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Mokryn O, Abbey A, Marmor Y, Shahar Y. Evaluating the dynamic interplay of social distancing policies regarding airborne pathogens through a temporal interaction-driven model that uses real-world and synthetic data. J Biomed Inform 2024; 151:104601. [PMID: 38307358 DOI: 10.1016/j.jbi.2024.104601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/18/2023] [Accepted: 01/27/2024] [Indexed: 02/04/2024]
Abstract
OBJECTIVE The recent SARS-CoV-2 pandemic has exhibited diverse patterns of spread across countries and communities, emphasizing the need to consider the underlying population dynamics in modeling its progression and the importance of evaluating the effectiveness of non-pharmaceutical intervention strategies in combating viral transmission within human communities. Such an understanding requires accurate modeling of the interplay between the community dynamics and the disease propagation dynamics within the community. METHODS We build on an interaction-driven model of an airborne disease over contact networks that we have defined. Using the model, we evaluate the effectiveness of temporal, spatial, and spatiotemporal social distancing policies. Temporal social distancing involves a pure dilation of the timeline while preserving individual activity potential and thus prolonging the period of interaction; spatial distancing corresponds to social distancing pods; and spatiotemporal distancing pertains to the situation in which fixed subgroups of the overall group meet at alternate times. We evaluate these social distancing policies over real-world interactions' data and over history-preserving synthetic temporal random networks. Furthermore, we evaluate the policies for the disease's with different number of initial patients, corresponding to either the phase in the progression of the infection through a community or the number of patients infected together at the initial infection event. We expand our model to consider the exposure to viral load, which we correlate with the meetings' duration. RESULTS Our results demonstrate the superiority of decreasing social interactions (i.e., time dilation) within the community over partial isolation strategies, such as the spatial distancing pods and the spatiotemporal distancing strategy. In addition, we found that slow-spreading pathogens (i.e., pathogens that require a longer exposure to infect) spread roughly at the same rate as fast-spreading ones in highly active communities. This result is surprising since the pathogens may follow different paths. However, we demonstrate that the dilation of the timeline considerably slows the spread of the slower pathogens. CONCLUSIONS Our results demonstrate that the temporal dynamics of a community have a more significant effect on the spread of the disease than the characteristics of the spreading processes.
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Affiliation(s)
- Osnat Mokryn
- Department of Information Systems, University of Haifa, Israel.
| | - Alex Abbey
- Department of Information Systems, University of Haifa, Israel
| | - Yanir Marmor
- Department of Information Systems, University of Haifa, Israel
| | - Yuval Shahar
- Department of Software and Information Systems Engineering, Ben Gurion University, Beer-Sheva, Israel
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2
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Kim TH, Song MJ, Lim SY, Lee YJ, Cho YJ. Factors related to lung function outcomes in critically ill COVID-19 patients in South Korea. Acute Crit Care 2024; 39:100-107. [PMID: 38476063 PMCID: PMC11002626 DOI: 10.4266/acc.2023.00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND New variants of the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic continue to emerge. However, little is known about the effect of these variants on clinical outcomes. This study evaluated the risk factors for poor pulmonary lung function test (PFT). METHODS The study retrospectively analyzed 87 patients in a single hospital and followed up by performing PFTs at an outpatient clinic from January 2020 to December 2021. COVID-19 variants were categorized as either a non-delta variant (November 13, 2020-July 6, 2021) or the delta variant (July 7, 2021-January 29, 2022). RESULTS The median age of the patients was 62 years, and 56 patients (64.4%) were male. Mechanical ventilation (MV) was provided for 52 patients, and 36 (41.4%) had restrictive lung defects. Forced vital capacity (FVC) and diffusion capacity of the lung for carbon monoxide (DLCO ) were lower in patients on MV. Male sex (odds ratio [OR], 0.228) and MV (OR, 4.663) were significant factors for decreased DLCO . The duration of MV was associated with decreased FVC and DLCO . However, the type of variant did not affect the decrease in FVC (P=0.750) and DLCO (P=0.639). CONCLUSIONS Among critically ill COVID-19 patients, 40% had restrictive patterns with decreased DLCO . The reduction of PFT was associated with MV, type of variants.
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Affiliation(s)
- Tae Hun Kim
- 1Division of Pulmonary Medicine, Department of Internal Medicine, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu, Korea
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Myung Jin Song
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Sung Yoon Lim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Yeon Joo Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Young-Jae Cho
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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3
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Zhang L, Cao H, Medlin K, Pearson J, Aristotelous AC, Chen A, Wessler T, Forest MG. Computational Modeling Insights into Extreme Heterogeneity in COVID-19 Nasal Swab Data. Viruses 2023; 16:69. [PMID: 38257769 PMCID: PMC10820884 DOI: 10.3390/v16010069] [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: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024] Open
Abstract
Throughout the COVID-19 pandemic, an unprecedented level of clinical nasal swab data from around the globe has been collected and shared. Positive tests have consistently revealed viral titers spanning six orders of magnitude! An open question is whether such extreme population heterogeneity is unique to SARS-CoV-2 or possibly generic to viral respiratory infections. To probe this question, we turn to the computational modeling of nasal tract infections. Employing a physiologically faithful, spatially resolved, stochastic model of respiratory tract infection, we explore the statistical distribution of human nasal infections in the immediate 48 h of infection. The spread, or heterogeneity, of the distribution derives from variations in factors within the model that are unique to the infected host, infectious variant, and timing of the test. Hypothetical factors include: (1) reported physiological differences between infected individuals (nasal mucus thickness and clearance velocity); (2) differences in the kinetics of infection, replication, and shedding of viral RNA copies arising from the unique interactions between the host and viral variant; and (3) differences in the time between initial cell infection and the clinical test. Since positive clinical tests are often pre-symptomatic and independent of prior infection or vaccination status, in the model we assume immune evasion throughout the immediate 48 h of infection. Model simulations generate the mean statistical outcomes of total shed viral load and infected cells throughout 48 h for each "virtual individual", which we define as each fixed set of model parameters (1) and (2) above. The "virtual population" and the statistical distribution of outcomes over the population are defined by collecting clinically and experimentally guided ranges for the full set of model parameters (1) and (2). This establishes a model-generated "virtual population database" of nasal viral titers throughout the initial 48 h of infection of every individual, which we then compare with clinical swab test data. Support for model efficacy comes from the sampling of infection dynamics over the virtual population database, which reproduces the six-order-of-magnitude clinical population heterogeneity. However, the goal of this study is to answer a deeper biological and clinical question. What is the impact on the dynamics of early nasal infection due to each individual physiological feature or virus-cell kinetic mechanism? To answer this question, global data analysis methods are applied to the virtual population database that sample across the entire database and de-correlate (i.e., isolate) the dynamic infection outcome sensitivities of each model parameter. These methods predict the dominant, indeed exponential, driver of population heterogeneity in dynamic infection outcomes is the latency time of infected cells (from the moment of infection until onset of viral RNA shedding). The shedding rate of the viral RNA of infected cells in the shedding phase is a strong, but not exponential, driver of infection. Furthermore, the unknown timing of the nasal swab test relative to the onset of infection is an equally dominant contributor to extreme population heterogeneity in clinical test data since infectious viral loads grow from undetectable levels to more than six orders of magnitude within 48 h.
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Affiliation(s)
- Leyi Zhang
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Han Cao
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen Medlin
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason Pearson
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Simulations Plus, Inc., 6 Davis Dr., Durham, NC 27709, USA
| | | | - Alexander Chen
- Department of Mathematics, California State University, Dominguez Hills, CA 90747, USA
| | - Timothy Wessler
- Department of Applied Mathematics, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - M. Gregory Forest
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Departments of Applied Physical Sciences and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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4
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Hijano DR, Ferrolino JA, Gu Z, Brazelton JN, Zhu H, Suganda S, Glasgow HL, Dallas RH, Allison KJ, Maron G, Darji H, Tang L, Fabrizio TP, Webby RJ, Hayden RT. Digital PCR to Measure SARS-CoV-2 RNA, Variants, and Outcomes in Youth. J Pediatric Infect Dis Soc 2023; 12:618-626. [PMID: 37956414 PMCID: PMC10725239 DOI: 10.1093/jpids/piad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND The role of SARS-CoV-2 viral load in predicting contagiousness, disease severity, transmissibility, and clinical decision-making continues to be an area of great interest. However, most studies have been in adults and have evaluated SARS-CoV-2 loads using cycle thresholds (Ct) values, which are not standardized preventing consistent interpretation critical to understanding clinical impact and utility. Here, a quantitative SARS-CoV-2 reverse-transcription digital PCR (RT-dPCR) assay normalized to WHO International Units was applied to children at risk of severe disease diagnosed with COVID-19 at St. Jude Children's Research Hospital between March 28, 2020, and January 31, 2022. METHODS Demographic and clinical information from children, adolescents, and young adults treated at St. Jude Children's Research Hospital were abstracted from medical records. Respiratory samples underwent SARS-CoV-2 RNA quantitation by RT-dPCR targeting N1 and N2 genes, with sequencing to determine the genetic lineage of infecting virus. RESULTS Four hundred and sixty-two patients aged 0-24 years (median 11 years old) were included during the study period. Most patients were infected by the omicron variant (43.72%), followed by ancestral strain (22.29%), delta (13.20%), and alpha (2.16%). Viral load at presentation ranged from 2.49 to 9.14 log10 IU/mL, and higher viral RNA loads were associated with symptoms (OR 1.32; CI 95% 1.16-1.49) and respiratory disease (OR 1.23; CI 95% 1.07-1.41). Viral load did not differ by SARS-CoV-2 variant, vaccination status, age, or baseline diagnosis. CONCLUSIONS SARS-CoV-2 RNA loads predict the presence of symptomatic and respiratory diseases. The use of standardized, quantitative methods is feasible, allows for replication, and comparisons across institutions, and has the potential to facilitate consensus quantitative thresholds for risk stratification and treatment.
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Affiliation(s)
- Diego R Hijano
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jose A Ferrolino
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Zhengming Gu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jessica N Brazelton
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Haiqing Zhu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Sri Suganda
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Heather L Glasgow
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ronald H Dallas
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Kim J Allison
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Maron
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Himani Darji
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Li Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Thomas P Fabrizio
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Richard J Webby
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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Yang X, Shi F, Zhang J, Gao H, Chen S, Olatosi B, Weissman S, Li X. Disease severity of COVID-19 in different phases of the pandemic: Do healthcare workers have better outcomes? Vaccine X 2023; 15:100377. [PMID: 37681205 PMCID: PMC10480519 DOI: 10.1016/j.jvacx.2023.100377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Background This study aimed to characterize and compare the demographics, clinical profile, and COVID-19 outcomes between healthcare workers (HCWs) and non-HCWs COVID-19 patients diagnosed in different phases of the pandemic defined by the vaccine rollout policy and different variants that circulated in South Carolina (SC). Methods Extracted from the statewide electronic health record data, we analyzed the clinical outcome of 34,502 HCWs and 1,071,020 non-HCWs adults diagnosed with SARS-CoV-2 between March 2, 2020 to April 14, 2022. Logistic regression models were used to explore the association between different pandemic phases and COVID-19 severity-related outcomes. Results Substantial reductions in mortality were observed following the vaccine rollout in non-HCWs and HCWs. Compared to the pre-vaccination period, non-HCWs patients diagnosed during post-vaccination with Alpha predominance (adjusted odds ratio [aOR]: 1.10; 95%CI: 1.04-1.16) were more likely to be hospitalized, but the reduced mortality rates were observed in all post-vaccination periods. Regarding HCWs, a reduced mortality rate was only observed in the pre-Alpha (aOR: 0.33; 95%CI: 0.13-0.84) and Omicron periods (aOR: 0.21; 95%CI: 0.05-0.89). Conclusions The declining protection effect of vaccines informs the importance of early promotion of the booster dose of the COVID-19 vaccine for HCWs who have more occupational exposure.
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Affiliation(s)
- Xueying Yang
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Department of Health Promotion, Education and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Fanghui Shi
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Department of Health Promotion, Education and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Jiajia Zhang
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Haoyuan Gao
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Shujie Chen
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Bankole Olatosi
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Sharon Weissman
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Department of Internal Medicine, School of Medicine, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoming Li
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Department of Health Promotion, Education and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
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Bruckhaus AA, Zhang Y, Salehi S, Abedi A, Duncan D. Relationships between COVID-19 healthcare outcomes and county characteristics in the U.S. for Delta (B.1.617.2) and Omicron (B.1.1.529 and BA.1.1) variants. Front Public Health 2023; 11:1252668. [PMID: 38045980 PMCID: PMC10693294 DOI: 10.3389/fpubh.2023.1252668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Background COVID-19 is constantly evolving, and highly populated communities consist of many different characteristics that may contribute to COVID-19 health outcomes. Therefore, we aimed to (1) quantify the relationships between county characteristics and severe and non-severe county-level health outcomes related to COVID-19. We also aimed to (2) compare these relationships across time periods where the Delta (B.1.617.2) and Omicron (B.1.1.529 and BA.1.1) variants were dominant in the U.S. Methods We used multiple regression to measure the strength of relationships between healthcare outcomes and county characteristics in the 50 most populous U.S. counties. Results We found many different significant predictors including the proportion of a population vaccinated, median household income, population density, and the proportion of residents aged 65+, but mainly found that socioeconomic factors and the proportion of a population vaccinated play a large role in the dynamics of the spread and severity of COVID-19 in communities with high populations. Discussion The present study shines light on the associations between public health outcomes and county characteristics and how these relationships change throughout Delta and Omicron's dominance. It is important to understand factors underlying COVID-19 health outcomes to prepare for future health crises.
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Affiliation(s)
- Alexander A. Bruckhaus
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
| | - Yujia Zhang
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
| | - Sana Salehi
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
| | - Aidin Abedi
- USC Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Rancho Research Institute, Rancho Los Amigos National Rehabilitation Center, Downey, CA, United States
| | - Dominique Duncan
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
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Ellis LP, Hess O, Huynh KLA, Bearman G, Kang L, Doern CD. A comparison of severity of illness between the SARS-CoV-2 Omicron variant and Delta variant. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e188. [PMID: 38028915 PMCID: PMC10654945 DOI: 10.1017/ash.2023.453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 12/01/2023]
Abstract
Background The COVID-19 pandemic has disproportionally affected traditionally marginalized groups. Both the Delta and Omicron variants raised concern amongst public health officials due to potentially higher infectivity rates and disease severity than prior variants. This study sought to compare disease severity between adults infected with the Omicron variant and adults infected with the Delta variant who presented to the Emergency Department at an academic, safety-net hospital in Virginia. Methods This retrospective cohort study used electronic medical record data of patients who presented to the Emergency Department and received a positive SARS-CoV-2 test between September 1, 2021, and January 31, 2022. Positive tests were stratified by genotypic variant through whole genome sequencing. Participants with the Omicron variant were propensity scores matched with individuals with the Delta variant. Results Among 500 Delta and 500 Omicron participants, 279 propensity score-matched pairs were identified. Participants were predominantly unvaccinated, with medical comorbidities, and self-identified as Black. Individuals infected with the Delta variant had more severe disease compared to those with the Omicron variant, regardless of vaccination status. Patients with kidney, liver, and respiratory disease, as well as cancer, are at higher risk for severe disease. Patients with 2 doses of COVID-19 immunization trended toward less severe disease. Conclusions Overall, these data further support the literature regarding the disproportionate effects of the COVID-19 pandemic on vulnerable patient populations - such as those with limited access to care, people of color, and those with chronic medical conditions - and can be used to inform public health interventions.
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Affiliation(s)
- Laura Peyton Ellis
- Obstetrics and Gynecology Residency Program, University of Connecticut, Farmington, CT, USA
| | - Olivia Hess
- School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Khoa Le Anh Huynh
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Gonzalo Bearman
- Richard P. Wenzel Professor of Medicine, Chair, Division of Infectious Diseases, Virginia Commonwealth University, Richmond, VA, USA
- Antimicrobial Stewardship and Healthcare Epidemiology, Cambridge University Press, Cambridge, UK
| | - Le Kang
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Christopher D. Doern
- Microbiology & Pathology and Pediatrics, Virginia Commonwealth University, Richmond, VA, USA
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Ribeiro RM, Choudhary MC, Deo R, Giganti MJ, Moser C, Ritz J, Greninger AL, Regan J, Flynn JP, Wohl DA, Currier JS, Eron JJ, Hughes MD, Smith DM, Chew KW, Daar ES, Perelson AS, Li JZ. Variant-Specific Viral Kinetics in Acute COVID-19. J Infect Dis 2023; 228:S136-S143. [PMID: 37650233 PMCID: PMC10469346 DOI: 10.1093/infdis/jiad314] [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] [Indexed: 09/01/2023] Open
Abstract
Understanding variant-specific differences in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral kinetics may explain differences in transmission efficiency and provide insights on pathogenesis and prevention. We evaluated SARS-CoV-2 kinetics from nasal swabs across multiple variants (Alpha, Delta, Epsilon, Gamma) in placebo recipients of the ACTIV-2/A5401 trial. Delta variant infection led to the highest maximum viral load and shortest time from symptom onset to viral load peak. There were no significant differences in time to viral clearance across the variants. Viral decline was biphasic with first- and second-phase decays having half-lives of 11 hours and 2.5 days, respectively, with differences among variants, especially in the second phase. These results suggest that while variant-specific differences in viral kinetics exist, post-peak viral load all variants appeared to be efficiently cleared by the host. Clinical Trials Registration. NCT04518410.
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Affiliation(s)
- Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico
| | - Manish C Choudhary
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Rinki Deo
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Mark J Giganti
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Carlee Moser
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Justin Ritz
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | - James Regan
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - James P Flynn
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - David A Wohl
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill
| | - Judith S Currier
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Joseph J Eron
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill
| | - Michael D Hughes
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California
| | - Kara W Chew
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Eric S Daar
- Lundquist Institute, Harbor-UCLA Medical Center, Torrance, California
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
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9
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Dimcheff DE, Blair CN, Zhu Y, Chappell JD, Gaglani M, McNeal T, Ghamande S, Steingrub JS, Shapiro NI, Duggal A, Busse LW, Frosch AEP, Peltan ID, Hager DN, Gong MN, Exline MC, Khan A, Wilson JG, Qadir N, Ginde AA, Douin DJ, Mohr NM, Mallow C, Martin ET, Johnson NJ, Casey JD, Stubblefield WB, Gibbs KW, Kwon JH, Talbot HK, Halasa N, Grijalva CG, Baughman A, Womack KN, Hart KW, Swan SA, Surie D, Thornburg NJ, McMorrow ML, Self WH, Lauring AS. Total and Subgenomic RNA Viral Load in Patients Infected With SARS-CoV-2 Alpha, Delta, and Omicron Variants. J Infect Dis 2023; 228:235-244. [PMID: 36883903 PMCID: PMC10420395 DOI: 10.1093/infdis/jiad061] [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: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic and subgenomic RNA levels are frequently used as a correlate of infectiousness. The impact of host factors and SARS-CoV-2 lineage on RNA viral load is unclear. METHODS Total nucleocapsid (N) and subgenomic N (sgN) RNA levels were measured by quantitative reverse transcription polymerase chain reaction (RT-qPCR) in specimens from 3204 individuals hospitalized with coronavirus disease 2019 (COVID-19) at 21 hospitals. RT-qPCR cycle threshold (Ct) values were used to estimate RNA viral load. The impact of time of sampling, SARS-CoV-2 variant, age, comorbidities, vaccination, and immune status on N and sgN Ct values were evaluated using multiple linear regression. RESULTS Mean Ct values at presentation for N were 24.14 (SD 4.53) for non-variants of concern, 25.15 (SD 4.33) for Alpha, 25.31 (SD 4.50) for Delta, and 26.26 (SD 4.42) for Omicron. N and sgN RNA levels varied with time since symptom onset and infecting variant but not with age, comorbidity, immune status, or vaccination. When normalized to total N RNA, sgN levels were similar across all variants. CONCLUSIONS RNA viral loads were similar among hospitalized adults, irrespective of infecting variant and known risk factors for severe COVID-19. Total N and subgenomic RNA N viral loads were highly correlated, suggesting that subgenomic RNA measurements add little information for the purposes of estimating infectivity.
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Affiliation(s)
- Derek E Dimcheff
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher N Blair
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Manjusha Gaglani
- Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Tresa McNeal
- Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Shekhar Ghamande
- Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Jay S Steingrub
- Department of Medicine, Baystate Medical Center, Springfield, Massachusetts, USA
| | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Abhijit Duggal
- Department of Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Anne E P Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, Minnesota, USA
| | - Ithan D Peltan
- Department of Medicine, Intermountain Medical Center, Murray, Utah, USA
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - David N Hager
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michelle N Gong
- Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Matthew C Exline
- Department of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Akram Khan
- Department of Medicine, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Jennifer G Wilson
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Nida Qadir
- Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Adit A Ginde
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - David J Douin
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Nicholas M Mohr
- Department of Emergency Medicine, University of Iowa, Iowa City, Iowa, USA
| | | | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicholas J Johnson
- Department of Emergency Medicine and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington, USA
| | - Jonathan D Casey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - William B Stubblefield
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kevin W Gibbs
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jennie H Kwon
- Department of Medicine, Washington University, St Louis, Missouri, USA
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kimberly W Hart
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Diya Surie
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natalie J Thornburg
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Meredith L McMorrow
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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10
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Marmor Y, Abbey A, Shahar Y, Mokryn O. Assessing individual risk and the latent transmission of COVID-19 in a population with an interaction-driven temporal model. Sci Rep 2023; 13:12955. [PMID: 37563358 PMCID: PMC10415258 DOI: 10.1038/s41598-023-39817-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Interaction-driven modeling of diseases over real-world contact data has been shown to promote the understanding of the spread of diseases in communities. This temporal modeling follows the path-preserving order and timing of the contacts, which are essential for accurate modeling. Yet, other important aspects were overlooked. Various airborne pathogens differ in the duration of exposure needed for infection. Also, from the individual perspective, Covid-19 progression differs between individuals, and its severity is statistically correlated with age. Here, we enrich an interaction-driven model of Covid-19 and similar airborne viral diseases with (a) meetings duration and (b) personal disease progression. The enriched model enables predicting outcomes at both the population and the individual levels. It further allows predicting individual risk of engaging in social interactions as a function of the virus characteristics and its prevalence in the population. We further showed that the enigmatic nature of asymptomatic transmission stems from the latent effect of the network density on this transmission and that asymptomatic transmission has a substantial impact only in sparse communities.
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Affiliation(s)
- Yanir Marmor
- Information Systems, University of Haifa, Haifa, Israel
| | - Alex Abbey
- Information Systems, University of Haifa, Haifa, Israel
| | - Yuval Shahar
- Software and Information Systems Engineering, Ben Gurion University, Beer Sheva, Israel
| | - Osnat Mokryn
- Information Systems, University of Haifa, Haifa, Israel.
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11
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Tarantino N, Litvinova E, Samri A, Soulié C, Morin V, Rousseau A, Dorgham K, Parizot C, Bonduelle O, Beurton A, Miyara M, Ghillani P, Mayaux J, Lhote R, Lacorte JM, Marcelin AG, Amoura Z, Luyt CE, Gorochov G, Guihot A, Vieillard V. Identification of natural killer markers associated with fatal outcome in COVID-19 patients. Front Cell Infect Microbiol 2023; 13:1165756. [PMID: 37342247 PMCID: PMC10277643 DOI: 10.3389/fcimb.2023.1165756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/18/2023] [Indexed: 06/22/2023] Open
Abstract
Introduction Increasing evidence has shown that coronavirus disease 19 (COVID-19) severity is driven by a dysregulated immunological response. Previous studies have demonstrated that natural killer (NK) cell dysfunction underpins severe illness in COVID-19 patients, but have lacked an in-depth analysis of NK cell markers as a driver of death in the most critically ill patients. Methods We enrolled 50 non-vaccinated hospitalized patients infected with the initial virus or the alpha variant of SARS-CoV-2 with moderate or severe illness, to evaluate phenotypic and functional features of NK cells. Results Here, we show that, consistent with previous studies, evolution NK cells from COVID-19 patients are more activated, with the decreased activation of natural cytotoxicity receptors and impaired cytotoxicity and IFN-γ production, in association with disease regardless of the SARS-CoV-2 strain. Fatality was observed in 6 of 17 patients with severe disease; NK cells from all of these patients displayed a peculiar phenotype of an activated memory-like phenotype associated with massive TNF-α production. Discussion These data suggest that fatal COVID-19 infection is driven by an uncoordinated inflammatory response in part mediated by a specific subset of activated NK cells.
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Affiliation(s)
- Nadine Tarantino
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
| | - Elena Litvinova
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Département d’Immunologie, Paris, France
| | - Assia Samri
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
| | - Cathia Soulié
- Sorbonne Université, Inserm, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), Assistance Publique – Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, Paris, France
| | - Véronique Morin
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
| | - Alice Rousseau
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
| | - Karim Dorgham
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
| | - Christophe Parizot
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Département d’Immunologie, Paris, France
| | - Olivia Bonduelle
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
| | - Alexandra Beurton
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Médecine Intensive-Réanimation et Pneumologie, Paris, France
- Sorbonne Université, Inserm UMRS Neurophysiologie Respiratoire Expérimentale et Clinique, Assistance Publique – Hôpitaux de Paris (AP-HP), Paris, France
| | - Makoto Miyara
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Département d’Immunologie, Paris, France
| | - Pascale Ghillani
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Département d’Immunologie, Paris, France
| | - Julien Mayaux
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Médecine Intensive-Réanimation et Pneumologie, Paris, France
| | - Raphael Lhote
- Service de Médecine Interne 2, Institut E3M, Assistance Publique – Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Paris, France
| | - Jean-Marc Lacorte
- Sorbonne Université, Inserm, UMRS1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France
- Service de Biochimie Endocrinienne et Oncologique, Assistance Publique – Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, Inserm, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), Assistance Publique – Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, Paris, France
| | - Zahir Amoura
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
- Service de Médecine Interne 2, Institut E3M, Assistance Publique – Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Paris, France
| | - Charles-Edouard Luyt
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Médecine Intensive-Réanimation et Pneumologie, Paris, France
- Service de Médecine Interne 2, Institut E3M, Assistance Publique – Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Paris, France
| | - Guy Gorochov
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Département d’Immunologie, Paris, France
| | - Amélie Guihot
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Département d’Immunologie, Paris, France
| | - Vincent Vieillard
- Sorbonne Université, Inserm, CNRS, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, Paris, France
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12
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Pearson J, Wessler T, Chen A, Boucher RC, Freeman R, Lai SK, Pickles R, Forest MG. Modeling identifies variability in SARS-CoV-2 uptake and eclipse phase by infected cells as principal drivers of extreme variability in nasal viral load in the 48 h post infection. J Theor Biol 2023; 565:111470. [PMID: 36965846 PMCID: PMC10033495 DOI: 10.1016/j.jtbi.2023.111470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/25/2023]
Abstract
The SARS-CoV-2 coronavirus continues to evolve with scores of mutations of the spike, membrane, envelope, and nucleocapsid structural proteins that impact pathogenesis. Infection data from nasal swabs, nasal PCR assays, upper respiratory samples, ex vivo cell cultures and nasal epithelial organoids reveal extreme variabilities in SARS-CoV-2 RNA titers within and between the variants. Some variabilities are naturally prone to clinical testing protocols and experimental controls. Here we focus on nasal viral load sensitivity arising from the timing of sample collection relative to onset of infection and from heterogeneity in the kinetics of cellular infection, uptake, replication, and shedding of viral RNA copies. The sources of between-variant variability are likely due to SARS-CoV-2 structural protein mutations, whereas within-variant population variability is likely due to heterogeneity in cellular response to that particular variant. With the physiologically faithful, agent-based mechanistic model of inhaled exposure and infection from (Chen et al., 2022), we perform statistical sensitivity analyses of the progression of nasal viral titers in the first 0-48 h post infection, focusing on three kinetic mechanisms. Model simulations reveal shorter latency times of infected cells (including cellular uptake, viral RNA replication, until the onset of viral RNA shedding) exponentially accelerate nasal viral load. Further, the rate of infectious RNA copies shed per day has a proportional influence on nasal viral load. Finally, there is a very weak, negative correlation of viral load with the probability of infection per virus-cell encounter, the model proxy for spike-receptor binding affinity.
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Affiliation(s)
- Jason Pearson
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy Wessler
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alex Chen
- Department of Mathematics, California State University-Dominguez Hills, Carson, CA 90747, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel K Lai
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27606, USA; Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Raymond Pickles
- Marsico Lung Institute, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Gregory Forest
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Department of Applied Physical Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27606, USA.
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13
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Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS CENTRAL SCIENCE 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
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Affiliation(s)
- Sizhu
Amelia Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Bashir Khan
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bing Bai
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - James A. Nieman
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
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14
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Silva JDP, Lima ABD, Alvim LB, Malta FSV, Mendonça CPTB, Carvalho AHBD, Rios JSH, Fonseca PLC, Queiroz DC, Santos LCGDAE, Ferreira ACDS, Souza RPD, Aguiar RSD, Zauli DAG. Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil. Viruses 2023; 15:v15041017. [PMID: 37112997 PMCID: PMC10145299 DOI: 10.3390/v15041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The introduction of SARS-CoV-2 variants of concern (VOCs) in Brazil has been associated with major impacts on the epidemiological and public health scenario. In this study, 291,571 samples were investigated for SARS-CoV-2 variants from August 2021 to March 2022 (the highest peak of positive cases) in four geographical regions of Brazil. To identify the frequency, introduction, and dispersion of SARS-CoV-2 variants in 12 Brazilian capitals, VOCs defining spike mutations were identified in 35,735 samples through genotyping and viral genome sequencing. Omicron VOC was detected in late November 2021 and replaced the Delta VOC in approximately 3.5 weeks. We estimated viral load differences between SARS-CoV-2 Delta and Omicron through the evaluation of the RT-qPCR cycle threshold (Ct) score in 77,262 samples. The analysis demonstrated that the Omicron VOC has a lower viral load in infected patients than the Delta VOC. Analyses of clinical outcomes in 17,586 patients across the country indicated that individuals infected with Omicron were less likely to need ventilatory support. The results of our study reinforce the importance of surveillance programs at the national level and showed the introduction and faster dispersion of Omicron over Delta VOC in Brazil without increasing the numbers of severe cases of COVID-19.
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Affiliation(s)
- Joice do Prado Silva
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | - Aline Brito de Lima
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | - Luige Biciati Alvim
- Departamento de Produtos e Inovação, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | | | | | | | | | - Paula Luize Camargos Fonseca
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Daniel Costa Queiroz
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Luíza Campos Guerra de Araújo E Santos
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Renan Pedra de Souza
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Renato Santana de Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro 22281-100, Brazil
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15
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Rao R, Musante CJ, Allen R. A quantitative systems pharmacology model of the pathophysiology and treatment of COVID-19 predicts optimal timing of pharmacological interventions. NPJ Syst Biol Appl 2023; 9:13. [PMID: 37059734 PMCID: PMC10102696 DOI: 10.1038/s41540-023-00269-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/09/2023] [Indexed: 04/16/2023] Open
Abstract
A quantitative systems pharmacology (QSP) model of the pathogenesis and treatment of SARS-CoV-2 infection can streamline and accelerate the development of novel medicines to treat COVID-19. Simulation of clinical trials allows in silico exploration of the uncertainties of clinical trial design and can rapidly inform their protocols. We previously published a preliminary model of the immune response to SARS-CoV-2 infection. To further our understanding of COVID-19 and treatment, we significantly updated the model by matching a curated dataset spanning viral load and immune responses in plasma and lung. We identified a population of parameter sets to generate heterogeneity in pathophysiology and treatment and tested this model against published reports from interventional SARS-CoV-2 targeting mAb and antiviral trials. Upon generation and selection of a virtual population, we match both the placebo and treated responses in viral load in these trials. We extended the model to predict the rate of hospitalization or death within a population. Via comparison of the in silico predictions with clinical data, we hypothesize that the immune response to virus is log-linear over a wide range of viral load. To validate this approach, we show the model matches a published subgroup analysis, sorted by baseline viral load, of patients treated with neutralizing Abs. By simulating intervention at different time points post infection, the model predicts efficacy is not sensitive to interventions within five days of symptom onset, but efficacy is dramatically reduced if more than five days pass post symptom onset prior to treatment.
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Affiliation(s)
- Rohit Rao
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA.
| | - Cynthia J Musante
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Richard Allen
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
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16
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Feng Q, Cui Q, Xiao Z, Liu Z, Fan S. Maternal and Perinatal Outcomes of SARS-CoV-2 and Variants in Pregnancy. MATERNAL-FETAL MEDICINE 2023. [DOI: 10.1097/fm9.0000000000000189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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17
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SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19. Diagnostics (Basel) 2023; 13:diagnostics13030559. [PMID: 36766664 PMCID: PMC9913917 DOI: 10.3390/diagnostics13030559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.
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18
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Temporal Series Analysis of Population Cycle Threshold Counts as a Predictor of Surge in Cases and Hospitalizations during the SARS-CoV-2 Pandemic. Viruses 2023; 15:v15020421. [PMID: 36851635 PMCID: PMC9959442 DOI: 10.3390/v15020421] [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: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Tools to predict surges in cases and hospitalizations during the COVID-19 pandemic may help guide public health decisions. Low cycle threshold (CT) counts may indicate greater SARS-CoV-2 concentrations in the respiratory tract, and thereby may be used as a surrogate marker of enhanced viral transmission. Several population studies have found an association between the oscillations in the mean CT over time and the evolution of the pandemic. For the first time, we applied temporal series analysis (Granger-type causality) to validate the CT counts as an epidemiological marker of forthcoming pandemic waves using samples and analyzing cases and hospital admissions during the third pandemic wave (October 2020 to May 2021) in Madrid. A total of 22,906 SARS-CoV-2 RT-PCR-positive nasopharyngeal swabs were evaluated; the mean CT value was 27.4 (SD: 2.1) (22.2% below 20 cycles). During this period, 422,110 cases and 36,727 hospital admissions were also recorded. A temporal association was found between the CT counts and the cases of COVID-19 with a lag of 9-10 days (p ≤ 0.01) and hospital admissions by COVID-19 (p < 0.04) with a lag of 2-6 days. According to a validated method to prove associations between variables that change over time, the short-term evolution of average CT counts in the population may forecast the evolution of the COVID-19 pandemic.
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Teyssou E, Marot S, Cocherie T, Fauchois A, Abdi B, Todesco E, Akhavan S, Pourcher V, Calvez V, Marcelin AG, Soulie C. Prolonged replication of BA.1 and BA.2 Omicron lineages compared to Delta variant in nasopharyngeal samples from COVID-19 patients. Infect Dis Now 2023; 53:104629. [PMID: 36323397 PMCID: PMC9618294 DOI: 10.1016/j.idnow.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVES We aimed to characterize and compare the viral loads (VL) of the Omicron BA.1 and BA.2 lineages and the Delta variant in nasopharyngeal samples from newly diagnosed COVID-19 patients and their kinetics over time. PATIENTS AND METHODS The kinetics of the VL were measured on the CT data from 215 SARS-CoV-2 positive patients who presented at least two positive PCRs a day apart and were screened for SARS-CoV-2 viral lineages. RESULTS We observed no significant difference in median CT value during the first diagnostic test between the Delta variant and the two Omicron lineages. However, the kinetics of CT decreases for the BA.1 and BA.2 lineage were significantly lengthier in time than the kinetics for the Delta variant. The BA.2 lineage presented lower median CT value (-2 CT) (inversely proportional to the VL) than the BA.1 lineage. CONCLUSIONS BA.2 Omicron lineage presented higher VL than BA.1 Omicron lineage at diagnostic. Omicron BA.1 and BA.2 lineages have more prolonged replication than the Delta variant.
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Affiliation(s)
- Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France.
| | - Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Théophile Cocherie
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Antoine Fauchois
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Basma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Eve Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Sepideh Akhavan
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Valérie Pourcher
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Service des maladies infectieuse, F-75013 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Cathia Soulie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France.
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20
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Fernández-de-Las-Peñas C, Cuadrado ML, Gómez-Mayordomo V, García-Azorín D, Arendt-Nielsen L. Headache as a COVID-19 onset symptom or Post-COVID symptom according to the SARS-CoV-2 Variant. Expert Rev Neurother 2023; 23:179-186. [PMID: 36857191 DOI: 10.1080/14737175.2023.2185138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
INTRODUCTION COVID19 associated headaches are highly common and there is currently an unmet need to better understand their association with SARSCoV2 variants. Headaches are a prevalent symptom in the acute phase of COVID19 and are associated with a better prognosis and better immune response. They are also a relevant post-COVID symptom. AREAS COVERED This article analyses the differences in the prevalence of headache as an onset symptom and in post-COVID headache among the different SARS-CoV-2 variants: the historical strain, Alpha, Delta and Omicron. The different pathophysiological mechanisms by which SARS-CoV-2 infection may cause headache are also discussed. EXPERT OPINION The presence of headache at the acute phase is a risk factor for post-COVID headache, whereas a history of primary headache does not appear to be associated with post-COVID headache. The prevalence of headache as an onset symptom appears to be variable for the different SARS-CoV-2 variants, but current data are inconclusive. However, the current evidence also suggests that headache represents a prevalent symptom in the acute and post-infection COVID-19 phase, regardless of SARS-CoV-2 variant.
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Affiliation(s)
- César Fernández-de-Las-Peñas
- Department of Physical Therapy, Occupational Therapy, Physical Medicine and Rehabilitation, Universidad Rey Juan Carlos (URJC), Madrid. Spain
- Center for Neuroplasticity and Pain (CNAP), SMI, Department of Health Science and Technology, Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Maria L Cuadrado
- Department of Neurology, Hospital Clínico San Carlos, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Victor Gómez-Mayordomo
- Department of Neurology, Institute of Neurosciences, Vithas Madrid La Milagrosa University Hospital. Madrid, Spain
| | - David García-Azorín
- Headache Unit, Department of Neurology, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
- Neuroscience Research Unit, Institute for Biomedical Research of Salamanca, Salamanca, Spain
| | - Lars Arendt-Nielsen
- Center for Neuroplasticity and Pain (CNAP), SMI, Department of Health Science and Technology, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Medical Gastroenterology, AMech-Sense, alborg University Hospital, Aalborg, Denmark
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21
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Lim MJR, Yeo J, Fong KY, Eng SWO, Fu S, Tan BYQ, Yeo LLL, Nga VDW, Yeo TT. Characteristics of subarachnoid hemorrhage associated with COVID-19 infection: A systematic review and descriptive analysis. J Stroke Cerebrovasc Dis 2023; 32:106904. [PMID: 36442281 PMCID: PMC9678815 DOI: 10.1016/j.jstrokecerebrovasdis.2022.106904] [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: 08/06/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Subarachnoid hemorrhage (SAH) has been reported as a neurological manifestation in 0.1% of COVID-19 patients. This systematic review investigated the outcomes and predictive factors of SAH in patients with COVID-19. MATERIALS AND METHODS An electronic literature search was conducted on PubMed, Embase, and Scopus from inception to 10th September 2021. Studies reporting SAH in COVID-19 patients were included. Demographic characteristics, risk factors for disease, severity of COVID-19, and mortality of SAH in COVID-19 patients were analyzed. Subgroup analyses stratified by COVID-19 severity and mortality were conducted. RESULTS 17 case reports, 11 case series, and 2 retrospective cohort studies, with a total of 345 cases of SAH in COVID-19 patients, were included for analysis. Most published cases were reported in the US. Mean age was 55±18.4 years, and 162 patients (48.5%) were female. 242 patients (73.8%) had severe-to-critical COVID-19, 56.7% had aneurysmal SAH, 71.4% were on anticoagulation, and 10.8% underwent surgical treatment. 136 out of 333 patients (40.8%) died. Among patients with severe-to-critical COVID-19, 11 out of 18 (61.1%) died, and 8 out of 8 (100.0%) were non-aneurysmal SAH. CONCLUSIONS SAH is a rare but morbid occurrence in COVID-19. The mortality rate of COVID-SAH patients was 40.8%, with a higher prevalence of severe-to-critical COVID-19 (100% versus 53.8%) and non-aneurysmal SAH (85.7% versus 44.6%) among COVID-SAH deaths. Given the changing landscape of COVID-19 variants, further studies investigating the association between COVID-19 and SAH may be warranted to identify the long-term effects of COVID-19.
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Affiliation(s)
- Mervyn Jun Rui Lim
- Division of Neurosurgery, University Surgical Centre, National University Hospital, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Corresponding author at: Division of Neurosurgery, University Surgical Centre, National University Hospital, National University Health Systems Tower Block, 1E Kent Ridge Rd, 119228, Singapore
| | - Jonathan Yeo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Corresponding author at: Division of Neurosurgery, University Surgical Centre, National University Hospital, National University Health Systems Tower Block, 1E Kent Ridge Rd, 119228, Singapore
| | - Khi Yung Fong
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sean Wai-Onn Eng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shuning Fu
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Benjamin Yong-Qiang Tan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Leonard Leong Litt Yeo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Vincent Diong Weng Nga
- Division of Neurosurgery, University Surgical Centre, National University Hospital, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tseng Tsai Yeo
- Division of Neurosurgery, University Surgical Centre, National University Hospital, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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22
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Richardson SI, Kgagudi P, Manamela NP, Kaldine H, Venter EM, Pillay T, Lambson BE, van der Mescht MA, Hermanus T, Balla SR, de Beer Z, de Villiers TR, Bodenstein A, van den Berg G, du Pisanie M, Burgers WA, Ntusi NAB, Abdullah F, Ueckermann V, Rossouw TM, Boswell MT, Moore PL. Antibody-dependent cellular cytotoxicity against SARS-CoV-2 Omicron sub-lineages is reduced in convalescent sera regardless of infecting variant. Cell Rep Med 2023; 4:100910. [PMID: 36603577 PMCID: PMC9771750 DOI: 10.1016/j.xcrm.2022.100910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/16/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.4 and BA.5 variants caused major waves of infections. Here, we assess the sensitivity of BA.4 to binding, neutralization, and antibody-dependent cellular cytotoxicity (ADCC) potential, measured by FcγRIIIa signaling, in convalescent donors infected with four previous variants of SARS-CoV-2, as well as in post-vaccination breakthrough infections (BTIs) caused by Delta or BA.1. We confirm that BA.4 shows high-level neutralization resistance regardless of the infecting variant. However, BTIs retain activity against BA.4, albeit at reduced titers. BA.4 sensitivity to ADCC is reduced compared with other variants but with smaller fold losses compared with neutralization and similar patterns of cross-reactivity. Overall, the high neutralization resistance of BA.4, even to antibodies from BA.1 infection, provides an immunological mechanism for the rapid spread of BA.4 immediately after a BA.1-dominated wave. Furthermore, although ADCC potential against BA.4 is reduced, residual activity may contribute to observed protection from severe disease.
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Affiliation(s)
- Simone I Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Kgagudi
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Nelia P Manamela
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Haajira Kaldine
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Elizabeth M Venter
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thanusha Pillay
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwen E Lambson
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mieke A van der Mescht
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Tandile Hermanus
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sashkia R Balla
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | | | | | - Marizane du Pisanie
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology; University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Ntobeko A B Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Fareed Abdullah
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Veronica Ueckermann
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Theresa M Rossouw
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael T Boswell
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Penny L Moore
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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23
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Zhou K, Hu B, Zhao X, Chi H, Pan J, Zheng Y, Bi X, Chen M, Xie J, Xu J, Tung TH, Shen B, Zhu H. Longitudinal observation of viral load in patients infected with Omicron variant and its relationship with clinical symptoms. Front Microbiol 2023; 13:1037733. [PMID: 36713203 PMCID: PMC9880150 DOI: 10.3389/fmicb.2022.1037733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
Objective In 2022, a new coronavirus variant (Omicron) infection epidemic broke out in Shanghai, China. However, it is unclear whether the duration of this omicron variant is different from that of the prototype strain. Methods We retrospectively analyzed 157 cases of Omicron variant infection in Taizhou Public Health Center from March 29, 2022, to April 18, 2022, and observed the dynamics of nucleic acid Ct values during the admission and discharge of patients. Clinical and laboratory indicators of these patients were also obtained. Results Compared to the prototype strain, the Omicron variant showed a broad population susceptibility in infected individuals (regardless of age and presence of underlying disease) and had slight damage to the immune system and renal function; the viral loads peaked was 2-3 days from disease onset; the median duration of omicron variant was 15-18 days; the nucleic acid Ct value of nasopharyngeal swabs of infected patients is lower than that of throat swabs, and the Ct value of oropharyngeal swabs is unstable during the recovery period. Conclusion Therefore, we found that the time to peak viral load of this Omicron variant was 2-3 days after the onset of the disease, and the duration was 15-18 days; symptomatic patients had higher viral load and longer hospitalization time. This finding will provide a basis for understanding omicron variants and formulating the national prevention and control strategy.
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Affiliation(s)
- Kai Zhou
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Bingjie Hu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Xinzhuan Zhao
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Hongbo Chi
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Juan Pan
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Yufen Zheng
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Xiaojie Bi
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Mengyuan Chen
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Jicheng Xie
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Jiaqin Xu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Tao-Hsin Tung
- Evidence-based Medicine Center, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Bo Shen
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China,*Correspondence: Bo Shen,
| | - Hongguo Zhu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China,Hongguo Zhu,
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24
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Alamri SS, Alsaieedi A, Khouqeer Y, Afeef M, Alharbi S, Algaissi A, Alghanmi M, Altorki T, Zawawi A, Alfaleh MA, Hashem AM, Alhabbab R. The importance of combining serological testing with RT-PCR assays for efficient detection of COVID-19 and higher diagnostic accuracy. PeerJ 2023; 11:e15024. [PMID: 37065688 PMCID: PMC10103696 DOI: 10.7717/peerj.15024] [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: 09/19/2022] [Accepted: 02/17/2023] [Indexed: 04/18/2023] Open
Abstract
Misdiagnosing suspected COVID-19 individuals could largely contribute to the viruses transmission, therefore, making an accurate diagnosis of infected subjects vital in minimizing and containing the disease. Although RT-PCR is the standard method in detecting COVID-19, it is associated with some limitations, including possible false negative results. Therefore, serological testing has been suggested as a complement assay to RT-PCR to support the diagnosis of acute infections. In this study, 15 out of 639 unvaccinated healthcare workers (HCWs) were tested negative for COVID-19 by RT-PCR and were found seropositive for SARS-CoV-2 nucleocapsid protein-specific IgM and IgG antibodies. These participants underwent additional confirmatory RT-PCR and SARS-CoV-2 spike-specific ELISA tests. Of the 15 individuals, nine participants were found negative by second RT-PCR but seropositive for anti-spike IgM and IgG antibodies and neutralizing antibodies confirming their acute infection. At the time of collection, these nine individuals were in close contact with COVID-19-confirmed patients, with 77.7% reporting COVID-19-related symptoms. These results indicate that including serological tests in the current testing profile can provide better outcomes and help contain the spread of the virus by increasing diagnostic accuracy to prevent future outbreaks rapidly.
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Affiliation(s)
- Sawsan S. Alamri
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahdab Alsaieedi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yousef Khouqeer
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Marwah Afeef
- Study & Research Department, King Fahad General Hospital, Jeddah, Saudi Arabia
| | - Samiyah Alharbi
- Intensive Care Unit, King Fahad General Hospital, Jeddah, Saudi Arabia
| | - Abdullah Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Medical Research Centre, Jazan University, Jazan, Saudi Arabia
| | - Maimonah Alghanmi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tarfa Altorki
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ayat Zawawi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohamed A. Alfaleh
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M. Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rowa Alhabbab
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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25
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Kitagawa H, Nomura T, Kaiki Y, Kakimoto M, Nazmul T, Omori K, Shigemoto N, Sakaguchi T, Ohge H. Viable SARS-CoV-2 detected in the air of hospital rooms of patients with COVID-19 with an early infection. Int J Infect Dis 2023; 126:73-78. [PMID: 36356797 PMCID: PMC9640214 DOI: 10.1016/j.ijid.2022.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES This study assessed the concentration of SARS-CoV-2 in the air of hospital rooms occupied by patients with COVID-19 who had viable SARS-CoV-2 in nasopharyngeal (NP) samples in early infection. METHODS Between July and October 2021, NP swabs were collected from 20 patients with early SARS-CoV-2 infection admitted to a tertiary hospital in Japan. Air samples were collected from their rooms, tested for SARS-CoV-2 RNA, and cultured to determine potential infectivity. RESULTS The NP swab samples of 18 patients were positive for viable SARS-CoV-2 (median concentration: 4.0 × 105 tissue culture infectious dose 50/ml). In the air samples, viral RNA (median concentration: 1.1 × 105 copies/m3) was detected in 12/18 (67%) patients, and viable virus (median concentration: 8.9 × 102 tissue culture infectious dose 50/m3) was detected in 5/18 (28%) patients. The median time between illness onset and sampling was 3 days. The RNA concentration was significantly higher in samples wherein viable SARS-CoV-2 was detected than in samples in which viable virus was not detected (P-value = 0.027). CONCLUSION Viable SARS-CoV-2 can be detected in the air surrounding patients with early SARS-CoV-2 infection. Health care workers should pay attention to infection control when caring for patients with early SARS-CoV-2 infection.
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Affiliation(s)
- Hiroki Kitagawa
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan,Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan,Corresponding author: Hiroki Kitagawa, Department of Infectious Diseases, Hiroshima University Hospital, Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan
| | - Toshihito Nomura
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan,Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuki Kaiki
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masaki Kakimoto
- Department of General Internal Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Tanuza Nazmul
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Keitaro Omori
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Norifumi Shigemoto
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan,Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan,Translational Research Center, Hiroshima University, Hiroshima, Japan
| | - Takemasa Sakaguchi
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
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26
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Choi G, Lim AY, Choi S, Park K, Lee SY, Kim JH. Viral shedding patterns of symptomatic SARS-CoV-2 infections by periods of variant predominance and vaccination status in Gyeonggi Province, Korea. Epidemiol Health 2022; 45:e2023008. [PMID: 36596734 PMCID: PMC10581894 DOI: 10.4178/epih.e2023008] [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: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES We compared the viral cycle threshold (Ct) values of infected patients to better understand viral kinetics by vaccination status during different periods of variant predominance in Gyeonggi Province, Korea. METHODS We obtained case-specific data from the coronavirus disease 2019 (COVID-19) surveillance system, Gyeonggi in-depth epidemiological report system, and Health Insurance Review & Assessment Service from January 2020 to January 2022. We defined periods of variant predominance and explored Ct values by analyzing viral sequencing test results. Using a generalized additive model, we performed a nonlinear regression analysis to determine viral kinetics over time. RESULTS Cases in the Delta variant's period of predominance had higher viral shedding patterns than cases in other periods. The temporal change of viral shedding did not vary by vaccination status in the Omicron-predominant period, but viral shedding decreased in patients who had completed their third vaccination in the Delta-predominant period. During the Delta-predominant and Omicron-predominant periods, the time from symptom onset to peak viral shedding based on the E gene was approximately 2.4 days (95% confidence interval [CI], 2.2 to 2.5) and 2.1 days (95% CI, 2.0 to 2.1), respectively. CONCLUSIONS In one-time tests conducted to diagnose COVID-19 in a large population, although no adjustment for individual characteristics was conducted, it was confirmed that viral shedding differed by the predominant strain and vaccination history. These results show the value of utilizing hundreds of thousands of test data produced at COVID-19 screening test centers.
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Affiliation(s)
- Gawon Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Ah-Young Lim
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Sojin Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Kunhee Park
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Soon Young Lee
- Department of Preventive Medicine and Public Health, Ajou University School of Medicine, Suwon, Korea
| | - Jong-Hun Kim
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
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27
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Zhang X, Chen S, Cao Z, Yao Y, Yu J, Zhou J, Gao G, He P, Dong Z, Zhong J, Luo J, Wei H, Zhang H. Increased pathogenicity and aerosol transmission for one SARS-CoV-2 B.1.617.2 Delta variant over the wild-type strain in hamsters. Virol Sin 2022; 37:796-803. [PMID: 36182073 PMCID: PMC9519367 DOI: 10.1016/j.virs.2022.09.008] [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: 02/17/2022] [Accepted: 09/26/2022] [Indexed: 12/27/2022] Open
Abstract
During the two-year pandemic of coronavirus disease 2019 (COVID-19), its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been evolving. SARS-CoV-2 Delta, a variant of concern, has become the dominant circulating strain worldwide within just a few months. Here, we performed a comprehensive analysis of a new B.1.617.2 Delta strain (Delta630) compared with the early WIV04 strain (WIV04) in vitro and in vivo, in terms of replication, infectivity, pathogenicity, and transmission in hamsters. When inoculated intranasally, Delta630 led to more pronounced weight loss and more severe disease in hamsters. Moreover, 40% mortality occurred about one week after infection with 104 PFU of Delta630, whereas no deaths occurred even after infection with 105 PFU of WIV04 or other strains belonging to the Delta variant. Moreover, Delta630 outgrew over WIV04 in the competitive aerosol transmission experiment. Taken together, the Delta630 strain showed increased replication ability, pathogenicity, and transmissibility over WIV04 in hamsters. To our knowledge, this is the first SARS-CoV-2 strain that causes death in a hamster model, which could be an asset for the efficacy evaluation of vaccines and antivirals against infections of SARS-CoV-2 Delta strains. The underlying molecular mechanisms of increased virulence and transmission await further analysis.
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Affiliation(s)
- Xinghai Zhang
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China,Corresponding authors
| | - Shaohong Chen
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China,University of Chinese Academy of Sciences, Beijing, 101409, China
| | - Zengguo Cao
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yanfeng Yao
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Junping Yu
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Junhui Zhou
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China,University of Chinese Academy of Sciences, Beijing, 101409, China
| | - Ge Gao
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ping He
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China,University of Chinese Academy of Sciences, Beijing, 101409, China
| | - Zhuo Dong
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan, 430040, China
| | - Jie Zhong
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan, 430040, China
| | - Jing Luo
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan, 430040, China
| | - Hongping Wei
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China,Corresponding authors
| | - Huajun Zhang
- State Key Laboratory of Virology, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China,Corresponding authors
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28
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Choi CW, Sung HK, Jeong JY, Lim DH, Choi J, Kwon HC, Nam S, Kim Y, Chin B. Changing Features of Liver Injury in COVID-19 Patients: Impact of Infection with the SARS-CoV-2 Delta (B.1.617.2) Variants. Infect Chemother 2022; 54:744-756. [PMID: 36596683 PMCID: PMC9840963 DOI: 10.3947/ic.2022.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND There is growing evidence that abnormal liver function tests (LFTs) are common in patients with coronavirus disease 2019 (COVID-19). However, it is not known whether viral involvement in the liver differs according to the strain. We investigated the impact on liver injury in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta (B.1.617.2) variants. MATERIALS AND METHODS We conducted a single-center, retrospective cohort study, including 372 patients admitted during the pre-Delta period (PDP: between February 1 and November 30, 2020) and 137 patients admitted during the Delta period (DP: between August 1 and August 31, 2021). Initial liver injury was defined as alanine aminotransferase (ALT) or aspartate aminotransferase (AST) levels ≥3 × the upper limit of normal (ULN) or alkaline phosphatase (ALP) or total bilirubin ≥2 × the ULN within 3 days from admission. RESULTS Of 509 patients with COVID-19 included in our study, 38 (7.5%) patients had initial liver injury. The DP group had a significantly higher rate of initial liver injury than the PDP group (PDP: 5.9% vs. DP: 11.7%, P = 0.028). The DP group (adjusted odds ratio [aOR]: 2.737, 95% confidence interval [CI]: 1.322 - 5.666) was independently associated with initial liver injury. During hospitalization, 160 (31.4%) patients had severe COVID-19. The DP group and initial liver injury had higher odds of progressing to severe COVID-19 (aOR: 2.664, 95% CI: 1.526 - 4.648, and aOR: 4.409, 95% CI: 1.816 - 10.707, respectively). The mediation analysis suggested that initial liver injury mediates the relationship between SARS-CoV-2 Delta variant infection and severe COVID-19 (unstandardized beta coefficient = 0.980, Standard error = 0.284, P = 0.001). CONCLUSION Initial liver injury is more common in COVID-19 patients with Delta variants. Also, Delta variants and initial liver injury are associated with poor clinical outcomes.
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Affiliation(s)
- Chang Wan Choi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Ho Kyung Sung
- National Emergency Medical Center, National Medical Center, Seoul, Korea.,Research Institute for Public Health, National Medical Center, Seoul, Korea
| | - Jae Yoon Jeong
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Dae Hyun Lim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Jongkyoung Choi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Hyeok Choon Kwon
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Seongwoo Nam
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Yeonjae Kim
- Division of Infectious Diseases, Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - BumSik Chin
- Division of Infectious Diseases, Department of Internal Medicine, National Medical Center, Seoul, Korea
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29
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Dabisch PA, Sanjak JS, Boydston JA, Yeager J, Herzog A, Biryukov J, Beck K, Do D, Seman BG, Green B, Bohannon JK, Holland B, Miller D, Ammons T, Freeburger D, Miller S, Jenkins T, Rippeon S, Miller J, Clarke D, Manan E, Patty A, Rhodes K, Sweeney T, Winpigler M, Altamura LA, Zimmerman H, Hail AS, Wahl V, Hevey M. Comparison of Dose-Response Relationships for Two Isolates of SARS-CoV-2 in a Nonhuman Primate Model of Inhalational COVID-19. J Aerosol Med Pulm Drug Deliv 2022; 35:296-306. [PMID: 36318785 PMCID: PMC9807281 DOI: 10.1089/jamp.2022.0043] [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] [Indexed: 12/05/2022] Open
Abstract
Background: As the COVID-19 pandemic has progressed, numerous variants of SARS-CoV-2 have arisen, with several displaying increased transmissibility. Methods: The present study compared dose-response relationships and disease presentation in nonhuman primates infected with aerosols containing an isolate of the Gamma variant of SARS-CoV-2 to the results of our previous study with the earlier WA-1 isolate of SARS-CoV-2. Results: Disease in Gamma-infected animals was mild, characterized by dose-dependent fever and oronasal shedding of virus. Differences were observed in shedding in the upper respiratory tract between Gamma- and WA-1-infected animals that have the potential to influence disease transmission. Specifically, the estimated median doses for shedding of viral RNA or infectious virus in nasal swabs were approximately 10-fold lower for the Gamma variant than the WA-1 isolate. Given that the median doses for fever were similar, this suggests that there is a greater difference between the median doses for viral shedding and fever for Gamma than for WA-1 and potentially an increased range of doses for Gamma over which asymptomatic shedding and disease transmission are possible. Conclusions: These results complement those of previous studies, which suggested that differences in exposure dose may help to explain the range of clinical disease presentations observed in individuals with COVID-19, highlighting the importance of public health measures designed to limit exposure dose, such as masking and social distancing. The dose-response data provided by this study are important to inform disease transmission and hazard modeling, as well as to inform dose selection in future studies examining the efficacy of therapeutics and vaccines in animal models of inhalational COVID-19.
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Affiliation(s)
- Paul A. Dabisch
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA.,Address correspondence to: Paul A. Dabisch, PhD, National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, for the U.S. Department of Homeland Security, 8300 Research Plaza, Frederick, MD 21701, USA
| | - Jaleal S. Sanjak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jeremy A. Boydston
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - John Yeager
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | | | - Jennifer Biryukov
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Katie Beck
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Danh Do
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Brittany G. Seman
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Brian Green
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Jordan K. Bohannon
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Brian Holland
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - David Miller
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Taylor Ammons
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Denise Freeburger
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Susan Miller
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Tammy Jenkins
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Sherry Rippeon
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - James Miller
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - David Clarke
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Emmanuel Manan
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Ashley Patty
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Kim Rhodes
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Tina Sweeney
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Michael Winpigler
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Louis A. Altamura
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Heather Zimmerman
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Alec S. Hail
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
| | - Michael Hevey
- National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute, U.S. Department of Homeland Security, Frederick, Maryland, USA
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Deng J, Ma Y, Liu Q, Du M, Liu M, Liu J. Association of Infection with Different SARS-CoV-2 Variants during Pregnancy with Maternal and Perinatal Outcomes: A Systematic Review and Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192315932. [PMID: 36498007 PMCID: PMC9740636 DOI: 10.3390/ijerph192315932] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/26/2022] [Accepted: 11/27/2022] [Indexed: 05/30/2023]
Abstract
The aim of this study is to review the currently available data, and to explore the association of infection with different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants during pregnancy with maternal and perinatal outcomes in the real world. Observational cohort studies were analyzed that described the maternal and perinatal outcomes of infection with different SARS-CoV-2 variants during pregnancy. Random-effects inverse-variance models were used to evaluate the pooled prevalence (PP) and its 95% confidence interval (CI) for maternal and perinatal outcomes. Random effects were used to estimate the pooled odds ratios (OR) and their 95% CI for different outcomes between Delta and pre-Delta periods, and between Omicron and Delta periods. Eighteen studies, involving a total of 133,058 cases of SARS-CoV-2 infection during pregnancy (99,567 cases of SARS-CoV-2 wild type or pre-variant infection and 33,494 cases of SARS-CoV-2 variant infections), were included in this meta-analysis. Among pregnant women with SARS-CoV-2 infections, the PPs for required respiratory support, severe or critical illness, intensive care unit (ICU) admission, maternal death, and preterm birth <37 weeks were, respectively, 27.24% (95%CI, 20.51−33.97%), 24.96% (95%CI, 15.96−33.96%), 11.31% (95%CI, 4.00−18.61%), 4.20% (95%CI, 1.43−6.97%), and 33.85% (95%CI, 21.54−46.17%) in the Delta period, which were higher than those in the pre-Delta period, while the corresponding PPs were, respectively, 10.74% (95%CI, 6.05−15.46%), 11.99% (95%CI, 6.23−17.74%), 4.17% (95%CI, 1.53−6.80%), 0.63% (95%CI, 0.05−1.20%), and 18.58% (95%CI, 9.52−27.65%). The PPs for required respiratory support, severe or critical illness, and ICU admission were, respectively, 2.63% (95%CI, 0.98−4.28%), 1.11% (95%CI, 0.29−1.94%), and 1.83% (95%CI, 0.85−2.81%) in the Omicron period, which were lower than those in the pre-Delta and Delta periods. These results suggest that Omicron infections are associated with less severe maternal and neonatal adverse outcomes, though maternal ICU admission, the need for respiratory support, and preterm birth did also occur with Omicron infections. Since Omicron is currently the predominant strain globally, and has the highest rates of transmission, it is still important to remain vigilant in protecting the vulnerable populations of mothers and infants. In particular, obstetricians and gynecologists should not ignore the adverse risks of maternal ICU admission, respiratory support, and preterm births in pregnant patients with SARS-CoV-2 infections, in order to protect the health of mothers and infants.
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Affiliation(s)
- Jie Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Address No. 38, Xueyuan Road, Haidian District, Beijing 100191, China
| | - Yirui Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Address No. 38, Xueyuan Road, Haidian District, Beijing 100191, China
| | - Qiao Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Address No. 38, Xueyuan Road, Haidian District, Beijing 100191, China
| | - Min Du
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Address No. 38, Xueyuan Road, Haidian District, Beijing 100191, China
| | - Min Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Address No. 38, Xueyuan Road, Haidian District, Beijing 100191, China
| | - Jue Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Address No. 38, Xueyuan Road, Haidian District, Beijing 100191, China
- Institute for Global Health and Development, Peking University, Address No. 5, Yiheyuan Road, Haidian District, Beijing 100871, China
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31
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Long-COVID Symptoms in Individuals Infected with Different SARS-CoV-2 Variants of Concern: A Systematic Review of the Literature. Viruses 2022; 14:v14122629. [PMID: 36560633 PMCID: PMC9785120 DOI: 10.3390/v14122629] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
The association of SARS-CoV-2 variants with long-COVID symptoms is still scarce, but new data are appearing at a fast pace. This systematic review compares the prevalence of long-COVID symptoms according to relevant SARS-CoV-2 variants in COVID-19 survivors. The MEDLINE, CINAHL, PubMed, EMBASE and Web of Science databases, as well as the medRxiv and bioRxiv preprint servers, were searched up to 25 October 2022. Case-control and cohort studies analyzing the presence of post-COVID symptoms appearing after an acute SARS-CoV-2 infection by the Alpha (B.1.1.7), Delta (B.1.617.2) or Omicron (B.1.1.529/BA.1) variants were included. Methodological quality was assessed using the Newcastle-Ottawa Scale. From 430 studies identified, 5 peer-reviewed studies and 1 preprint met the inclusion criteria. The sample included 355 patients infected with the historical variant, 512 infected with the Alpha variant, 41,563 infected with the Delta variant, and 57,616 infected with the Omicron variant. The methodological quality of all studies was high. The prevalence of long-COVID was higher in individuals infected with the historical variant (50%) compared to those infected with the Alpha, Delta or Omicron variants. It seems that the prevalence of long-COVID in individuals infected with the Omicron variant is the smallest, but current data are heterogeneous, and long-term data have, at this stage, an obviously shorter follow-up compared with the earlier variants. Fatigue is the most prevalent long-COVID symptom in all SARS-CoV-2 variants, but pain is likewise prevalent. The available data suggest that the infection with the Omicron variant results in fewer long-COVID symptoms compared to previous variants; however, the small number of studies and the lack of the control of cofounders, e.g., reinfections or vaccine status, in some studies limit the generality of the results. It appears that individuals infected with the historical variant are more likely to develop long-COVID symptomatology.
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32
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Yang R, Cheng J, Song X, Pan Y, Wang H, Li J, He X, Gou J, Zhang G. Characteristics of COVID-19 (Delta Variant)/HIV Co-infection: A Cross-sectional Study in Henan Province, China. INTENSIVE CARE RESEARCH 2022; 2:96-107. [PMID: 36407473 PMCID: PMC9666970 DOI: 10.1007/s44231-022-00018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
Abstract
Background Since the end of July 2021, SARS-CoV-2 (Delta variant) invaded Henan Province, China, causing a rapid COVID-19 spread in the province. Among them, the clinical features of COVID-19 (Delta Variant)/HIV co-infection have attracted our attention. Methods We included 12 COVID-19 patients living with HIV (human immunodeficiency virus) from July 30, 2021 to September 17, 2021 in Henan Province, China. Demographic, clinical, laboratory, and computed tomography (CT) imaging data were dynamically collected from first nucleic acid positive to hospital discharge. Laboratory findings included SARS-CoV-2 viral load, HIV viral load, IgM, IgG, cytokines, lymphocyte subpopulation, ferritin, etc. Statistical analyses were performed using IBM SPSS version 26·0 and GraphPad Prism version 9·0. Results It was founded that the low Ct value persisted for about 21 days, and the viral shedding time (turn negative time) of the patients was 32·36 ± 2·643 days. Furthermore, chest CT imaging revealed that lesions were obviously and rapidly absorbed. It was surprising that IgM levels were statistically higher in patients taking azvudine or convalescent plasma than in patients not taking these drugs (P < 0·001, P = 0·0002, respectively). IgG levels were significantly higher in patients treated with the combined medication of BRII/196 and BRII/198 than in those not treated with these drugs (P = 0·0029). IgM was significantly higher in those with low HIV viral load than those with high HIV viral load (P < 0·001). In addition, as treatment progressed and patients' condition improved, IL-17a showed a decreasing trend. Conclusions Based on this study, we found that HIV infection might not exacerbate COVID-19 severity. Supplementary Information The online version contains supplementary material available at 10.1007/s44231-022-00018-z.
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Affiliation(s)
- Rui Yang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe East Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Jiuling Cheng
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe East Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Xiangjin Song
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe East Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Yuanwei Pan
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan People’s Republic of China
| | - Huaqi Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe East Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Jing Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe East Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Xudong He
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe East Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Jianjun Gou
- Department of General Surgery, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe East Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Guojun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe East Road, Zhengzhou, 450052 Henan People’s Republic of China
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Xie Y, Challis JK, Oloye FF, Asadi M, Cantin J, Brinkmann M, McPhedran KN, Hogan N, Sadowski M, Jones PD, Landgraff C, Mangat C, Servos MR, Giesy JP. RNA in Municipal Wastewater Reveals Magnitudes of COVID-19 Outbreaks across Four Waves Driven by SARS-CoV-2 Variants of Concern. ACS ES&T WATER 2022; 2:1852-1862. [PMID: 37552734 PMCID: PMC8887651 DOI: 10.1021/acsestwater.1c00349] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 05/07/2023]
Abstract
There are no standardized protocols for quantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater to date, especially for population normalization. Here, a pipeline was developed, applied, and assessed to quantify SARS-CoV-2 and key variants of concern (VOCs) RNA in wastewater at Saskatoon, Canada. Normalization approaches using recovery ratio and extraction efficiency, wastewater parameters, or population indicators were assessed by comparing to daily numbers of new cases. Viral load was positively correlated with daily new cases reported in the sewershed. Wastewater surveillance (WS) had a lead time of approximately 7 days, which indicated surges in the number of new cases. WS revealed the variant α and δ driving the third and fourth wave, respectively. The adjustment with the recovery ratio and extraction efficiency improved the correlation between viral load and daily new cases. Normalization of viral concentration to concentrations of the artificial sweetener acesulfame K improved the trend of viral load during the Christmas and New Year holidays when populations were dynamic and variable. Acesulfame K performed better than pepper mild mottle virus, creatinine, and ammonia for population normalization. Hence, quality controls to characterize recovery ratios and extraction efficiencies and population normalization with acesulfame are promising for precise WS programs supporting decision-making in public health.
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Affiliation(s)
- Yuwei Xie
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Jonathan K. Challis
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Femi F. Oloye
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
| | - Jenna Cantin
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Markus Brinkmann
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Kerry N. McPhedran
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Natacha Hogan
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- College of Agriculture and Bioresources, Department of
Animal and Poultry Sciences, University of Saskatchewan,
Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department,
City of Saskatoon, Saskatoon, Saskatchewan S7M 1X5,
Canada
| | - Paul D. Jones
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology
Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
R3E 3R2, Canada
- Food Science Department, University of
Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chand Mangat
- Antimicrobial Resistance and Nosocomial Infections,
National Microbiology Laboratory, Public Health Agency of
Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Mark R. Servos
- Department of Biology, University of
Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - John P. Giesy
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Department of Veterinary Biomedical Sciences,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4,
Canada
- Department of Environmental Sciences,
Baylor University, Waco, Texas 76706, United
States
- Department of Zoology and Center for Integrative
Toxicology, Michigan State University, East Lansing, Michigan
48824, United States
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Meurisse M, Van Oyen H, Blot K, Catteau L, Serrien B, Klamer S, Cauët E, Robert A, Van Goethem N. Evaluating methodological approaches to assess the severity of infection with SARS-CoV-2 variants: scoping review and applications on Belgian COVID-19 data. BMC Infect Dis 2022; 22:839. [DOI: 10.1186/s12879-022-07777-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Differences in the genetic material of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may result in altered virulence characteristics. Assessing the disease severity caused by newly emerging variants is essential to estimate their impact on public health. However, causally inferring the intrinsic severity of infection with variants using observational data is a challenging process on which guidance is still limited. We describe potential limitations and biases that researchers are confronted with and evaluate different methodological approaches to study the severity of infection with SARS-CoV-2 variants.
Methods
We reviewed the literature to identify limitations and potential biases in methods used to study the severity of infection with a particular variant. The impact of different methodological choices is illustrated by using real-world data of Belgian hospitalized COVID-19 patients.
Results
We observed different ways of defining coronavirus disease 2019 (COVID-19) disease severity (e.g., admission to the hospital or intensive care unit versus the occurrence of severe complications or death) and exposure to a variant (e.g., linkage of the sequencing or genotyping result with the patient data through a unique identifier versus categorization of patients based on time periods). Different potential selection biases (e.g., overcontrol bias, endogenous selection bias, sample truncation bias) and factors fluctuating over time (e.g., medical expertise and therapeutic strategies, vaccination coverage and natural immunity, pressure on the healthcare system, affected population groups) according to the successive waves of COVID-19, dominated by different variants, were identified. Using data of Belgian hospitalized COVID-19 patients, we were able to document (i) the robustness of the analyses when using different variant exposure ascertainment methods, (ii) indications of the presence of selection bias and (iii) how important confounding variables are fluctuating over time.
Conclusions
When estimating the unbiased marginal effect of SARS-CoV-2 variants on the severity of infection, different strategies can be used and different assumptions can be made, potentially leading to different conclusions. We propose four best practices to identify and reduce potential bias introduced by the study design, the data analysis approach, and the features of the underlying surveillance strategies and data infrastructure.
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van Hensbergen M, den Heijer CDJ, Mujakovic S, Dukers-Muijrers NHTM, Wolffs PFG, van Loo IHM, Hoebe CJPA. Evaluation of symptomatology and viral load among residents and healthcare staff in long-term care facilities: A coronavirus disease 2019 retrospective case-cohort study. PLoS One 2022; 17:e0276796. [PMID: 36327239 PMCID: PMC9632776 DOI: 10.1371/journal.pone.0276796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Objectives We evaluated COVID-19 symptoms, case fatality rate (CFR), and viral load among all Long-Term Care Facility (LTCF) residents and staff in South Limburg, the Netherlands (February 2020-June 2020, wildtype SARS-CoV-2 Wuhan strain). Methods Patient information was gathered via regular channels used to notify the public health services. Ct-values were obtained from the Maastricht University Medical Centre laboratory. Logistic regression analyses were performed to assess associations between COVID-19, symptoms, CFR, and viral load. Results Of 1,457 staff and 1,540 residents, 35.1% and 45.2% tested positive for COVID-19. Symptoms associated with COVID-19 for female staff were fever, cough, muscle ache and loss of taste and smell. Associated symptoms for men were cough, and loss of taste and smell. Associated symptoms for residents were subfebrility, fatigue, and fever for male residents only. LTCF residents had a higher mean viral load compared to staff. Male residents had a higher CFR (35.8%) compared to women (22.5%). Female residents with Ct-values 31 or less had increased odds of mortality. Conclusions Subfebrility and fatigue seem to be associated with COVID-19 in LTCF residents. Therefore, physicians should also consider testing residents who (only) show aspecific symptoms whenever available resources prohibit testing of all residents. Viral load was higher in residents compared to staff, and higher in male residents compared to female residents. All COVID-19 positive male residents, as well as female residents with a medium to high viral load (Ct-values 31 or lower) should be monitored closely, as these groups have an overall increased risk of mortality.
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Affiliation(s)
- Mitch van Hensbergen
- Department of Sexual Health, Infectious Diseases, and Environmental Health, South Limburg Public Health Service, Limburg, The Netherlands
- Faculty of Health, Medicine and Life Sciences, Department of Social Medicine, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, Limburg, The Netherlands
- * E-mail:
| | - Casper D. J. den Heijer
- Department of Sexual Health, Infectious Diseases, and Environmental Health, South Limburg Public Health Service, Limburg, The Netherlands
- Faculty of Health, Medicine and Life Sciences, Department of Social Medicine, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, Limburg, The Netherlands
- Faculty of Health, Medicine and Life Sciences, Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, Limburg, the Netherlands
| | - Suhreta Mujakovic
- Department of Sexual Health, Infectious Diseases, and Environmental Health, South Limburg Public Health Service, Limburg, The Netherlands
| | - Nicole H. T. M. Dukers-Muijrers
- Department of Sexual Health, Infectious Diseases, and Environmental Health, South Limburg Public Health Service, Limburg, The Netherlands
- Faculty of Health, Medicine and Life Sciences, Department of Health Promotion, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, Limburg, the Netherlands
| | - Petra F. G. Wolffs
- Faculty of Health, Medicine and Life Sciences, Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, Limburg, the Netherlands
| | - Inge H. M. van Loo
- Faculty of Health, Medicine and Life Sciences, Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, Limburg, the Netherlands
| | - Christian J. P. A. Hoebe
- Department of Sexual Health, Infectious Diseases, and Environmental Health, South Limburg Public Health Service, Limburg, The Netherlands
- Faculty of Health, Medicine and Life Sciences, Department of Social Medicine, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, Limburg, The Netherlands
- Faculty of Health, Medicine and Life Sciences, Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, Limburg, the Netherlands
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Comparison of SARS-CoV-2 viral load in asymptomatic and symptomatic children attended in a referral public pediatric hospital in Argentina. Rev Argent Microbiol 2022:S0325-7541(22)00082-7. [PMID: 36402614 PMCID: PMC9618439 DOI: 10.1016/j.ram.2022.09.002] [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: 03/11/2022] [Revised: 07/15/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
At present, different reports have shown that children reach similar SARS-CoV-2 viral load (VL) levels compared to adults; however, the impact of VL on children remains ambiguous when asymptomatic versus symptomatic cases are compared. Thus, the aim of this study was to assess VL at the time of diagnosis in asymptomatic and symptomatic SARS-CoV-2 infected children. VL analysis was retrospectively carried out from nasopharyngeal swabs on 82 SARS-CoV-2 infected children, from March to October 2020. Of the 82 children, 31 were asymptomatic. Symptomatic patients had significantly higher VL values compared to asymptomatic ones (median = 7.41 vs 4.35 log10 copies/ml, respectively). Notwithstanding, 8 out of 31 asymptomatic children had high VL levels, overlapping levels observed above the first quartile in the symptomatic group. Analysis of different age groups revealed that median VL values were higher in the symptomatic groups, although there was only a significant difference in children younger than 5 years of age. On the other hand, there was no significant difference between the VL values from the 82 SARS-CoV-2 infected children according to age, sex, underlying disease, symptoms or severity of COVID-19 related disease. This study emphasizes the importance of VL analysis in SARS-CoV-2 infected children, who could contribute to viral spread in the community. This concern could be extended to healthcare workers, who are in contact with children.
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Niu Y, Luo L, Yang S, Abudurusuli G, Wang X, Zhao Z, Rui J, Li Z, Deng B, Liu W, Zhang Z, Li K, Liu C, Li P, Huang J, Yang T, Wang Y, Chen T, Li Q. Comparison of epidemiological characteristics and transmissibility of different strains of COVID-19 based on the incidence data of all local outbreaks in China as of March 1, 2022. Front Public Health 2022; 10:949594. [PMID: 36187650 PMCID: PMC9521362 DOI: 10.3389/fpubh.2022.949594] [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: 05/21/2022] [Accepted: 08/29/2022] [Indexed: 01/21/2023] Open
Abstract
Background The epidemiological characteristics and transmissibility of Coronavirus Disease 2019 (COVID-19) may undergo changes due to the mutation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) strains. The purpose of this study is to compare the differences in the outbreaks of the different strains with regards to aspects such as epidemiological characteristics, transmissibility, and difficulties in prevention and control. Methods COVID-19 data from outbreaks of pre-Delta strains, the Delta variant and Omicron variant, were obtained from the Chinese Center for Disease Control and Prevention (CDC). Case data were collected from China's direct-reporting system, and the data concerning outbreaks were collected by on-site epidemiological investigators and collated by the authors of this paper. Indicators such as the effective reproduction number (R eff), time-dependent reproduction number (R t), rate of decrease in transmissibility (RDT), and duration from the illness onset date to the diagnosed date (D ID )/reported date (D IR ) were used to compare differences in transmissibility between pre-Delta strains, Delta variants and Omicron variants. Non-parametric tests (namely the Kruskal-Wallis H and Mean-Whitney U tests) were used to compare differences in epidemiological characteristics and transmissibility between outbreaks of different strains. P < 0.05 indicated that the difference was statistically significant. Results Mainland China has maintained a "dynamic zero-out strategy" since the first case was reported, and clusters of outbreaks have occurred intermittently. The strains causing outbreaks in mainland China have gone through three stages: the outbreak of pre-Delta strains, the outbreak of the Delta variant, and outbreaks involving the superposition of Delta and Omicron variant strains. Each outbreak of pre-Delta strains went through two stages: a rising stage and a falling stage, Each outbreak of the Delta variant and Omicron variant went through three stages: a rising stage, a platform stage and a falling stage. The maximum R eff value of Omicron variant outbreaks was highest (median: 6.7; ranged from 5.3 to 8.0) and the differences were statistically significant. The RDT value of outbreaks involving pre-Delta strains was smallest (median: 91.4%; [IQR]: 87.30-94.27%), and the differences were statistically significant. The D ID and D IR for all strains was mostly in a range of 0-2 days, with more than 75%. The range of duration for outbreaks of pre-Delta strains was the largest (median: 20 days, ranging from 1 to 61 days), and the differences were statistically significant. Conclusion With the evolution of the virus, the transmissibility of the variants has increased. The transmissibility of the Omicron variant is higher than that of both the pre-Delta strains and the Delta variant, and is more difficult to suppress. These findings provide us with get a more clear and precise picture of the transmissibility of the different variants in the real world, in accordance with the findings of previous studies. R eff is more suitable than R t for assessing the transmissibility of the disease during an epidemic outbreak.
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Affiliation(s)
- Yan Niu
- Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Shiting Yang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Guzainuer Abudurusuli
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Xiaoye Wang
- Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zeyu Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Jia Rui
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Zhuoyang Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Bin Deng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Weikang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Zhe Zhang
- School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Kangguo Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Chan Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Peihua Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Jiefeng Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Tianlong Yang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Yao Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Tianmu Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China,Tianmu Chen
| | - Qun Li
- Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, China,*Correspondence: Qun Li
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Hamill V, Noll L, Lu N, Tsui WNT, Porter EP, Gray M, Sebhatu T, Goerl K, Brown S, Palinski R, Thomason S, Almes K, Retallick J, Bai J. Molecular detection of SARS-CoV-2 strains and differentiation of Delta variant strains. Transbound Emerg Dis 2022; 69:2879-2889. [PMID: 34964565 PMCID: PMC9240106 DOI: 10.1111/tbed.14443] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/03/2021] [Accepted: 12/22/2021] [Indexed: 12/20/2022]
Abstract
The Delta variant of SARS-CoV-2 has now become the predominant strain in the global COVID-19 pandemic. Strain coverage of some detection assays developed during the early pandemic stages has declined due to periodic mutations in the viral genome. We have developed a real-time RT-PCR (RT-qPCR) for SARS-CoV-2 detection that provides nearly 100% strain coverage, and differentiation of highly transmissible Delta variant strains. All full or nearly full (≥28 kb) SARS-CoV-2 genomes (n = 403,812), including 6422 Delta and 280 Omicron variant strains, were collected from public databases at the time of analysis and used for assay design. The two amino acid deletions in the spike gene (S-gene, Δ156-157) that is characteristic of the Delta variant were targeted during the assay design. Although strain coverage for the Delta variant was very high (99.7%), detection coverage for non-Delta wild-type strains was 93.9%, mainly due to the confined region of design. To increase strain coverage of the assay, the design for CDC N1 target was added to the assay. In silico analysis of 403,812 genomes indicated a 95.4% strain coverage for the CDC N1 target, however, in combination with our new non-Delta S-gene target, total coverage for non-Delta wild-type strains increased to 99.8%. A human 18S rRNA gene was also analyzed and used as an internal control. The final four-plex RT-qPCR assay generated PCR amplification efficiencies between 95.4% and 102.0% with correlation coefficients (R2 ) of >0.99 for cloned positive controls; Delta and non-Delta human clinical samples generated PCR efficiencies of 93.4%-97.0% and R2 > 0.99. The assay also detects 98.6% of 280 Omicron sequences. Assay primers and probes have no match to other closely related human coronaviruses, and did not produce a signal from samples positive to selected animal coronaviruses. Genotypes of selected clinical samples identified by the RT-qPCR were confirmed by Sanger sequencing.
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Affiliation(s)
- Vaughn Hamill
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Wai Ning Tiffany Tsui
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Elizabeth Poulsen Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Mark Gray
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Tesfaalem Sebhatu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Kyle Goerl
- Lafene Health Center, Kansas State University, Manhattan, KS 66506, United States
| | - Susan Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Rachel Palinski
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Sasha Thomason
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Kelli Almes
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Jamie Retallick
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
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Lina L, Zhendong G, Sevalie S, Fangfang Z, Dawei Z, Weiwei C, Xiao L, Zongzheng Z. Comparison of the amount of SARS-CoV-2 exhaled by Delta and Omicron patients. J Infect 2022; 85:573-607. [PMID: 36044946 PMCID: PMC9420242 DOI: 10.1016/j.jinf.2022.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Liu Lina
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Guo Zhendong
- Tropical Infectious Disease Prevention and Control Center, Freetown, Sierra Leone
| | - Stephen Sevalie
- No. 34 Military Hospital, Wilberforce, Freetown, Sierra Leone
| | - Zhang Fangfang
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhang Dawei
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Chen Weiwei
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China.
| | - Li Xiao
- Tropical Infectious Disease Prevention and Control Center, Freetown, Sierra Leone.
| | - Zhao Zongzheng
- Tropical Infectious Disease Prevention and Control Center, Freetown, Sierra Leone.
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40
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A comprehensive modelling approach to estimate the transmissibility of coronavirus and its variants from infected subjects in indoor environments. Sci Rep 2022; 12:14164. [PMID: 35986061 PMCID: PMC9389491 DOI: 10.1038/s41598-022-17693-z] [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: 04/30/2022] [Accepted: 07/29/2022] [Indexed: 12/04/2022] Open
Abstract
A central issue in assessing the airborne risk of COVID-19 infections in indoor spaces pertains to linking the viral load in infected subjects to the lung deposition probability in exposed individuals through comprehensive aerosol dynamics modelling. In this paper, we achieve this by combining aerosol processes (evaporation, dispersion, settling, lung deposition) with a novel double Poisson model to estimate the probability that at least one carrier particle containing at least one virion will be deposited in the lungs and infect a susceptible individual. Multiple emission scenarios are considered. Unlike the hitherto used single Poisson models, the double Poisson model accounts for fluctuations in the number of carrier particles deposited in the lung in addition to the fluctuations in the virion number per carrier particle. The model demonstrates that the risk of infection for 10-min indoor exposure increases from 1 to 50% as the viral load in the droplets ejected from the infected subject increases from 2 × 108 to 2 × 1010 RNA copies/mL. Being based on well-established aerosol science and statistical principles, the present approach puts airborne risk assessment methodology on a sound formalistic footing, thereby reducing avoidable epistemic uncertainties in estimating relative transmissibilities of different coronavirus variants quantified by different viral loads.
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41
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Pezzotti G, Ohgitani E, Fujita Y, Imamura H, Shin-Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Nishimura I, Mazda O. Raman Fingerprints of the SARS-CoV-2 Delta Variant and Mechanisms of Its Instantaneous Inactivation by Silicon Nitride Bioceramics. ACS Infect Dis 2022; 8:1563-1581. [PMID: 35819780 PMCID: PMC9305655 DOI: 10.1021/acsinfecdis.2c00200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 02/06/2023]
Abstract
Raman spectroscopy uncovered molecular scale markers of the viral structure of the SARS-CoV-2 Delta variant and related viral inactivation mechanisms at the biological interface with silicon nitride (Si3N4) bioceramics. A comparison of Raman spectra collected on the TY11-927 variant (lineage B.1.617.2; simply referred to as the Delta variant henceforth) with those of the JPN/TY/WK-521 variant (lineage B.1.617.1; referred to as the Kappa variant or simply as the Japanese isolate henceforth) revealed the occurrence of key mutations of the spike receptor together with profound structural differences in the molecular structure/symmetry of sulfur-containing amino acid and altered hydrophobic interactions of the tyrosine residue. Additionally, different vibrational fractions of RNA purines and pyrimidines and dissimilar protein secondary structures were also recorded. Despite mutations, hydrolytic reactions at the surface of silicon nitride (Si3N4) bioceramics induced instantaneous inactivation of the Delta variant at the same rate as that of the Kappa variant. Contact between virions and micrometric Si3N4 particles yielded post-translational deimination of arginine spike residues, methionine sulfoxidation, tyrosine nitration, and oxidation of RNA purines to form formamidopyrimidines. Si3N4 bioceramics proved to be a safe and effective inorganic compound for instantaneous environmental sanitation.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
- Department of Immunology, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
465 Kajii-cho, Kyoto 602-8566, Japan
- Department of Orthopedic Surgery, Tokyo
Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, 160-0023 Tokyo,
Japan
- Center for Advanced Medical Engineering and
Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka
565-0854, Japan
- Institute of Biomaterials and Bioengineering,
Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai,
Chiyoda-ku, Tokyo 101-0062, Japan
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
- Biomedical Research Center, Kyoto Institute
of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yuki Fujita
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
| | - Masaharu Shin-Ya
- Department of Immunology, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
465 Kajii-cho, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
| | - Ichiro Nishimura
- Division of Advanced Prosthodontics, The Jane and
Jerry Weintraub Center for Reconstructive Biotechnology, UCLA School of
Dentistry, Los Angeles, California 90095, United
States
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
465 Kajii-cho, Kyoto 602-8566, Japan
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42
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Moyo-Gwete T, Madzivhandila M, Mkhize NN, Kgagudi P, Ayres F, Lambson BE, Manamela NP, Richardson SI, Makhado Z, van der Mescht MA, de Beer Z, de Villiers TR, Burgers WA, Ntusi NAB, Rossouw T, Ueckermann V, Boswell MT, Moore PL. Shared N417-Dependent Epitope on the SARS-CoV-2 Omicron, Beta, and Delta Plus Variants. J Virol 2022; 96:e0055822. [PMID: 35867572 PMCID: PMC9364786 DOI: 10.1128/jvi.00558-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, several variants of concern (VOCs) have arisen which are defined by multiple mutations in their spike proteins. These VOCs have shown variable escape from antibody responses and have been shown to trigger qualitatively different antibody responses during infection. By studying plasma from individuals infected with either the original D614G, Beta, or Delta variants, we showed that the Beta and Delta variants elicit antibody responses that are overall more cross-reactive than those triggered by D614G. Patterns of cross-reactivity varied, and the Beta and Delta variants did not elicit cross-reactive responses to each other. However, Beta-elicited plasma was highly cross-reactive against Delta Plus (Delta+), which differs from Delta by a single K417N mutation in the receptor binding domain, suggesting that the plasma response targets the N417 residue. To probe this further, we isolated monoclonal antibodies from a Beta-infected individual with plasma responses against Beta, Delta+, and Omicron, which all possess the N417 residue. We isolated an N417-dependent antibody, 084-7D, which showed similar neutralization breadth to the plasma. The 084-7D MAb utilized the IGHV3-23*01 germ line gene and had somatic hypermutations similar to those of previously described public antibodies which target the 417 residue. Thus, we have identified a novel antibody which targets a shared epitope found on three distinct VOCs, enabling their cross-neutralization. Understanding antibodies targeting escape mutations, such as K417N, which repeatedly emerge through convergent evolution in SARS-CoV-2 variants, may aid in the development of next-generation antibody therapeutics and vaccines. IMPORTANCE The evolution of SARS-CoV-2 has resulted in variants of concern (VOCs) with distinct spike mutations conferring various immune escape profiles. These variable mutations also influence the cross-reactivity of the antibody response mounted by individuals infected with each of these variants. This study sought to understand the antibody responses elicited by different SARS-CoV-2 variants and to define shared epitopes. We show that Beta and Delta infections resulted in antibody responses that were more cross-reactive than the original D614G variant, but they had differing patterns of cross-reactivity. We further isolated an antibody from Beta infection which targeted the N417 site, enabling cross-neutralization of Beta, Delta+, and Omicron, all of which possess this residue. The discovery of antibodies which target escape mutations common to multiple variants highlights conserved epitopes to target in future vaccines and therapeutics.
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Affiliation(s)
- Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mashudu Madzivhandila
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonhlanhla N. Mkhize
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Kgagudi
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Frances Ayres
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwen E. Lambson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nelia P. Manamela
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simone I. Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Makhado
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mieke A. van der Mescht
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | | | | | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Ntobeko A. B. Ntusi
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Theresa Rossouw
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Veronica Ueckermann
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Michael T. Boswell
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Penny L. Moore
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
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Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TSF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, MacInnis BL, Johnson J, Springer M, Happi CT, Sabeti PC, Myhrvold C. Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nat Biomed Eng 2022; 6:932-943. [PMID: 35637389 PMCID: PMC9398993 DOI: 10.1038/s41551-022-00889-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/01/2022] [Indexed: 02/03/2023]
Abstract
The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
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Affiliation(s)
- Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - A'Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michelle E Grunberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Priya P Pillai
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Sreekar Mantena
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gaeun Kim
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Gregory Kocher
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Justin S Lee
- Biotechnology Cores Facility Branch, Division of Scientific Resources, National Center for Emerging and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy Johnson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Karron RA, Hetrich MK, Na YB, Knoll MD, Schappell E, Meece J, Hanson E, Tong S, Lee JS, Veguilla V, Dawood FS. Assessment of Clinical and Virological Characteristics of SARS-CoV-2 Infection Among Children Aged 0 to 4 Years and Their Household Members. JAMA Netw Open 2022; 5:e2227348. [PMID: 36044218 PMCID: PMC9434363 DOI: 10.1001/jamanetworkopen.2022.27348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
IMPORTANCE Few studies have prospectively assessed SARS-CoV-2 community infection in children aged 0 to 4 years. Information about SARS-CoV-2 incidence and clinical and virological features in young children could help guide prevention and mitigation strategies. OBJECTIVE To assess SARS-CoV-2 incidence, clinical and virological features, and symptoms in a prospective household cohort and to compare viral load by age group, symptoms, and SARS-CoV-2 lineage in young children, older children, and adults. DESIGN, SETTING, AND PARTICIPANTS This prospective cohort study enrolled 690 participants from 175 Maryland households with 1 or more children aged 0 to 4 years between November 24, 2020, and October 15, 2021. For 8 months after enrollment, participants completed weekly symptom questionnaires and submitted self-collected nasal swabs for SARS-CoV-2 qualitative real-time reverse transcriptase polymerase chain reaction (RT-PCR) testing, quantitative RT-PCR testing, and viral lineage determination. For the analyses, SARS-CoV-2 Alpha and Delta lineages were considered variants of interest or concern. Sera collected at enrollment and at approximately 4 months and 8 months after enrollment were assayed for SARS-CoV-2 spike and nucleocapsid protein antibodies. MAIN OUTCOMES AND MEASURES Incidence, clinical and virological characteristics, and symptoms of SARS-CoV-2 infection by age group and correlations between (1) highest detected viral load and symptom frequency and (2) highest detected viral load and SARS-CoV-2 lineage. RESULTS Among 690 participants (355 [51.4%] female and 335 [48.6%] male), 256 individuals (37.1%) were children aged 0 to 4 years, 100 (14.5%) were children aged 5 to 17 years, and 334 (48.4%) were adults aged 18 to 74 years. A total of 15 participants (2.2%) were Asian, 24 (3.5%) were Black, 603 (87.4%) were White, 43 (6.2%) were multiracial, and 5 (0.7%) were of other races; 33 participants (4.8%) were Hispanic, and 657 (95.2%) were non-Hispanic. Overall, 54 participants (7.8%) had SARS-CoV-2 infection during the surveillance period, including 22 of 256 children (8.6%) aged 0 to 4 years, 11 of 100 children (11.0%) aged 5 to 17 years, and 21 of 334 adults (6.3%). Incidence rates per 1000 person-weeks were 2.25 (95% CI, 1.28-3.65) infections among children aged 0 to 4 years, 3.48 (95% CI, 1.59-6.61) infections among children aged 5 to 17 years, and 1.08 (95% CI, 0.52-1.98) infections among adults. Children aged 0 to 17 years with SARS-CoV-2 infection were more frequently asymptomatic (11 of 30 individuals [36.7%]) compared with adults (3 of 21 individuals [14.3%]), with children aged 0 to 4 years most frequently asymptomatic (7 of 19 individuals [36.8%]). The highest detected viral load did not differ between asymptomatic vs symptomatic individuals overall (median [IQR], 2.8 [1.5-3.3] log10 copies/mL vs 2.8 [1.8-4.4] log10 copies/mL) or by age group (median [IQR] for ages 0-4 years, 2.7 [2.4-4.4] log10 copies/mL; ages 5-17 years: 2.4 [1.1-4.0] log10 copies/mL; ages 18-74 years: 2.9 [1.9-4.6] log10 copies/mL). The number of symptoms was significantly correlated with viral load among adults (R = 0.69; P < .001) but not children (ages 0-4 years: R = 0.02; P = .91; ages 5-17 years: R = 0.18; P = .58). The highest detected viral load was greater among those with Delta variant infections (median [IQR], 4.4 [3.9-5.1] log10 copies/mL) than those with infections from variants not of interest or concern (median [IQR], 1.9 [1.1-3.6] log10 copies/mL; P = .009) or those with Alpha variant infections (median [IQR], 2.6 [2.3-3.4] log10 copies/mL; P = .006). CONCLUSIONS AND RELEVANCE In this study, SARS-CoV-2 infections were frequently asymptomatic among children aged 0 to 4 years; the presence and number of symptoms did not correlate with viral load. These findings suggest that symptom screening may be insufficient to prevent outbreaks involving young children.
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Affiliation(s)
- Ruth A. Karron
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Marissa K. Hetrich
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Yu Bin Na
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Maria Deloria Knoll
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth Schappell
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Jennifer Meece
- Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | | | - Suxiang Tong
- COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Justin S. Lee
- COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Vic Veguilla
- COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Fatimah S. Dawood
- COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia
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45
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Orendáčová M, Kvašňák E. Effects of vaccination, new SARS-CoV-2 variants and reinfections on post-COVID-19 complications. Front Public Health 2022; 10:903568. [PMID: 35968477 PMCID: PMC9372538 DOI: 10.3389/fpubh.2022.903568] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Post-COVID-19 complications involve a variety of long-lasting health complications emerging in various body systems. Since the prevalence of post-COVID-19 complications ranges from 8-47% in COVID-19 survivors, it represents a formidable challenge to COVID-19 survivors and the health care system. Post-COVID-19 complications have already been studied in the connection to risk factors linked to their higher probability of occurrence and higher severity, potential mechanisms underlying the pathogenesis of post-COVID-19 complications, and their functional and structural correlates. Vaccination status has been recently revealed to represent efficient prevention from long-term and severe post-COVID-19 complications. However, the exact mechanisms responsible for vaccine-induced protection against severe and long-lasting post-COVID-19 complications remain elusive. Also, to the best of our knowledge, the effects of new SARS-CoV-2 variants and SARS-CoV-2 reinfections on post-COVID-19 complications and their underlying pathogenesis remain to be investigated. This hypothesis article will be dedicated to the potential effects of vaccination status, SARS-CoV-2 reinfections, and new SARS-CoV-2 variants on post-COVID-19 complications and their underlying mechanisms Also, potential prevention strategies against post-COVID complications will be discussed.
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Affiliation(s)
- Mária Orendáčová
- Department of Medical Biophysics and Medical Informatics, Third Faculty of Medicine, Charles University in Prague, Prague, Czechia
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Rodriguez J, Price O, Jennings R, Creel A, Eaton S, Chesnutt J, McClellan G, Batni SR. A Novel Framework for Modeling Person-to-Person Transmission of Respiratory Diseases. Viruses 2022; 14:v14071567. [PMID: 35891547 PMCID: PMC9322782 DOI: 10.3390/v14071567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/27/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
From the beginning of the COVID-19 pandemic, researchers assessed the impact of the disease in terms of loss of life, medical load, economic damage, and other key metrics of resiliency and consequence mitigation; these studies sought to parametrize the critical components of a disease transmission model and the resulting analyses were informative but often lacked critical parameters or a discussion of parameter sensitivities. Using SARS-CoV-2 as a case study, we present a robust modeling framework that considers disease transmissibility from the source through transport and dispersion and infectivity. The framework is designed to work across a range of particle sizes and estimate the generation rate, environmental fate, deposited dose, and infection, allowing for end-to-end analysis that can be transitioned to individual and population health models. In this paper, we perform sensitivity analysis on the model framework to demonstrate how it can be used to advance and prioritize research efforts by highlighting critical parameters for further analyses.
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Affiliation(s)
- Jason Rodriguez
- Applied Research Associates, Inc. (ARA), 4300 San Mateo Blvd NE, Suite A220, Albuquerque, NM 87110, USA; (J.R.); (O.P.); (R.J.); (A.C.); (S.E.); (J.C.); (G.M.)
| | - Owen Price
- Applied Research Associates, Inc. (ARA), 4300 San Mateo Blvd NE, Suite A220, Albuquerque, NM 87110, USA; (J.R.); (O.P.); (R.J.); (A.C.); (S.E.); (J.C.); (G.M.)
| | - Rachel Jennings
- Applied Research Associates, Inc. (ARA), 4300 San Mateo Blvd NE, Suite A220, Albuquerque, NM 87110, USA; (J.R.); (O.P.); (R.J.); (A.C.); (S.E.); (J.C.); (G.M.)
| | - Amy Creel
- Applied Research Associates, Inc. (ARA), 4300 San Mateo Blvd NE, Suite A220, Albuquerque, NM 87110, USA; (J.R.); (O.P.); (R.J.); (A.C.); (S.E.); (J.C.); (G.M.)
| | - Sarah Eaton
- Applied Research Associates, Inc. (ARA), 4300 San Mateo Blvd NE, Suite A220, Albuquerque, NM 87110, USA; (J.R.); (O.P.); (R.J.); (A.C.); (S.E.); (J.C.); (G.M.)
| | - Jennifer Chesnutt
- Applied Research Associates, Inc. (ARA), 4300 San Mateo Blvd NE, Suite A220, Albuquerque, NM 87110, USA; (J.R.); (O.P.); (R.J.); (A.C.); (S.E.); (J.C.); (G.M.)
| | - Gene McClellan
- Applied Research Associates, Inc. (ARA), 4300 San Mateo Blvd NE, Suite A220, Albuquerque, NM 87110, USA; (J.R.); (O.P.); (R.J.); (A.C.); (S.E.); (J.C.); (G.M.)
| | - Sweta R. Batni
- Defense Threat Reduction Agency (DTRA), 8725 John J. Kingman Road #6201, Fort Belvoir, VA 22060, USA
- Correspondence:
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47
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Patrick C, Upadhyay V, Lucas A, Mallela KM. Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain. J Mol Biol 2022; 434:167622. [PMID: 35533762 PMCID: PMC9076029 DOI: 10.1016/j.jmb.2022.167622] [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: 01/10/2022] [Revised: 04/21/2022] [Accepted: 04/29/2022] [Indexed: 12/16/2022]
Abstract
Among the five known SARS-CoV-2 variants of concern, Delta is the most virulent leading to severe symptoms and increased mortality among infected people. Our study seeks to examine how the biophysical parameters of the Delta variant correlate to the clinical observations. Receptor binding domain (RBD) is the first point of contact with the human host cells and is the immunodominant form of the spike protein. Delta variant RBD contains two novel mutations L452R and T478K. We examined the effect of single as well as the double mutations on RBD expression in human Expi293 cells, RBD stability using urea and thermal denaturation, and RBD binding to angiotensin converting enzyme 2 (ACE2) receptor and to neutralizing antibodies using isothermal titration calorimetry. Delta variant RBD showed significantly higher expression compared to the wild-type RBD, and the increased expression is due to L452R mutation. Despite their non-conservative nature, none of the mutations significantly affected RBD structure and stability. All mutants showed similar binding affinity to ACE2 and to Class 1 antibodies (CC12.1 and LY-CoV016) as that of the wild-type. Delta double mutant L452R/T478K showed no binding to Class 2 antibodies (P2B-2F6 and LY-CoV555) and a hundred-fold weaker binding to a Class 3 antibody (REGN10987), and the decreased antibody binding is determined by the L452R mutation. These results indicate that the immune escape from neutralizing antibodies, rather than increased receptor binding, is the main biophysical parameter that determined the fitness landscape of the Delta variant RBD.
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Affiliation(s)
| | | | | | - Krishna M.G. Mallela
- Corresponding author at: Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd, MS C238-V20, Aurora, CO 80045, USA
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48
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Batchi-Bouyou AL, Djontu JC, Vouvoungui JC, Mfoutou Mapanguy CC, Lobaloba Ingoba L, Mougany JS, Boumpoutou KR, Diafouka-Kietela S, Ampa R, Ntoumi F. Assessment of neutralizing antibody responses after natural SARS-CoV-2 infection and vaccination in congolese individuals. BMC Infect Dis 2022; 22:610. [PMID: 35831798 PMCID: PMC9277981 DOI: 10.1186/s12879-022-07593-y] [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: 02/08/2022] [Accepted: 06/13/2022] [Indexed: 12/29/2022] Open
Abstract
Background Assessing immune responses after vaccination is part of the evaluation package of vaccine effectiveness in the real world. Regarding SARS-CoV-2, neutralizing antibody levels has been shown to be a good indicator of antibody immune response boosting. So far, limited data have been reported from Africa including in Central Africa. The objective of this study was to provide data on anti-S1 spike total IgG and neutralizing antibodies in vaccinated and non-vaccinated including naturally infected Congolese population during B.1.214.1 and B.1.617.2 variant waves. Methods Recruited patients were divided into 4 groups: (1) Naturally infected by the B.1.214.1 variant on January 2021 and followed up until September 2021. These patients have been vaccinated at month 07 and then followed up for 2 months post vaccination; (2) Naturally infected by the B.1.617.2 variant from June 2021; (3) unvaccinated SARS-CoV-2 individuals with no history of prior SARS-CoV-2 infection; (4) fully vaccinated individuals with sinopharm/BBIP-CorV or Janssen/Ad26.COV2.S. SARS-CoV-2 was detected by qRT-PCR and sequenced using Next-Generation Sequencing. ELISA method was used for detecting IgG, and neutralizing Antibody against SARS-CoV-2 antigens using commercial neutralizing assay. Results Individuals infected by the B.1214.1 variant elicited consistently high IgG titers at 02, 03 and 06 months. Two months post vaccination with BBIP-CorV, participants showed a significant increase by × 2.5 fold (p < 0.0001) of total IgG and X1.5 fold for neutralizing antibody capacity. This study showed that natural infection with B1.617.2 (delta) variant was more immunogenic compared to those being infected with B1.214.2 variant. We found a significantly higher concentration in anti-SARS-CoV-2 IgG (p < 0.0002) and antibodies neutralization capacity (P < 0.0001) in fully vaccinated compared to unvaccinated participants. Two months post vaccination, individuals who received Janssen/Ad26.COV2.S presented higher (p = 0.01) total IgG to spike protein compared to BBIP-CorV. Conclusion Both natural infection and vaccination with BBIP-CorV and Janssen/Ad26.COV2.S induced antibody response in Congolese population. In addition, Janssen/Ad26.COV2.S was more immunogenic than Sinopharm/BBIP-CorV. There is a need to investigate the duration of these antibodies both in previously infected and naive vaccinated Congolese to allow public heath stakeholders to make evidence-based decision on vaccine schedule for the Congolese population.
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Affiliation(s)
- Armel Landry Batchi-Bouyou
- Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Campus OMS, Djoué, Brazzaville, Republic of Congo.,Faculty of Sciences and Techniques, University Marien Ngouabi, Brazzaville, Republic of Congo
| | - Jean Claude Djontu
- Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Campus OMS, Djoué, Brazzaville, Republic of Congo
| | | | - Claujens Chastel Mfoutou Mapanguy
- Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Campus OMS, Djoué, Brazzaville, Republic of Congo.,Faculty of Sciences and Techniques, University Marien Ngouabi, Brazzaville, Republic of Congo
| | - Line Lobaloba Ingoba
- Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Campus OMS, Djoué, Brazzaville, Republic of Congo.,Faculty of Sciences and Techniques, University Marien Ngouabi, Brazzaville, Republic of Congo
| | - Jiré Séphora Mougany
- Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Campus OMS, Djoué, Brazzaville, Republic of Congo.,Faculty of Sciences and Techniques, University Marien Ngouabi, Brazzaville, Republic of Congo
| | - Kamal Rauchelvy Boumpoutou
- Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Campus OMS, Djoué, Brazzaville, Republic of Congo
| | - Steve Diafouka-Kietela
- Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Campus OMS, Djoué, Brazzaville, Republic of Congo
| | - Raoul Ampa
- Faculty of Sciences and Techniques, University Marien Ngouabi, Brazzaville, Republic of Congo
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Campus OMS, Djoué, Brazzaville, Republic of Congo. .,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.
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49
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Time-Series Associations between Public Interest in COVID-19 Variants and National Vaccination Rate: A Google Trends Analysis. Behav Sci (Basel) 2022; 12:bs12070223. [PMID: 35877293 PMCID: PMC9312257 DOI: 10.3390/bs12070223] [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: 06/07/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
The emergence of a constantly mutating novel virus has led to considerable public anxiety amid the COVID-19 pandemic. Information seeking is a common strategy to cope with pandemic anxiety. Using Google Trends analysis, this study investigated public interest in COVID-19 variants and its temporal associations with the disease-prevention measure of vaccination during the initial COVID-19 vaccine rollout period (13 December 2020 to 25 September 2021). Public interest was operationalized as the relative search volume of online queries of variant-related terms in the countries first affected by the Alpha, Beta, and Delta variants: the UK, South Africa, and India, respectively. The results show that public interest in COVID-19 variants was greater during the Delta-variant-predominant period than before this period. The time-series cross-correlation analysis revealed positive temporal associations (i.e., greater such public interest was accompanied by an increase in national vaccination rate) tended to occur more frequently and at earlier time lags than the negative temporal associations. This study yielded new findings regarding the temporal changes in public interest in COVID-19 variants, and the between-country variations in these public interest changes can be explained by differences in the rate and pace of vaccination among the countries of interest.
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50
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Puhach O, Adea K, Hulo N, Sattonnet P, Genecand C, Iten A, Jacquérioz F, Kaiser L, Vetter P, Eckerle I, Meyer B. Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2. Nat Med 2022. [PMID: 35395151 DOI: 10.1101/2022.01.10.22269010] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Infectious viral load (VL) expelled as droplets and aerosols by infected individuals partly determines transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RNA VL measured by qRT-PCR is only a weak proxy for infectiousness. Studies on the kinetics of infectious VL are important to understand the mechanisms behind the different transmissibility of SARS-CoV-2 variants and the effect of vaccination on transmission, which allows guidance of public health measures. In this study, we quantified infectious VL in individuals infected with SARS-CoV-2 during the first five symptomatic days by in vitro culturability assay in unvaccinated or vaccinated individuals infected with pre-variant of concern (pre-VOC) SARS-CoV-2, Delta or Omicron BA.1. Unvaccinated individuals infected with pre-VOC SARS-CoV-2 had lower infectious VL than Delta-infected unvaccinated individuals. Full vaccination (defined as >2 weeks after receipt of the second dose during the primary vaccination series) significantly reduced infectious VL for Delta breakthrough cases compared to unvaccinated individuals. For Omicron BA.1 breakthrough cases, reduced infectious VL was observed only in boosted but not in fully vaccinated individuals compared to unvaccinated individuals. In addition, infectious VL was lower in fully vaccinated Omicron BA.1-infected individuals compared to fully vaccinated Delta-infected individuals, suggesting that mechanisms other than increased infectious VL contribute to the high infectiousness of SARS-CoV-2 Omicron BA.1. Our findings indicate that vaccines may lower transmission risk and, therefore, have a public health benefit beyond the individual protection from severe disease.
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Affiliation(s)
- Olha Puhach
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Kenneth Adea
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Nicolas Hulo
- Service for Biomathematical and Biostatistical Analyses, Institute of Genetics and Genomics, University of Geneva, Geneva, Switzerland
| | - Pascale Sattonnet
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Camille Genecand
- Cantonal Health Service, General Directorate for Health, Geneva, Switzerland
| | - Anne Iten
- Service of Prevention and Infection Control, Directorate of Medicine and Quality, Geneva University Hospitals, Geneva, Switzerland
| | - Frédérique Jacquérioz
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- Division of Tropical and Humanitarian Medicine, Geneva University Hospitals, Geneva, Switzerland
- Primary Care Division, Geneva University Hospitals, Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Pauline Vetter
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
| | - Isabella Eckerle
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
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