV, Korchevaya ER, Ammour YI, Smirnova DI, Sokolova OS, Glukhov GS, Moiseenko AV, Zubarev IV, Samoilikov RV, Leneva IA, Svitich OA, Zverev VV, Faizuloev EB. Immunogenic properties of SARS-CoV-2 inactivated by ultraviolet light. Arch Virol 2022; 167:2181-2191. [PMID: 35857146 PMCID: PMC9296761 DOI: 10.1007/s00705-022-05530-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/25/2022] [Indexed: 11/23/2022]
Abstract
Vaccination against COVID-19 is the most effective method of controlling the spread of SARS-CoV-2 and reducing mortality from this disease. The development of vaccines with high protective activity against a wide range of SARS-CoV-2 antigenic variants remains relevant. In this regard, evaluation of the effectiveness of physical methods of virus inactivation, such as ultraviolet irradiation (UV) of the virus stock, remains relevant. This study demonstrates that the UV treatment of SARS-CoV-2 completely inactivates its infectivity while preserving its morphology, antigenic properties, and ability to induce the production of virus-neutralizing antibodies in mice through immunization. Thus, the UV inactivation of SARS-CoV-2 makes it possible to obtain viral material similar in its antigenic and immunogenic properties to the native antigen, which can be used both for the development of diagnostic test systems and for the development of an inactivated vaccine against COVID-19.
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Affiliation(s)
- A V Gracheva
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - E R Korchevaya
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - Yu I Ammour
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - D I Smirnova
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - O S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - G S Glukhov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - A V Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.,N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - I V Zubarev
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - R V Samoilikov
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - I A Leneva
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - O A Svitich
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.,F.F. Erisman Institute of Public Health, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - V V Zverev
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.,F.F. Erisman Institute of Public Health, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Evgeny B Faizuloev
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.
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14
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Gómez-Carballa A, Rivero-Calle I, Pardo-Seco J, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Cebey-López M, Barral-Arca R, Rodriguez-Tenreiro C, Dacosta-Urbieta A, Bello X, Pischedda S, Currás-Tuala MJ, Viz-Lasheras S, Martinón-Torres F, Salas A. A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity. ENVIRONMENTAL RESEARCH 2022; 210:112890. [PMID: 35202626 PMCID: PMC8861187 DOI: 10.1016/j.envres.2022.112890] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/11/2022] [Accepted: 02/02/2022] [Indexed: 05/08/2023]
Abstract
Coronavirus Disease-19 (COVID-19) symptoms range from mild to severe illness; the cause for this differential response to infection remains unknown. Unravelling the immune mechanisms acting at different levels of the colonization process might be key to understand these differences. We carried out a multi-tissue (nasal, buccal and blood; n = 156) gene expression analysis of immune-related genes from patients affected by different COVID-19 severities, and healthy controls through the nCounter technology. Mild and asymptomatic cases showed a powerful innate antiviral response in nasal epithelium, characterized by activation of interferon (IFN) pathway and downstream cascades, successfully controlling the infection at local level. In contrast, weak macrophage/monocyte driven innate antiviral response and lack of IFN signalling activity were present in severe cases. Consequently, oral mucosa from severe patients showed signals of viral activity, cell arresting and viral dissemination to the lower respiratory tract, which ultimately could explain the exacerbated innate immune response and impaired adaptative immune responses observed at systemic level. Results from saliva transcriptome suggest that the buccal cavity might play a key role in SARS-CoV-2 infection and dissemination in patients with worse prognosis. Co-expression network analysis adds further support to these findings, by detecting modules specifically correlated with severity involved in the abovementioned biological routes; this analysis also provides new candidate genes that might be tested as biomarkers in future studies. We also found tissue specific severity-related signatures mainly represented by genes involved in the innate immune system and cytokine/chemokine signalling. Local immune response could be key to determine the course of the systemic response and thus COVID-19 severity. Our findings provide a framework to investigate severity host gene biomarkers and pathways that might be relevant to diagnosis, prognosis, and therapy.
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Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - José Gómez-Rial
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Laboratorio de Inmunología. Servicio de Análisis Clínicos. Hospital Clínico Universitario (SERGAS), Galicia, Spain
| | - Carmen Rivero-Velasco
- Intensive Medicine Department, Hospital Clìnico Universitario de Santiago de Compostela, Galicia, Spain
| | - Nuria Rodríguez-Núñez
- Pneumology Department, Hospital Clìnico Universitario de Santiago de Compostela, Galicia, Spain
| | - Gema Barbeito-Castiñeiras
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Hugo Pérez-Freixo
- Preventive Medicine Department, Hospital Clínico Universitario de Santiago de Compostela, Spain
| | - Miriam Cebey-López
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ruth Barral-Arca
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Carmen Rodriguez-Tenreiro
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Dacosta-Urbieta
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Xabier Bello
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sara Pischedda
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - María José Currás-Tuala
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sandra Viz-Lasheras
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
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15
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Liu J, Mao Q, Wu X, He Q, Bian L, Bai Y, Wang Z, Wang Q, Zhang J, Liang Z, Xu M. Considerations for the Feasibility of Neutralizing Antibodies as a Surrogate Endpoint for COVID-19 Vaccines. Front Immunol 2022; 13:814365. [PMID: 35572565 PMCID: PMC9092276 DOI: 10.3389/fimmu.2022.814365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/31/2022] [Indexed: 01/02/2023] Open
Abstract
To effectively control and prevent the pandemic of coronavirus disease 2019 (COVID-19), suitable vaccines have been researched and developed rapidly. Currently, 31 COVID-19 vaccines have been approved for emergency use or authorized for conditional marketing, with more than 9.3 billion doses of vaccines being administered globally. However, the continuous emergence of variants with high transmissibility and an ability to escape the immune responses elicited by vaccines poses severe challenges to the effectiveness of approved vaccines. Hundreds of new COVID-19 vaccines based on different technology platforms are in need of a quick evaluation for their efficiencies. Selection and enrollment of a suitable sample of population for conducting these clinical trials is often challenging because the pandemic so widespread and also due to large scale vaccination. To overcome these hurdles, methods of evaluation of vaccine efficiency based on establishment of surrogate endpoints could expedite the further research and development of vaccines. In this review, we have summarized the studies on neutralizing antibody responses and effectiveness of the various COVID-19 vaccines. Using this data we have analyzed the feasibility of establishing surrogate endpoints for evaluating the efficacy of vaccines based on neutralizing antibody titers. The considerations discussed here open up new avenues for devising novel approaches and strategies for the research and develop as well as application of COVID-19 vaccines.
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Affiliation(s)
- Jianyang Liu
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | - Qunying Mao
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | - Xing Wu
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | - Qian He
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | - Lianlian Bian
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | - Yu Bai
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | | | - Qian Wang
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | - Jialu Zhang
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | - Zhenglun Liang
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
| | - Miao Xu
- National Institutes for Food and Drug Control, Beijing, China
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, China
- NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, China
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16
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Cheikh Ismail L, Osaili TM, Mohamad MN, Al Marzouqi A, Habib-Mourad C, Abu Jamous DO, Ali HI, Al Sabbah H, Hasan H, Hassan H, Stojanovska L, Hashim M, AlHaway M, Qasrawi R, Shaker Obaid RR, Al Daour R, Saleh ST, Al Dhaheri AS. Assessment of Dietary and Lifestyle Responses After COVID-19 Vaccine Availability in Selected Arab Countries. Front Nutr 2022; 9:849314. [PMID: 35495916 PMCID: PMC9048021 DOI: 10.3389/fnut.2022.849314] [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: 01/05/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
Background The COVID-19 pandemic has been consistently associated with unhealthy lifestyle behaviors and dietary practices. This study aimed to assess the dietary and lifestyle behaviors of adults after COVID-19 vaccine availability and their attitude toward the vaccine in selected Arab countries. Methods A cross-sectional survey-based study was conducted between October 2021 and December 2021 using Google Forms (n = 2259). A multi-component questionnaire was used to collect socio-demographic characteristics, attitudes toward the COVID-19 vaccine, and behavioral, dietary, and lifestyle responses after easing the restriction. Participants were given a score based on the sum of positive dietary and lifestyle changes. The generalized linear models were used to identify the association between positive dietary and lifestyle changes score and sociodemographic characteristics. Results Weight gain during the pandemic was reported by 39.5% of the participants, 36.1% reported ever getting infected with the COVID-19 virus, and 85% received at least one dose of the vaccine. The key adverse reactions of the COVID-19 vaccine were fatigue, headache, and joint pain, and the main reason for vaccination was protection against infection. Most participants were concerned about the vaccine side effects (45.8%) and inadequate testing (50.7%). After easing of restriction, 54.3% of the participants reduced the frequency of disinfecting objects, and 58.3% joined social events. Most dietary and lifestyle behaviors remained unchanged after vaccine availability but there was an increase in the time spent behind the screen for work (50.1%) and entertainment (42.9%). The results of the multivariate regression analyses revealed that older participants (p = 0.001), those with higher education (p = 0.010), and those working from home (p = 0.040) were more likely to have higher positive dietary and lifestyle changes scores. Conclusion Although most participants were concerned about vaccine safety, low vaccine hesitancy rates were observed among the study sample. The availability of the COVID-19 vaccines resulted in loosening some of the safety social measures among Arab adults but the negative impact of the pandemic on dietary and lifestyle behaviors remained unaltered.
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Affiliation(s)
- Leila Cheikh Ismail
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Tareq M. Osaili
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Maysm N. Mohamad
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Amina Al Marzouqi
- Department of Health Services Administration, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Carla Habib-Mourad
- Department of Nutrition and Food Sciences, Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon
| | - Dima O. Abu Jamous
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Habiba I. Ali
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Haleama Al Sabbah
- College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Hayder Hasan
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Hussein Hassan
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Lily Stojanovska
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
| | - Mona Hashim
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Muna AlHaway
- Blood Transfusion and Research Center, Emirates Health Services, Dubai, United Arab Emirates
| | - Radwan Qasrawi
- Department of Computer Science, Al-Quds University, Jerusalem, Palestine
- Department of Computer Engineering, Istinye University, Istanbul, Turkey
| | - Reyad R. Shaker Obaid
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Rameez Al Daour
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Sheima T. Saleh
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Ayesha S. Al Dhaheri
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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17
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Evaluation of BNT162b2 Vaccine Effectiveness in Galicia, Northwest Spain. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074039. [PMID: 35409724 PMCID: PMC8998680 DOI: 10.3390/ijerph19074039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 11/17/2022]
Abstract
Investigating vaccine effectiveness (VE) in real-world conditions is crucial, especially its variation across different settings and populations. We undertook a test-negative control study in Galicia (Northwest Spain) to assess BNT162b2 effectiveness against acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection as well as COVID-19 associated hospitalization, intensive care unit (ICU) admission and mortality. A total of 44,401 positive and 817,025 negative SARS-CoV-2 test results belonging to adults were included. Adjusted odds ratios of vaccination and their 95% confidence interval (CI) were estimated using multivariate logistic-regression models. BNT162b2 showed high effectiveness in reducing SARS-CoV-2 infections in all age categories, reaching maximum VE ≥ 14 days after administering the second dose [18-64 years: VE = 92.9% (95%CI: 90.2-95.1); 65-79 years: VE = 85.8% (95%CI: 77.3-91.9), and ≥80 years: VE = 91.4% (95%CI: 87.9-94.1)]. BNT162b2 also demonstrated effectiveness in preventing COVID-19 hospitalization for all age categories, with VE more pronounced for those aged ≥80 years [VE = 60.0% (95%CI: 49.4-68.3)]. Moreover, there was a considerable reduction in ICU admission [VE = 88.0% (95%CI: 74.6-95.8)] and mortality [VE = 38.0% (95%CI: 15.9-55.4)] in the overall population. BNT162b2 showed substantial protection against SARS-CoV-2 infections and COVID-19 severity. Our findings would prove useful for systematic reviews and meta-analysis on COVID-19 VE.
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18
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Gräf T, Bello G, Venas TMM, Pereira EC, Paixão ACD, Appolinario LR, Lopes RS, Mendonça ACDF, da Rocha ASB, Motta FC, Gregianini TS, Salvato RS, Fernandes SB, Rovaris DB, Cavalcanti AC, Leite AB, Riediger I, Debur MDC, Bernardes AFL, Ribeiro-Rodrigues R, Grinsztejn B, Alves do Nascimento V, de Souza VC, Gonçalves L, da Costa CF, Mattos T, Dezordi FZ, Wallau GL, Naveca FG, Delatorre E, Siqueira MM, Resende PC. Identification of a novel SARS-CoV-2 P.1 sub-lineage in Brazil provides new insights about the mechanisms of emergence of variants of concern. Virus Evol 2022; 7:veab091. [PMID: 35039782 PMCID: PMC8754780 DOI: 10.1093/ve/veab091] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/25/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022] Open
Abstract
One of the most remarkable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) features is the significant number of mutations they acquired. However, the specific factors that drove the emergence of such variants since the second half of 2020 are not fully resolved. In this study, we describe a new SARS-CoV-2 P.1 sub-lineage circulating in Brazil, denoted here as Gamma-like-II, that as well as the previously described lineage Gamma-like-I shares several lineage-defining mutations with the VOC Gamma. Reconstructions of ancestor sequences support that most lineage-defining mutations of the Spike (S) protein, including those at the receptor-binding domain (RBD), accumulated at the first P.1 ancestor. In contrast, mutations outside the S protein were mostly fixed at subsequent steps. Our evolutionary analyses estimate that P.1-ancestral strains carrying RBD mutations of concern probably circulated cryptically in the Amazonas for several months before the emergence of the VOC Gamma. Unlike the VOC Gamma, the other P.1 sub-lineages displayed a much more restricted dissemination and accounted for a low fraction (<2 per cent) of SARS-CoV-2 infections in Brazil in 2021. The stepwise diversification of lineage P.1 through multiple inter-host transmissions is consistent with the hypothesis that partial immunity acquired from natural SARS-CoV-2 infections in heavily affected regions might have been a major driving force behind the natural selection of some VOCs. The lag time between the emergence of the P.1 ancestor and the expansion of the VOC Gamma and the divergent epidemic trajectories of P.1 sub-lineages support a complex interplay between the emergence of mutations of concern and viral spread in Brazil.
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Affiliation(s)
- Tiago Gräf
- Plataforma de Vigilância Molecular, Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia 40296-710, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Taina Moreira Martins Venas
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Elisa Cavalcante Pereira
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Anna Carolina Dias Paixão
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Luciana Reis Appolinario
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Renata Serrano Lopes
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | | | - Alice Sampaio Barreto da Rocha
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Fernando Couto Motta
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Tatiana Schäffer Gregianini
- Laboratório Central de Saúde Pública do Estado do Rio Grande do Sul (LACEN-RS), Porto Alegre 90610-000, Brazil
| | - Richard Steiner Salvato
- Laboratório Central de Saúde Pública do Estado do Rio Grande do Sul (LACEN-RS), Porto Alegre 90610-000, Brazil
| | - Sandra Bianchini Fernandes
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Florianópolis 88010-001, Brazil
| | - Darcita Buerger Rovaris
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Florianópolis 88010-001, Brazil
| | - Andrea Cony Cavalcanti
- Laboratório Central de Saúde Pública do Estado do Rio de Janeiro (LACEN-RJ), Rio de Janeiro 20231-000, Brazil
| | - Anderson Brandão Leite
- Laboratório Central de Saúde Pública do Estado de Alagoas (LACEN-AL), Maceió 57036-000, Brazil
| | - Irina Riediger
- Laboratório Central de Saúde Pública do Estado do Paraná (LACEN-PR), Curitiba 80045-150, Brazil
| | - Maria do Carmo Debur
- Laboratório Central de Saúde Pública do Estado do Paraná (LACEN-PR), Curitiba 80045-150, Brazil
| | | | - Rodrigo Ribeiro-Rodrigues
- Laboratório Central de Saúde Pública do Estado do Espírito Santo (LACEN-ES), Vitória 29052-121, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Valdinete Alves do Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ, Manaus, Amazonas 69027-070, Brazil
| | - Victor Costa de Souza
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ, Manaus, Amazonas 69027-070, Brazil
| | - Luciana Gonçalves
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ, Manaus, Amazonas 69027-070, Brazil
| | | | - Tirza Mattos
- Laboratório Central de Saúde Pública do Amazonas, Manaus 69020-040, Brazil
| | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fiocruz, Recife, Pernambuco 50670-420, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fiocruz, Recife, Pernambuco 50670-420, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ, Manaus, Amazonas 69027-070, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre 29500-000, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil
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19
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Siracusano G, Ruggiero A, Bisoffi Z, Piubelli C, Carbonare LD, Valenti MT, Mayora-Neto M, Temperton N, Lopalco L, Zipeto D. Different decay of antibody response and VOC sensitivity in naïve and previously infected subjects at 15 weeks following vaccination with BNT162b2. J Transl Med 2022; 20:22. [PMID: 34998405 PMCID: PMC8742572 DOI: 10.1186/s12967-021-03208-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/17/2021] [Indexed: 02/01/2023] Open
Abstract
Background COVID-19 vaccines have demonstrated effectiveness in reducing SARS-CoV-2 mild and severe outcomes. In vaccinated subjects with SARS-CoV-2 history, RBD-specific IgG and pseudovirus neutralization titers were rapidly recalled by a single BTN162b2 vaccine dose to higher levels than those in naïve recipients after the second dose, irrespective of waning immunity. In this study, we inspected the long-term kinetic and neutralizing responses of S-specific IgG induced by two administrations of BTN162b2 vaccine in infection-naïve subjects and in subjects previously infected with SARS-CoV-2. Methods Twenty-six naïve and 9 previously SARS-CoV-2 infected subjects during the second wave of the pandemic in Italy were enrolled for this study. The two groups had comparable demographic and clinical characteristics. By means of ELISA and pseudotyped-neutralization assays, we investigated the kinetics of developed IgG-RBD and their neutralizing activity against both the ancestral D614G and the SARS-CoV-2 variants of concern emerged later, respectively. The Wilcoxon matched pair signed rank test and the Kruskal–Wallis test with Dunn’s correction for multiple comparison were applied when needed. Results Although after 15 weeks from vaccination IgG-RBD dropped in all participants, naïve subjects experienced a more dramatic decline than those with previous SARS-CoV-2 infection. Neutralizing antibodies remained higher in subjects with SARS-CoV-2 history and conferred broad-spectrum protection. Conclusions These data suggest that hybrid immunity to SARS-CoV-2 has a relevant impact on the development of IgG-RBD upon vaccination. However, the rapid decay of vaccination-elicited antibodies highlights that the administration of a third dose is expected to boost the response and acquire high levels of cross-neutralizing antibodies. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03208-3.
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Affiliation(s)
- Gabriel Siracusano
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milan, Italy.
| | - Alessandra Ruggiero
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital Negrar, Verona, Italy.,Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital Negrar, Verona, Italy
| | | | | | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, ME7, 47B, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, ME7, 47B, UK
| | - Lucia Lopalco
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milan, Italy
| | - Donato Zipeto
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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20
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Poudel S, Ishak A, Perez-Fernandez J, Garcia E, León-Figueroa DA, Romaní L, Bonilla-Aldana DK, Rodriguez-Morales AJ. Highly mutated SARS-CoV-2 Omicron variant sparks significant concern among global experts - What is known so far? Travel Med Infect Dis 2021; 45:102234. [PMID: 34896326 PMCID: PMC8666662 DOI: 10.1016/j.tmaid.2021.102234] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Sujan Poudel
- Division of Research and Academic Affairs, Larkin Community Hospital, South Miami, USA
| | - Angela Ishak
- Division of Research and Academic Affairs, Larkin Community Hospital, South Miami, USA
| | - Javier Perez-Fernandez
- Program Director, Pulmonary and Critical Care Fellowship Training Program, Larkin University, Miami, USA
| | - Efrain Garcia
- Program Director, Infectious Disease Fellowship Training Program, Larkin Community Hospital, Miami, USA
| | - Darwin A León-Figueroa
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Chiclayo, Peru; Sociedad Científica Médico Estudiantil Peruana, Lima, Peru; Sociedad Científica de Estudiantes de Medicina Veritas (SCIEMVE), Chiclayo, Peru; Emerge, Unidad de Investigación en Enfermedades Emergentes y Cambio Climático, Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia. Lima, Peru
| | - Luccio Romaní
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Chiclayo, Peru; Sociedad Científica de Estudiantes de Medicina Veritas (SCIEMVE), Chiclayo, Peru; Emerge, Unidad de Investigación en Enfermedades Emergentes y Cambio Climático, Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia. Lima, Peru
| | - D Katterine Bonilla-Aldana
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación GISCA, Fundación Universitaria Autónoma de Las Américas, Pereira, Risaralda, Colombia; Latin American Network of Coronavirus Disease 2019 Research (LANCOVID), Pereira, 660003, Colombia; Institución Universitaria Visión de las Américas, Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Latin American Network of Coronavirus Disease 2019 Research (LANCOVID), Pereira, 660003, Colombia; Grupo de Investigacion Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de Las Americas, Pereira, Risaralda, Colombia; Universidad Cientifica Del Sur, Lima, Peru; School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia; Institución Universitaria Visión de las Américas, Pereira, Risaralda, Colombia.
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21
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Sariol CA, Serrano-Collazo C, Ortiz EJ, Pantoja P, Cruz L, Arana T, Atehortua D, Pabon-Carrero C, Espino AM. Limited Impact of Delta Variant's Mutations on the Effectiveness of Neutralization Conferred by Natural Infection or COVID-19 Vaccines in a Latino Population. Viruses 2021; 13:2405. [PMID: 34960674 PMCID: PMC8707683 DOI: 10.3390/v13122405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 pandemic has impacted public health systems all over the world. The Delta variant seems to possess enhanced transmissibility, but no clear evidence suggests it has increased virulence. Our data show that pre-exposed individuals had similar neutralizing activity against the authentic COVID-19 strain and the Delta and Epsilon variants. After only one vaccine dose, the neutralization capacity expanded to all tested variants in pre-exposed individuals. Healthy vaccinated individuals showed a limited breadth of neutralization. One vaccine dose did induce similar neutralizing antibodies against the Delta as against the authentic strain. However, even after two doses, this capacity only expanded to the Epsilon variant.
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Affiliation(s)
- Carlos A. Sariol
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (L.C.); (T.A.); (A.M.E.)
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (C.S.-C.); (E.J.O.); (P.P.)
- Department of Internal Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA
| | - Crisanta Serrano-Collazo
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (C.S.-C.); (E.J.O.); (P.P.)
| | - Edwin J. Ortiz
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (C.S.-C.); (E.J.O.); (P.P.)
- Puerto Rico Science, Technology and Research Trust, San Juan, PR 00927, USA; (D.A.); (C.P.-C.)
| | - Petraleigh Pantoja
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (C.S.-C.); (E.J.O.); (P.P.)
| | - Lorna Cruz
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (L.C.); (T.A.); (A.M.E.)
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (C.S.-C.); (E.J.O.); (P.P.)
| | - Teresa Arana
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (L.C.); (T.A.); (A.M.E.)
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (C.S.-C.); (E.J.O.); (P.P.)
| | - Dianne Atehortua
- Puerto Rico Science, Technology and Research Trust, San Juan, PR 00927, USA; (D.A.); (C.P.-C.)
| | - Christina Pabon-Carrero
- Puerto Rico Science, Technology and Research Trust, San Juan, PR 00927, USA; (D.A.); (C.P.-C.)
| | - Ana M. Espino
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936, USA; (L.C.); (T.A.); (A.M.E.)
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22
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Sariol CA, Serrano-Collazo C, Ortiz EJ, Pantoja P, Cruz L, Arana T, Atehortua D, Pabon-Carrero C, Espino AM. Limited impact of Delta variant’s mutations in the effectiveness of neutralization conferred by natural infection or COVID-19 vaccines in a Latino population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.10.25.21265422. [PMID: 34729566 PMCID: PMC8562550 DOI: 10.1101/2021.10.25.21265422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The SARS-CoV-2 pandemic has impacted public health systems all over the world. The Delta variant seems to possess enhanced transmissibility, but no clear evidence suggests it has increased virulence. Our data shows that pre-exposed individuals had similar neutralizing activity against the authentic COVID-19 strain and the Delta and Epsilon variants. After one vaccine dose, the neutralization capacity expands to all tested variants. Healthy vaccinated individuals showed a limited breadth of neutralization. One vaccine dose induced similar neutralizing antibodies against the Delta compared to the authentic strain. However, even after two doses, this capacity only expanded to the Epsilon variant.
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Affiliation(s)
- Carlos A. Sariol
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
- Department of Internal medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | - Crisanta Serrano-Collazo
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | - Edwin J. Ortiz
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
- Puerto Rico Science, Technology and Research Trust, PR, USA
| | - Petraleigh Pantoja
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | - Lorna Cruz
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | - Teresa Arana
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | | | | | - Ana M. Espino
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
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