201
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Samsunder N, de Vos M, Ngcapu S, Giandhari J, Lewis L, Kharsany AB, Carwood C, de Olveira T, Karim QA, Karim SA, Naidoo K, Escadafal C, Sivro A. Clinical evaluation of SARS-CoV-2 rapid antigen tests during the Omicron wave in South Africa. J Infect Dis 2022; 226:1412-1417. [PMID: 35921539 PMCID: PMC9384653 DOI: 10.1093/infdis/jiac333] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
We evaluated the performance of nasal and nasopharyngeal Standard Q COVID-19 Ag tests (SD Biosensor) and the Panbio COVID-19 Ag Rapid Test Device (nasal, Abbott) against the Abbott RealTime SARS-CoV-2 assay during the Omicron (21 M, 21K and 21L) wave in South Africa. Overall, all evaluated tests performed well with high level of sensitivity (ranging from 77.78-81.42%) and excellent specificity values (>99%). The sensitivity of rapid antigen tests increased above 90% in samples with Ct <20, and all three tests performed best within first week of symptom onset. The Panbio Ag test performed best in the context of Omicron 21L infections, that were also characterised by significantly lower Ct values compared to infections with 21K and 21 M.
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Affiliation(s)
- Natasha Samsunder
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | | | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Ayesha Bm Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,FIND, the global alliance for diagnostics, Geneva, Switzerland
| | - Cherie Carwood
- Epicentre AIDS Risk Management (Pty) Limited, Durban, South Africa
| | - Tulio de Olveira
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa.,Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.,Department of Global Health, University of Washington, Seattle, USA
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,Department of Epidemiology, Columbia University, New York City, USA
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,Department of Epidemiology, Columbia University, New York City, USA
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, South Africa
| | | | - Aida Sivro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
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202
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Chin AWH, Lai AMY, Peiris M, Man Poon LL. Increased Stability of SARS-CoV-2 Omicron Variant over Ancestral Strain. Emerg Infect Dis 2022; 28:1515-1517. [PMID: 35550234 PMCID: PMC9239870 DOI: 10.3201/eid2807.220428] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
As of April 2022, the Omicron BA.1 variant of concern of SARS-CoV-2 was spreading quickly around the world and outcompeting other circulating strains. We examined its stability on various surfaces and found that this Omicron variant is more stable than its ancestral strain on smooth and porous surfaces.
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203
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Sender R, Bar-On Y, Woo Park S, Noor E, Dushoff J, Milo R. The unmitigated profile of COVID-19 infectiousness. eLife 2022; 11:79134. [PMID: 35913120 PMCID: PMC9391043 DOI: 10.7554/elife.79134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Quantifying the temporal dynamics of infectiousness of individuals infected with SARS-CoV-2 is crucial for understanding the spread of COVID-19 and for evaluating the effectiveness of mitigation strategies. Many studies have estimated the infectiousness profile using observed serial intervals. However, statistical and epidemiological biases could lead to underestimation of the duration of infectiousness. We correct for these biases by curating data from the initial outbreak of the pandemic in China (when mitigation was minimal), and find that the infectiousness profile of the original strain is longer than previously thought. Sensitivity analysis shows our results are robust to model structure, assumed growth rate and potential observational biases. Although unmitigated transmission data is lacking for variants of concern (VOCs), previous analyses suggest that the alpha and delta variants have faster within-host kinetics, which we extrapolate to crude estimates of variant-specific unmitigated generation intervals. Knowing the unmitigated infectiousness profile of infected individuals can inform estimates of the effectiveness of isolation and quarantine measures. The framework presented here can help design better quarantine policies in early stages of future epidemics.
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Affiliation(s)
- Ron Sender
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yinon Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sang Woo Park
- Department of Ecology and Evolutionary, Princeton University, Princeton, United States
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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204
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Hakki S, Zhou J, Jonnerby J, Singanayagam A, Barnett JL, Madon KJ, Koycheva A, Kelly C, Houston H, Nevin S, Fenn J, Kundu R, Crone MA, Pillay TD, Ahmad S, Derqui-Fernandez N, Conibear E, Freemont PS, Taylor GP, Ferguson N, Zambon M, Barclay WS, Dunning J, Lalvani A, Badhan A, Varro R, Luca C, Quinn V, Cutajar J, Nichols N, Russell J, Grey H, Ketkar A, Miserocchi G, Tejpal C, Catchpole H, Nixon K, Di Biase B, Hopewell T, Narean JS, Samuel J, Timcang K, McDermott E, Bremang S, Hammett S, Evetts S, Kondratiuk A. Onset and window of SARS-CoV-2 infectiousness and temporal correlation with symptom onset: a prospective, longitudinal, community cohort study. THE LANCET RESPIRATORY MEDICINE 2022; 10:1061-1073. [PMID: 35988572 PMCID: PMC9388060 DOI: 10.1016/s2213-2600(22)00226-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/24/2022] [Accepted: 06/08/2022] [Indexed: 12/05/2022]
Abstract
Background Knowledge of the window of SARS-CoV-2 infectiousness is crucial in developing policies to curb transmission. Mathematical modelling based on scarce empirical evidence and key assumptions has driven isolation and testing policy, but real-world data are needed. We aimed to characterise infectiousness across the full course of infection in a real-world community setting. Methods The Assessment of Transmission and Contagiousness of COVID-19 in Contacts (ATACCC) study was a UK prospective, longitudinal, community cohort of contacts of newly diagnosed, PCR-confirmed SARS-CoV-2 index cases. Household and non-household exposed contacts aged 5 years or older were eligible for recruitment if they could provide informed consent and agree to self-swabbing of the upper respiratory tract. The primary objective was to define the window of SARS-CoV-2 infectiousness and its temporal correlation with symptom onset. We quantified viral RNA load by RT-PCR and infectious viral shedding by enumerating cultivable virus daily across the course of infection. Participants completed a daily diary to track the emergence of symptoms. Outcomes were assessed with empirical data and a phenomenological Bayesian hierarchical model. Findings Between Sept 13, 2020, and March 31, 2021, we enrolled 393 contacts from 327 households (the SARS-CoV-2 pre-alpha and alpha variant waves); and between May 24, 2021, and Oct 28, 2021, we enrolled 345 contacts from 215 households (the delta variant wave). 173 of these 738 contacts were PCR positive for more than one timepoint, 57 of which were at the start of infection and comprised the final study population. The onset and end of infectious viral shedding were captured in 42 cases and the median duration of infectiousness was 5 (IQR 3–7) days. Although 24 (63%) of 38 cases had PCR-detectable virus before symptom onset, only seven (20%) of 35 shed infectious virus presymptomatically. Symptom onset was a median of 3 days before both peak viral RNA and peak infectious viral load (viral RNA IQR 3–5 days, n=38; plaque-forming units IQR 3–6 days, n=35). Notably, 22 (65%) of 34 cases and eight (24%) of 34 cases continued to shed infectious virus 5 days and 7 days post-symptom onset, respectively (survival probabilities 67% and 35%). Correlation of lateral flow device (LFD) results with infectious viral shedding was poor during the viral growth phase (sensitivity 67% [95% CI 59–75]), but high during the decline phase (92% [86–96]). Infectious virus kinetic modelling suggested that the initial rate of viral replication determines the course of infection and infectiousness. Interpretation Less than a quarter of COVID-19 cases shed infectious virus before symptom onset; under a crude 5-day self-isolation period from symptom onset, two-thirds of cases released into the community would still be infectious, but with reduced infectious viral shedding. Our findings support a role for LFDs to safely accelerate deisolation but not for early diagnosis, unless used daily. These high-resolution, community-based data provide evidence to inform infection control guidance. Funding National Institute for Health and Care Research.
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205
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Wu Z, Wang C, Liu B, Liang C, Lu J, Li J, Tang X, Li C, Li T. Smartphone-Based High-Throughput Fiber-Integrated Immunosensing System for Point-of-Care Testing of the SARS-CoV-2 Nucleocapsid Protein. ACS Sens 2022; 7:1985-1995. [PMID: 35766020 PMCID: PMC9261833 DOI: 10.1021/acssensors.2c00754] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
To control the coronavirus disease 2019 (COVID-19) pandemic, there is an urgent need for simple, rapid, and reliable detection methods to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, especially in community hospitals or clinical centers. The SARS-CoV-2 nucleocapsid protein (NP) is an important index for diagnosis of COVID-19. Here, we proposed a smartphone-based high-throughput fiber-integrated immunosensing system (HFIS) for detecting the SARS-CoV-2 NP in serum samples within 45 min. For the testing of NP standards, the linear detection range was 7.8-1000 pg/mL, the limit of detection was 7.5 pg/mL, and the cut-off value was 8.923 pg/mL. Twenty-five serum samples from clinically diagnosed COVID-19 patients and 100 negative control samples from healthy blood donors were tested for SARS-CoV-2 NP by HFIS, and the obtained results were compared with those of ELISA and Simple Western analysis. The results showed that the HFIS sensitivity and specificity were 72% [95% confidence interval (CI): 52.42-85.72%] and 100% (95% CI: 96.11-100%), respectively, which significantly correlated with those from the commercial ELISA kit and Simple Western analysis. This portable high-throughput HFIS assay could be an alternative test for detecting SARS-CoV-2 NP in blood samples on site.
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Affiliation(s)
- Ze Wu
- Department of Transfusion Medicine, School of
Laboratory Medicine and Biotechnology, Southern Medical
University, Guangzhou 510515, P. R. China
- Department of Laboratory Medicine, Nanfang Hospital,
Southern Medical University, Guangzhou 510515, P. R.
China
| | - Cong Wang
- Department of Transfusion Medicine, School of
Laboratory Medicine and Biotechnology, Southern Medical
University, Guangzhou 510515, P. R. China
| | - Bochao Liu
- Department of Transfusion Medicine, School of
Laboratory Medicine and Biotechnology, Southern Medical
University, Guangzhou 510515, P. R. China
- Guangzhou Blood Center,
Guangzhou 510091, P. R. China
| | - Chaolan Liang
- Department of Transfusion Medicine, School of
Laboratory Medicine and Biotechnology, Southern Medical
University, Guangzhou 510515, P. R. China
| | - Jinhui Lu
- Department of Transfusion Medicine, School of
Laboratory Medicine and Biotechnology, Southern Medical
University, Guangzhou 510515, P. R. China
| | - Jinfeng Li
- Shenzhen Key Laboratory of Molecular Epidemiology,
Shenzhen Center for Disease Control and Prevention, Shenzhen
518054, P. R. China
| | - Xi Tang
- Department of Infection, The First
People’s Hospital of Foshan, Foshan 528010,
China
| | - Chengyao Li
- Department of Transfusion Medicine, School of
Laboratory Medicine and Biotechnology, Southern Medical
University, Guangzhou 510515, P. R. China
| | - Tingting Li
- Department of Transfusion Medicine, School of
Laboratory Medicine and Biotechnology, Southern Medical
University, Guangzhou 510515, P. R. China
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206
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Jefferson T, Heneghan CJ, Spencer E, Brassey J, Plüddemann A, Onakpoya I, Evans D, Conly J. A Hierarchical Framework for Assessing Transmission Causality of Respiratory Viruses. Viruses 2022; 14:1605. [PMID: 35893670 PMCID: PMC9332164 DOI: 10.3390/v14081605] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 01/03/2023] Open
Abstract
Systematic reviews of 591 primary studies of the modes of transmission for SARS-CoV-2 show significant methodological shortcomings and heterogeneity in the design, conduct, testing, and reporting of SARS-CoV-2 transmission. While this is partly understandable at the outset of a pandemic, evidence rules of proof for assessing the transmission of this virus are needed for present and future pandemics of viral respiratory pathogens. We review the history of causality assessment related to microbial etiologies with a focus on respiratory viruses and suggest a hierarchy of evidence to integrate clinical, epidemiologic, molecular, and laboratory perspectives on transmission. The hierarchy, if applied to future studies, should narrow the uncertainty over the twin concepts of causality and transmission of human respiratory viruses. We attempt to address the translational gap between the current research evidence and the assessment of causality in the transmission of respiratory viruses with a focus on SARS-CoV-2. Experimentation, consistency, and independent replication of research alongside our proposed framework provide a chain of evidence that can reduce the uncertainty over the transmission of respiratory viruses and increase the level of confidence in specific modes of transmission, informing the measures that should be undertaken to prevent transmission.
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Affiliation(s)
- Tom Jefferson
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK;
| | - Carl J. Heneghan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK; (C.J.H.); (E.S.); (A.P.)
| | - Elizabeth Spencer
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK; (C.J.H.); (E.S.); (A.P.)
| | - Jon Brassey
- Trip Database Ltd., Little Maristowe, Glasllwch Lane, Newport NP20 3PS, UK;
| | - Annette Plüddemann
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK; (C.J.H.); (E.S.); (A.P.)
| | - Igho Onakpoya
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK;
| | - David Evans
- Li Ka Shing Institute of Virology, Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - John Conly
- Centre for Antimicrobial Resistance, Alberta Health Services, Alberta Precision Laboratories, University of Calgary, Calgary, AB T2N 4N1, Canada;
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207
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Lin Y, Yue S, Yang Y, Yang S, Pan Z, Yang X, Gao L, Zhou J, Li Z, Hu L, Tang J, Wu Q, Lei S, Tian Q, Wang Y, Hao Y, Xu L, Huang Q, Zhu B, Chen Y, Chen X, Ye L. Nasal Spray of Neutralizing Monoclonal Antibody 35B5 Confers Potential Prophylaxis Against Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Small-Scale Clinical Trial. Clin Infect Dis 2022; 76:e336-e341. [PMID: 35666466 PMCID: PMC9214129 DOI: 10.1093/cid/ciac448] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs), especially the Delta and Omicron variants, have been reported to show significant resistance to approved neutralizing monoclonal antibodies (mAbs) and vaccines. We previously identified a mAb named 35B5 that harbors broad neutralization to SARS-CoV-2 VOCs. Herein, we explored the protection efficacy of a 35B5-based nasal spray against SARS-CoV-2 VOCs in a small-scale clinical trial. METHODS We enrolled 30 healthy volunteers who were nasally administered the modified 35B5 formulation. At 12, 24, 48, and 72 hours after nasal spray, the neutralization efficacy of nasal mucosal samples was assayed with pseudoviruses coated with SARS-CoV-2 spike protein of the wild-type strain or the Alpha, Beta, Delta, or Omicron variants. RESULTS The nasal mucosal samples collected within 24 hours after nasal spray effectively neutralized SARS-CoV-2 VOCs (including Delta and Omicron). Meanwhile, the protection efficacy was 60% effective and 20% effective at 48 and 72 hours after nasal spray, respectively. CONCLUSIONS A single nasal spray of 35B5 formation conveys 24-hour effective protection against SARS-CoV-2 VOCs, including the Alpha, Beta, Delta, or Omicron variants. Thus, 35B5 nasal spray might be potential in strengthening SARS-CoV-2 prevention, especially in high-risk populations. CLINICAL TRIALS REGISTRATION 2022-005-02-KY.
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Affiliation(s)
| | | | | | - Sen Yang
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Zhiwei Pan
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Xiaofan Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Leiqiong Gao
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jing Zhou
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Zhirong Li
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Li Hu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jianfang Tang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Qing Wu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Shun Lei
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Qin Tian
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yifei Wang
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Yaxing Hao
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Lifan Xu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Qizhao Huang
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Bo Zhu
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | | | | | - Lilin Ye
- Correspondence: L. Ye, Third Military Medical University, 30 Gaotanyan, Chongqing, 400038, China ()
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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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209
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210
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Phan T, Brozak S, Pell B, Gitter A, Mena KD, Kuang Y, Wu F. A simple SEIR-V model to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission using wastewater-based surveillance data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.07.17.22277721. [PMID: 35898336 PMCID: PMC9327624 DOI: 10.1101/2022.07.17.22277721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Wastewater-based surveillance (WBS) has been widely used as a public health tool to monitor SARS-CoV-2 transmission. However, epidemiological inference from WBS data remains understudied and limits its application. In this study, we have established a quantitative framework to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission through integrating WBS data into an SEIR-V model. We conceptually divide the individual-level viral shedding course into exposed, infectious, and recovery phases as an analogy to the compartments in population-level SEIR model. We demonstrated that the temperature effect on viral losses in the sewer can be straightforwardly incorporated in our framework. Using WBS data from the second wave of the pandemic (Oct 02, 2020 â€" Jan 25, 2021) in the Great Boston area, we showed that the SEIR-V model successfully recapitulates the temporal dynamics of viral load in wastewater and predicts the true number of cases peaked earlier and higher than the number of reported cases by 16 days and 8.6 folds ( R = 0.93), respectively. This work showcases a simple, yet effective method to bridge WBS and quantitative epidemiological modeling to estimate the prevalence and transmission of SARS-CoV-2 in the sewershed, which could facilitate the application of wastewater surveillance of infectious diseases for epidemiological inference and inform public health actions.
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Affiliation(s)
- Tin Phan
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico, USA
| | - Samantha Brozak
- School of Mathematical and Statistical Sciences, Arizona State University, Arizona, USA
| | - Bruce Pell
- Department of Mathematics and Computer Science, Lawrence Technological University, MI, USA
| | - Anna Gitter
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, Texas, USA 77030
| | - Kristina D. Mena
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, Texas, USA 77030
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, Arizona, USA
| | - Fuqing Wu
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, Texas, USA 77030
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211
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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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212
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Trougakos IP, Terpos E, Alexopoulos H, Politou M, Paraskevis D, Scorilas A, Kastritis E, Andreakos E, Dimopoulos MA. Adverse effects of COVID-19 mRNA vaccines: the spike hypothesis. Trends Mol Med 2022; 28:542-554. [PMID: 35537987 PMCID: PMC9021367 DOI: 10.1016/j.molmed.2022.04.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/27/2022] [Accepted: 04/08/2022] [Indexed: 11/27/2022]
Abstract
Vaccination is a major tool for mitigating the coronavirus disease 2019 (COVID-19) pandemic, and mRNA vaccines are central to the ongoing vaccination campaign that is undoubtedly saving thousands of lives. However, adverse effects (AEs) following vaccination have been noted which may relate to a proinflammatory action of the lipid nanoparticles used or the delivered mRNA (i.e., the vaccine formulation), as well as to the unique nature, expression pattern, binding profile, and proinflammatory effects of the produced antigens - spike (S) protein and/or its subunits/peptide fragments - in human tissues or organs. Current knowledge on this topic originates mostly from cell-based assays or from model organisms; further research on the cellular/molecular basis of the mRNA vaccine-induced AEs will therefore promise safety, maintain trust, and direct health policies.
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Affiliation(s)
- Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, 157 84, Greece.
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, National and Kapodistrian University of Athens, Athens, 115 28, Greece
| | - Harry Alexopoulos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, 157 84, Greece
| | - Marianna Politou
- Hematology Laboratory-Blood Bank, Aretaieio Hospital, School of Medicine, National and Kapodistrian University of Athens, 115 28, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 115 27, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, 157 01, Greece
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, National and Kapodistrian University of Athens, Athens, 115 28, Greece
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, 115 27, Greece
| | - Meletios A Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, National and Kapodistrian University of Athens, Athens, 115 28, Greece
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213
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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: 10.1101/2022.01.10.22269010v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
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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214
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Hybrid measurement of respiratory aerosol reveals a dominant coarse fraction resulting from speech that remains airborne for minutes. Proc Natl Acad Sci U S A 2022; 119:e2203086119. [PMID: 35727979 PMCID: PMC9245670 DOI: 10.1073/pnas.2203086119] [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] [Indexed: 12/12/2022] Open
Abstract
Respiratory droplets are widely recognized as the primary vehicle in viral respiratory disease transmission. Accurate information on their number and size distributions is important for appropriate mitigation strategies, for quantitative modeling of airborne disease transmission, and for evaluating the relative importance of droplets originating from saliva versus airway lining fluid. A straightforward experimental setup using inexpensive, readily available components is developed for simultaneous characterization of larger particles by video analysis of laser light scattering and monitoring of smaller sizes by an optical particle counter. Measurements indicate that in a healthy volunteer, the airborne mass of speech aerosol far exceeds that generated by breathing, even when accounting for faster sedimentation of the larger particles. Accurate measurements of the size and quantity of aerosols generated by various human activities in different environments are required for efficacious mitigation strategies and accurate modeling of respiratory disease transmission. Previous studies of speech droplets, using standard aerosol instrumentation, reported very few particles larger than 5 μm. This starkly contrasts with the abundance of such particles seen in both historical slide deposition measurements and more recent light scattering observations. We have reconciled this discrepancy by developing an alternative experimental approach that addresses complications arising from nucleated condensation. Measurements reveal that a large volume fraction of speech-generated aerosol has diameters in the 5- to 20-μm range, making them sufficiently small to remain airborne for minutes, not hours. This coarse aerosol is too large to penetrate the lower respiratory tract directly, and its relevance to disease transmission is consistent with the vast majority of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections initiating in the upper respiratory tract. Our measurements suggest that in the absence of symptoms such as coughing or sneezing, the importance of speech-generated aerosol in the transmission of respiratory diseases is far greater than generally recognized.
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215
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Characterizing SARS-CoV-2 Viral Clearance Kinetics to Improve the Design of Antiviral Pharmacometric Studies. Antimicrob Agents Chemother 2022; 66:e0019222. [PMID: 35736134 PMCID: PMC9295592 DOI: 10.1128/aac.00192-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A consensus methodology for the pharmacometric assessment of candidate SARS-CoV-2 antiviral drugs would be useful for comparing trial results and improving trial design. The time to viral clearance, assessed by serial qPCR of nasopharyngeal swab samples, has been the most widely reported measure of virological response in clinical trials, but it has not been compared formally with other metrics, notably model-based estimates of the rate of viral clearance. We analyzed prospectively gathered viral clearance profiles from 280 infection episodes in vaccinated and unvaccinated individuals. We fitted different phenomenological pharmacodynamic models (single exponential decay, bi-exponential, penalized splines) and found that the clearance rate, estimated from a mixed effects single exponential decay model, is a robust pharmacodynamic summary of viral clearance. The rate of viral clearance, estimated from viral densities during the first week following peak viral load, provides increased statistical power (reduced type 2 error) compared with time to clearance. Antiviral effects approximately equivalent to those with currently used and recommended SARS-CoV-2 antiviral treatments, notably nirmatrelvir and molnupiravir, can be detected from randomized trials with sample sizes of only 35 to 65 patients per arm. We recommend that pharmacometric antiviral assessments should be conducted in early COVID-19 illness with serial qPCR samples taken over 1 week.
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216
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Hagemann J, Onorato G, Seifen C, Becker S, Huppertz T, Olze H, Kuna P, Mullol J, Salmi ST, Fonseca J, Rouadi P, Zuberbier T, Bousquet J, Klimek L. Presentation of airway and general symptoms in Covid-19 caused by dominant SARS-CoV-2 variants: a follow-up on ARIA consensus. Allergy 2022; 77:10.1111/all.15416. [PMID: 35730253 PMCID: PMC9349691 DOI: 10.1111/all.15416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Jan Hagemann
- Department of Otolaryngology, Head and Neck SurgeryUniversitätsmedizin MainzMainzGermany
| | | | - Christopher Seifen
- Department of Otolaryngology, Head and Neck SurgeryUniversitätsmedizin MainzMainzGermany
| | - Sven Becker
- Department of Otolaryngology, Head and Neck SurgeryUniversitätsmedizin TübingenTübingenGermany
| | - Tilman Huppertz
- Department of Otolaryngology, Head and Neck SurgeryUniversitätsmedizin MainzMainzGermany
| | - Heidi Olze
- Department of OtolaryngologyCharité Universitätsmedizin Berlin, Humboldt‐Universität zu BerlinBerlinGermany
| | - Piotr Kuna
- Division of Internal Medicine, Asthma and AllergyBarlicki University Hospital, Medical University of LodzLodzPoland
| | - Joaquim Mullol
- Department of OtolaryngologyUniversity Hospital BercelonaBercelonaSpain
| | | | - Joao Fonseca
- Faculdade de Medicina da Universidade do PortoPortoPortugal
- Center for Research in Health Technologies and Information Systems, CINTESISUniversidade do PortoPortoPortugal
- Allergy UnitInstituto CUF Porto e Hospital CUF PortoPortoPortugal
- Health Information and Decision Sciences Department ‐ CIDES, Faculdade de MedicinaUniversidade do PortoPortoPortugal
| | - Philip Rouadi
- Department of Otolaryngology‐Head and Neck SurgeryEye and Ear University HospitalBeirutLebanon
| | - Torsten Zuberbier
- Department of OtolaryngologyCharité Universitätsmedizin Berlin, Humboldt‐Universität zu BerlinBerlinGermany
- Comprehensive Allergy CenterDepartment of Dermatology and AllergyBerlinGermany
| | - Jean Bousquet
- University Hospital MontpellierMontpellierFrance
- Comprehensive Allergy CenterDepartment of Dermatology and AllergyBerlinGermany
- MACVIA‐FranceMontpellierFrance
| | - Ludger Klimek
- Department of Otolaryngology, Head and Neck SurgeryUniversitätsmedizin MainzMainzGermany
- Center for Rhinology and AllergologyWiesbadenGermany
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217
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The Basic Reproduction Number and Delayed Action of T Cells for Patients Infected with SARS-CoV-2. MATHEMATICS 2022. [DOI: 10.3390/math10122017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
COVID-19 has been prevalent for the last two years. The transmission capacity of SARS-CoV-2 differs under the influence of different epidemic prevention policies, making it difficult to measure the infectivity of the virus itself. In order to evaluate the infectivity of SARS-CoV-2 in patients with different diseases, we constructed a viral kinetic model by adding the effects of T cells and antibodies. To analyze and compare the delay time of T cell action in patients with different symptoms, we constructed a delay differential equation model. Through the first model, we found that the basic reproduction number of severe patients is greater than that of mild patients, and accordingly, we constructed classification criteria for severe and mild patients. Through the second model, we found that the delay time of T cell action in severe patients is much longer than that in mild patients, and accordingly, we present suggestions for the prevention, diagnosis, and treatment of different patients.
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218
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Goławski M, Lewandowski P, Jabłońska I, Delijewski M. The Reassessed Potential of SARS-CoV-2 Attenuation for COVID-19 Vaccine Development—A Systematic Review. Viruses 2022; 14:v14050991. [PMID: 35632736 PMCID: PMC9146402 DOI: 10.3390/v14050991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Live-attenuated SARS-CoV-2 vaccines received relatively little attention during the COVID-19 pandemic. Despite this, several methods of obtaining attenuated coronaviruses are known. In this systematic review, the strategies of coronavirus attenuation, which may potentially be applied to SARS-CoV-2, were identified. PubMed, Scopus, Web of Science and Embase databases were searched to identify relevant articles describing attenuating mutations tested in vivo. In case of coronaviruses other than SARS-CoV-2, sequence alignment was used to exclude attenuating mutations that cannot be applied to SARS-CoV-2. Potential immunogenicity, safety and efficacy of the attenuated SARS-CoV-2 vaccine were discussed based on animal studies data. A total of 27 attenuation strategies, used to create 101 different coronaviruses, have been described in 56 eligible articles. The disruption of the furin cleavage site in the SARS-CoV-2 spike protein was identified as the most promising strategy. The replacement of core sequences of transcriptional regulatory signals, which prevents recombination with wild-type viruses, also appears particularly advantageous. Other important attenuating mutations encompassed mostly the prevention of evasion of innate immunity. Sufficiently attenuated coronaviruses typically caused no meaningful disease in susceptible animals and protected them from challenges with virulent virus. This indicates that attenuated COVID-19 vaccines may be considered as a potential strategy to fight the threat posed by SARS-CoV-2.
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Affiliation(s)
- Marcin Goławski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
- Correspondence:
| | - Piotr Lewandowski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
| | - Iwona Jabłońska
- Department of Biophysics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland;
| | - Marcin Delijewski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
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219
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Baselga M, Güemes A, Alba JJ, Schuhmacher AJ. SARS-CoV-2 Droplet and Airborne Transmission Heterogeneity. J Clin Med 2022; 11:2607. [PMID: 35566733 PMCID: PMC9099777 DOI: 10.3390/jcm11092607] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/21/2022] [Accepted: 05/03/2022] [Indexed: 12/13/2022] Open
Abstract
The spread dynamics of the SARS-CoV-2 virus have not yet been fully understood after two years of the pandemic. The virus's global spread represented a unique scenario for advancing infectious disease research. Consequently, mechanistic epidemiological theories were quickly dismissed, and more attention was paid to other approaches that considered heterogeneity in the spread. One of the most critical advances in aerial pathogens transmission was the global acceptance of the airborne model, where the airway is presented as the epicenter of the spread of the disease. Although the aerodynamics and persistence of the SARS-CoV-2 virus in the air have been extensively studied, the actual probability of contagion is still unknown. In this work, the individual heterogeneity in the transmission of 22 patients infected with COVID-19 was analyzed by close contact (cough samples) and air (environmental samples). Viral RNA was detected in 2/19 cough samples from patient subgroups, with a mean Ct (Cycle Threshold in Quantitative Polymerase Chain Reaction analysis) of 25.7 ± 7.0. Nevertheless, viral RNA was only detected in air samples from 1/8 patients, with an average Ct of 25.0 ± 4.0. Viral load in cough samples ranged from 7.3 × 105 to 8.7 × 108 copies/mL among patients, while concentrations between 1.1-4.8 copies/m3 were found in air, consistent with other reports in the literature. In patients undergoing follow-up, no viral load was found (neither in coughs nor in the air) after the third day of symptoms, which could help define quarantine periods in infected individuals. In addition, it was found that the patient's Ct should not be considered an indicator of infectiousness, since it could not be correlated with the viral load disseminated. The results of this work are in line with proposed hypotheses of superspreaders, which can attribute part of the heterogeneity of the spread to the oversized emission of a small percentage of infected people.
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Affiliation(s)
- Marta Baselga
- Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain; (M.B.); (A.G.); (J.J.A.)
| | - Antonio Güemes
- Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain; (M.B.); (A.G.); (J.J.A.)
- Department of Surgery, University of Zaragoza, 50009 Zaragoza, Spain
| | - Juan J. Alba
- Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain; (M.B.); (A.G.); (J.J.A.)
- Department of Mechanical Engineering, University of Zaragoza, 50018 Zaragoza, Spain
| | - Alberto J. Schuhmacher
- Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain; (M.B.); (A.G.); (J.J.A.)
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), 50018 Zaragoza, Spain
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220
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Wan Z, Lu R, Zhao Y, Zhang C. Diagnostic strategy of SARS-CoV-2 for containment under China's zero-COVID-19 policy. J Infect 2022; 85:e7-e9. [PMID: 35508273 PMCID: PMC9056992 DOI: 10.1016/j.jinf.2022.04.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 01/09/2023]
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221
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Rohrig A, Eyal N. A new day for human challenge trials? Trends Mol Med 2022; 28:531-532. [PMID: 35610124 PMCID: PMC9124157 DOI: 10.1016/j.molmed.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022]
Abstract
Two years into the coronavirus disease 2019 (COVID-19) pandemic and following several hot debates, the world’s first COVID-19 human challenge trial has recently been published by Killingley et al. We review its findings and explain why this particular juncture in time makes additional challenge trials for COVID-19 and for other diseases justified and important.
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Affiliation(s)
| | - Nir Eyal
- Center for Population-Level Bioethics, Rutgers University, New Brunswick, NJ, USA.
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222
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Puhach O, Adea K, Hulo N, Sattonnet P, Genecand C, Iten A, Bausch FJ, 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; 28:1491-1500. [PMID: 35395151 DOI: 10.1038/s41591-022-01816-0] [Citation(s) in RCA: 162] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/06/2022] [Indexed: 11/09/2022]
Abstract
Infectious viral load (VL) expelled as droplets and aerosols by infected individuals partly determines SARS-CoV-2 transmission. 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 to guide public health measures. In this study we quantified infectious VL in SARS-CoV-2 infected individuals during the first 5 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. Unvaccinated individuals infected with pre-VOC SARS-CoV-2 had lower infectious VL compared to Delta-infected unvaccinated individuals. Full vaccination (defined as >2weeks after reception of 2nd dose during primary vaccination series) significantly reduced infectious VL for Delta breakthrough cases compared to unvaccinated individuals. For Omicron breakthrough cases, reduced infectious VL was only observed in boosted but not in fully vaccinated individuals compared to unvaccinated subjects. In addition, infectious VL was lower in fully vaccinated Omicron- compared to fully vaccinated Delta-infected individuals, suggesting that other mechanisms than increased infectious VL contribute to the high infectiousness of SARS-CoV-2 Omicron. 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, University Hospital Geneva, HUG, Geneva, Switzerland
| | - Frédérique Jacquérioz Bausch
- 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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223
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Drug-Free Nasal Spray as a Barrier against SARS-CoV-2 and Its Delta Variant: In Vitro Study of Safety and Efficacy in Human Nasal Airway Epithelia. Int J Mol Sci 2022; 23:ijms23074062. [PMID: 35409423 PMCID: PMC8999825 DOI: 10.3390/ijms23074062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
The nasal epithelium is a key portal for infection by respiratory viruses such as SARS-CoV-2 and represents an important target for prophylactic and therapeutic interventions. In the present study, we test the safety and efficacy of a newly developed nasal spray (AM-301, marketed as Bentrio) against infection by SARS-CoV-2 and its Delta variant on an in vitro 3D-model of the primary human nasal airway epithelium. Safety was assessed in assays for tight junction integrity, cytotoxicity and cilia beating frequency. Efficacy against SARS-CoV-2 infection was evaluated in pre-viral load and post-viral load application on airway epithelium. No toxic effects of AM-301 on the nasal epithelium were found. Prophylactic treatment with AM-301 significantly reduced viral titer vs. controls over 4 days, reaching a maximum reduction of 99% in case of infection from the wild-type SARS-CoV-2 variant and more than 83% in case of the Delta variant. When AM-301 administration was started 24 h after infection, viral titer was reduced by about 12-folds and 3-folds on Day 4. The results suggest that AM-301 is safe and significantly decelerates SARS-CoV-2 replication in cell culture inhibition assays of prophylaxis (pre-viral load application) and mitigation (post-viral load application). Its physical (non-pharmaceutical) mechanism of action, safety and efficacy warrant additional investigations both in vitro and in vivo for safety and efficacy against a broad spectrum of airborne viruses and allergens.
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224
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Affiliation(s)
- Kathryn M Edwards
- Division of Infectious Diseases, Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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Ganti K, Ferreri LM, Lee CY, Bair CR, Delima GK, Holmes KE, Suthar MS, Lowen AC. Timing of exposure is critical in a highly sensitive model of SARS-CoV-2 transmission. PLoS Pathog 2022; 18:e1010181. [PMID: 35333914 PMCID: PMC8986102 DOI: 10.1371/journal.ppat.1010181] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/06/2022] [Accepted: 03/09/2022] [Indexed: 01/19/2023] Open
Abstract
Transmission efficiency is a critical factor determining the size of an outbreak of infectious disease. Indeed, the propensity of SARS-CoV-2 to transmit among humans precipitated and continues to sustain the COVID-19 pandemic. Nevertheless, the number of new cases among contacts is highly variable and underlying reasons for wide-ranging transmission outcomes remain unclear. Here, we evaluated viral spread in golden Syrian hamsters to define the impact of temporal and environmental conditions on the efficiency of SARS-CoV-2 transmission through the air. Our data show that exposure periods as brief as one hour are sufficient to support robust transmission. However, the timing after infection is critical for transmission success, with the highest frequency of transmission to contacts occurring at times of peak viral load in the donor animals. Relative humidity and temperature had no detectable impact on transmission when exposures were carried out with optimal timing and high inoculation dose. However, contrary to expectation, trends observed with sub-optimal exposure timing and lower inoculation dose suggest improved transmission at high relative humidity or high temperature. In sum, among the conditions tested, our data reveal the timing of exposure to be the strongest determinant of SARS-CoV-2 transmission success and implicate viral load as an important driver of transmission.
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Affiliation(s)
- Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Lucas M. Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Chung-Young Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Camden R. Bair
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Gabrielle K. Delima
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kate E. Holmes
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Mehul S. Suthar
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory-UGA Center of Excellence for Influenza Research and Surveillance [CEIRS], Atlanta, Georgia, United States of America
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory-UGA Center of Excellence for Influenza Research and Surveillance [CEIRS], Atlanta, Georgia, United States of America
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